AMR/search.json

[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"Creation of data","what":"Put everything together","title":"How to conduct AMR data analysis","text":"Using sample() function, can randomly select items objects defined earlier. let fake data reflect reality bit, also approximately define probabilities bacteria antibiotic results, using random_sir() function. Using left_join() function dplyr package, can ‘map’ gender patient ID using patients_table object created earlier: resulting data set contains 20 000 blood culture isolates. head() function can preview first 6 rows data set: Now, let’s start cleaning analysis!","code":"sample_size <- 20000 data <- data.frame(   date = sample(dates, size = sample_size, replace = TRUE),   patient_id = sample(patients, size = sample_size, replace = TRUE),   hospital = sample(     c(       \"Hospital A\",       \"Hospital B\",       \"Hospital C\",       \"Hospital D\"     ),     size = sample_size, replace = TRUE,     prob = c(0.30, 0.35, 0.15, 0.20)   ),   bacteria = sample(bacteria,     size = sample_size, replace = TRUE,     prob = c(0.50, 0.25, 0.15, 0.10)   ),   AMX = random_sir(sample_size, prob_sir = c(0.35, 0.60, 0.05)),   AMC = random_sir(sample_size, prob_sir = c(0.15, 0.75, 0.10)),   CIP = random_sir(sample_size, prob_sir = c(0.20, 0.80, 0.00)),   GEN = random_sir(sample_size, prob_sir = c(0.08, 0.92, 0.00)) ) data <- data %>% left_join(patients_table) head(data)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"cleaning-the-data","dir":"Articles","previous_headings":"","what":"Cleaning the data","title":"How to conduct AMR data analysis","text":"also created package dedicated data cleaning checking, called cleaner package. freq() function can used create frequency tables. example, gender variable: Frequency table Class: character Length: 20,000 Available: 20,000 (100%, NA: 0 = 0%) Unique: 2 Shortest: 1 Longest: 1 , can draw least two conclusions immediately. data scientists perspective, data looks clean: values M F. researchers perspective: slightly men. Nothing didn’t already know. data already quite clean, still need transform variables. bacteria column now consists text, want add variables based microbial IDs later . , transform column valid IDs. mutate() function dplyr package makes really easy: also want transform antibiotics, real life data don’t know really clean. .sir() function ensures reliability reproducibility kind variables. is_sir_eligible() can check columns probably columns SIR test results. Using mutate() across(), can apply transformation formal <rsi> class: Finally, apply EUCAST rules antimicrobial results. Europe, medical microbiological laboratories already apply rules. package features latest insights intrinsic resistance exceptional phenotypes. Moreover, eucast_rules() function can also apply additional rules, like forcing ampicillin = R amoxicillin/clavulanic acid = R. amoxicillin (column AMX) amoxicillin/clavulanic acid (column AMC) data generated randomly, rows undoubtedly contain AMX = S AMC = R, technically impossible. eucast_rules() fixes :","code":"data %>% freq(gender) data <- data %>%   mutate(bacteria = as.mo(bacteria)) is_sir_eligible(data) #> [1] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE colnames(data)[is_sir_eligible(data)] #> [1] \"AMX\" \"AMC\" \"CIP\" \"GEN\"  data <- data %>%   mutate(across(where(is_sir_eligible), as.sir)) data <- eucast_rules(data, col_mo = \"bacteria\", rules = \"all\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"adding-new-variables","dir":"Articles","previous_headings":"","what":"Adding new variables","title":"How to conduct AMR data analysis","text":"Now microbial ID, can add taxonomic properties:","code":"data <- data %>%   mutate(     gramstain = mo_gramstain(bacteria),     genus = mo_genus(bacteria),     species = mo_species(bacteria)   )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"first-isolates","dir":"Articles","previous_headings":"Adding new variables","what":"First isolates","title":"How to conduct AMR data analysis","text":"also need know isolates can actually use analysis. conduct analysis antimicrobial resistance, must include first isolate every patient per episode (Hindler et al., Clin Infect Dis. 2007). , easily get overestimate underestimate resistance antibiotic. Imagine patient admitted MRSA found 5 different blood cultures following weeks (yes, countries like Netherlands blood drawing policies). resistance percentage oxacillin isolates overestimated, included MRSA . clearly selection bias. Clinical Laboratory Standards Institute (CLSI) appoints follows: (…) preparing cumulative antibiogram guide clinical decisions empirical antimicrobial therapy initial infections, first isolate given species per patient, per analysis period (eg, one year) included, irrespective body site, antimicrobial susceptibility profile, phenotypical characteristics (eg, biotype). first isolate easily identified, cumulative antimicrobial susceptibility test data prepared using first isolate generally comparable cumulative antimicrobial susceptibility test data calculated methods, providing duplicate isolates excluded. M39-A4 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 4th Edition. CLSI, 2014. Chapter 6.4 AMR package includes methodology first_isolate() function able apply four different methods defined Hindler et al. 2007: phenotype-based, episode-based, patient-based, isolate-based. right method depends goals analysis, default phenotype-based method case method properly correct duplicate isolates. method also takes account antimicrobial susceptibility test results using all_microbials(). Read methods first_isolate() page. outcome function can easily added data: 61.6% suitable resistance analysis! can now filter filter() function, also dplyr package: future use, two syntaxes can shortened: end 12 322 isolates analysis. Now data looks like: Time analysis!","code":"data <- data %>%   mutate(first = first_isolate(info = TRUE)) #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for col_mo. #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient_id' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> => Found 12,322 'phenotype-based' first isolates (61.6% of total where a #>    microbial ID was available) data_1st <- data %>%   filter(first == TRUE) data_1st <- data %>%   filter_first_isolate() head(data_1st)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"analysing-the-data","dir":"Articles","previous_headings":"","what":"Analysing the data","title":"How to conduct AMR data analysis","text":"might want start getting idea data distributed. ’s important start, also decides continue analysis. Although package contains convenient function make frequency tables, exploratory data analysis (EDA) primary scope package. Use package like DataExplorer , read free online book Exploratory Data Analysis R Roger D. Peng.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dispersion-of-species","dir":"Articles","previous_headings":"Analysing the data","what":"Dispersion of species","title":"How to conduct AMR data analysis","text":"just get idea species distributed, create frequency table freq() function. created genus species column earlier based microbial ID. paste(), can concatenate together. freq() function can used like base R language intended: can used like dplyr way, easier readable: Frequency table Class: character Length: 12,322 Available: 12,322 (100%, NA: 0 = 0%) Unique: 4 Shortest: 16 Longest: 24","code":"freq(paste(data_1st$genus, data_1st$species)) data_1st %>% freq(genus, species)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"overview-of-different-bugdrug-combinations","dir":"Articles","previous_headings":"Analysing the data","what":"Overview of different bug/drug combinations","title":"How to conduct AMR data analysis","text":"Using tidyverse selections, can also select filter columns based antibiotic class : want get quick glance number isolates different bug/drug combinations, can use bug_drug_combinations() function: give crude numbers data. calculate antimicrobial resistance sensible way, also correcting results, use resistance() susceptibility() functions.","code":"data_1st %>%   filter(any(aminoglycosides() == \"R\")) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) data_1st %>%   bug_drug_combinations() %>%   head() # show first 6 rows data_1st %>%   select(bacteria, aminoglycosides()) %>%   bug_drug_combinations() #> ℹ For aminoglycosides() using column 'GEN' (gentamicin)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"resistance-percentages","dir":"Articles","previous_headings":"Analysing the data","what":"Resistance percentages","title":"How to conduct AMR data analysis","text":"functions resistance() susceptibility() can used calculate antimicrobial resistance susceptibility. specific analyses, functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() proportion_R() can used determine proportion specific antimicrobial outcome. functions contain minimum argument, denoting minimum required number test results returning value. functions otherwise return NA. default minimum = 30, following CLSI M39-A4 guideline applying microbial epidemiology. per EUCAST guideline 2019, calculate resistance proportion R (proportion_R(), equal resistance()) susceptibility proportion S (proportion_SI(), equal susceptibility()). functions can used : can used conjunction group_by() summarise(), dplyr package: course convenient know number isolates responsible percentages. purpose n_sir() can used, works exactly like n_distinct() dplyr package. counts isolates available every group (.e. values S, R): functions can also used get proportion multiple antibiotics, calculate empiric susceptibility combination therapies easily: curious resistance within certain antibiotic classes, use antibiotic class selector penicillins(), automatically include columns AMX AMC data: make transition next part, let’s see differences previously calculated combination therapies plotted:","code":"data_1st %>% resistance(AMX) #> [1] 0.5842396 data_1st %>%   group_by(hospital) %>%   summarise(amoxicillin = resistance(AMX)) data_1st %>%   group_by(hospital) %>%   summarise(     amoxicillin = resistance(AMX),     available = n_sir(AMX)   ) data_1st %>%   group_by(genus) %>%   summarise(     amoxiclav = susceptibility(AMC),     gentamicin = susceptibility(GEN),     amoxiclav_genta = susceptibility(AMC, GEN)   ) data_1st %>%   # group by hospital   group_by(hospital) %>%   #                / -> select all penicillins in the data for calculation   #                |              / -> use resistance() for all peni's per hospital   #                |              |           / -> print as percentages   summarise(across(penicillins(), resistance, as_percent = TRUE)) %>%   # format the antibiotic column names, using so-called snake case,   # so 'Amoxicillin/clavulanic acid' becomes 'amoxicillin_clavulanic_acid'   rename_with(set_ab_names, penicillins()) data_1st %>%   group_by(genus) %>%   summarise(     \"1. Amoxi/clav\" = susceptibility(AMC),     \"2. Gentamicin\" = susceptibility(GEN),     \"3. Amoxi/clav + genta\" = susceptibility(AMC, GEN)   ) %>%   # pivot_longer() from the tidyr package \"lengthens\" data:   tidyr::pivot_longer(-genus, names_to = \"antibiotic\") %>%   ggplot(aes(     x = genus,     y = value,     fill = antibiotic   )) +   geom_col(position = \"dodge2\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plots","dir":"Articles","previous_headings":"Analysing the data","what":"Plots","title":"How to conduct AMR data analysis","text":"show results plots, R users nowadays use ggplot2 package. package lets create plots layers. can read website. quick example look like syntaxes: AMR package contains functions extend ggplot2 package, example geom_sir(). automatically transforms data count_df() proportion_df() show results stacked bars. simplest shortest example:  Omit translate_ab = FALSE antibiotic codes (AMX, AMC, CIP, GEN) translated official names (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, gentamicin). group e.g. genus column add additional functions package, can create :  simplify , also created ggplot_sir() function, combines almost functions:","code":"ggplot(   data = a_data_set,   mapping = aes(     x = year,     y = value   ) ) +   geom_col() +   labs(     title = \"A title\",     subtitle = \"A subtitle\",     x = \"My X axis\",     y = \"My Y axis\"   )  # or as short as: ggplot(a_data_set) +   geom_bar(aes(year)) ggplot(data_1st) +   geom_sir(translate_ab = FALSE) # group the data on `genus` ggplot(data_1st %>% group_by(genus)) +   # create bars with genus on x axis   # it looks for variables with class `sir`,   # of which we have 4 (earlier created with `as.sir`)   geom_sir(x = \"genus\") +   # split plots on antibiotic   facet_sir(facet = \"antibiotic\") +   # set colours to the SIR interpretations (colour-blind friendly)   scale_sir_colours() +   # show percentages on y axis   scale_y_percent(breaks = 0:4 * 25) +   # turn 90 degrees, to make it bars instead of columns   coord_flip() +   # add labels   labs(     title = \"Resistance per genus and antibiotic\",     subtitle = \"(this is fake data)\"   ) +   # and print genus in italic to follow our convention   # (is now y axis because we turned the plot)   theme(axis.text.y = element_text(face = \"italic\")) data_1st %>%   group_by(genus) %>%   ggplot_sir(     x = \"genus\",     facet = \"antibiotic\",     breaks = 0:4 * 25,     datalabels = FALSE   ) +   coord_flip()"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-mic-and-disk-diffusion-values","dir":"Articles","previous_headings":"Analysing the data > Plots","what":"Plotting MIC and disk diffusion values","title":"How to conduct AMR data analysis","text":"AMR package also extends plot() ggplot2::autoplot() functions plotting minimum inhibitory concentrations (MIC, created .mic()) disk diffusion diameters (created .disk()). random_mic() random_disk() functions, can generate sampled values new data types (S3 classes) <mic> <disk>:   also specific, generating MICs likely found E. coli ciprofloxacin: plot() autoplot() function, can define microorganism antimicrobial agent way. add interpretation values according chosen guidelines (defaults latest EUCAST guideline). Default colours colour-blind friendly, maintaining convention e.g. ‘susceptible’ green ‘resistant’ red:   disk diffusion values, much difference plotting:  using ggplot2 package, now choosing latest implemented CLSI guideline (notice EUCAST-specific term “Susceptible, incr. exp.” changed “Intermediate”):","code":"mic_values <- random_mic(size = 100) mic_values #> Class 'mic' #>   [1] 0.25   0.5    0.125  0.125  16     32     0.002  >=256  0.025  1      #>  [11] 64     128    32     0.25   0.5    0.0625 128    >=256  8      0.002  #>  [21] 0.005  0.002  4      0.125  0.005  0.125  0.01   4      64     0.005  #>  [31] 32     0.002  0.25   0.002  0.0625 32     16     128    0.001  128    #>  [41] 0.001  0.5    0.025  0.5    128    4      0.005  0.25   0.125  0.002  #>  [51] 16     0.025  0.005  0.0625 4      32     0.005  4      0.025  0.001  #>  [61] 128    0.125  0.025  2      4      0.0625 0.001  8      0.25   0.025  #>  [71] 1      32     >=256  1      16     8      0.0625 0.01   2      0.005  #>  [81] 16     0.025  1      0.002  128    0.002  0.5    8      8      64     #>  [91] 128    0.01   0.005  16     0.002  0.005  >=256  8      0.002  0.25 # base R: plot(mic_values) # ggplot2: autoplot(mic_values) mic_values <- random_mic(size = 100, mo = \"E. coli\", ab = \"cipro\") # base R: plot(mic_values, mo = \"E. coli\", ab = \"cipro\") # ggplot2: autoplot(mic_values, mo = \"E. coli\", ab = \"cipro\") disk_values <- random_disk(size = 100, mo = \"E. coli\", ab = \"cipro\") disk_values #> Class 'disk' #>   [1] 28 18 29 27 31 26 27 30 31 18 30 25 17 20 20 31 22 22 30 26 24 26 23 28 28 #>  [26] 24 27 29 20 30 25 25 25 22 23 27 27 23 29 27 23 20 19 23 23 18 29 21 31 29 #>  [51] 19 31 27 27 31 20 22 28 31 19 21 30 28 21 24 21 20 20 19 27 26 30 19 24 29 #>  [76] 17 26 18 27 23 19 29 24 27 27 20 25 28 17 21 29 29 17 22 20 26 24 23 17 25 # base R: plot(disk_values, mo = \"E. coli\", ab = \"cipro\") autoplot(   disk_values,   mo = \"E. coli\",   ab = \"cipro\",   guideline = \"CLSI\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"independence-test","dir":"Articles","previous_headings":"Analysing the data","what":"Independence test","title":"How to conduct AMR data analysis","text":"next example uses example_isolates data set. data set included package contains 2,000 microbial isolates full antibiograms. reflects reality can used practise AMR data analysis. compare resistance amoxicillin/clavulanic acid (column AMC) ICU clinical wards. input fisher.test() can retrieved transformation like : can apply test now : can seen, p value practically zero (0.0000002263247), means amoxicillin/clavulanic acid resistance found isolates patients ICUs clinical wards really different. Author: Dr. Matthijs Berends","code":"# use package 'tidyr' to pivot data: library(tidyr)  check_AMC <- example_isolates %>%   filter(ward %in% c(\"ICU\", \"Clinical\")) %>% # filter on only these wards   select(ward, AMC) %>% # select the wards and amoxi/clav   group_by(ward) %>% # group on the wards   count_df(combine_SI = TRUE) %>% # count all isolates per group (ward)   pivot_wider(     names_from = ward, # transform output so \"ICU\" and \"Clinical\" are columns     values_from = value   ) %>%   select(ICU, Clinical) %>% # and only select these columns   as.matrix() # transform to a good old matrix for fisher.test()  check_AMC #>      ICU Clinical #> [1,] 396      942 #> [2,] 184      240 # do Fisher's Exact Test fisher.test(check_AMC) #>  #>  Fisher's Exact Test for Count Data #>  #> data:  check_AMC #> p-value = 2.263e-07 #> alternative hypothesis: true odds ratio is not equal to 1 #> 95 percent confidence interval: #>  0.435261 0.691614 #> sample estimates: #> odds ratio  #>  0.5485079"},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to apply EUCAST rules","text":"EUCAST rules? European Committee Antimicrobial Susceptibility Testing (EUCAST) states website: EUCAST expert rules tabulated collection expert knowledge intrinsic resistances, exceptional resistance phenotypes interpretive rules may applied antimicrobial susceptibility testing order reduce errors make appropriate recommendations reporting particular resistances. Europe, lot medical microbiological laboratories already apply rules (Brown et al., 2015). package features latest insights intrinsic resistance unusual phenotypes (v3.3, 2021). Moreover, eucast_rules() function use purpose can also apply additional rules, like forcing ampicillin = R isolates amoxicillin/clavulanic acid = R.","code":""},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to apply EUCAST rules","text":"rules can used discard impossible bug-drug combinations data. example, Klebsiella produces beta-lactamase prevents ampicillin (amoxicillin) working . words, practically every strain Klebsiella resistant ampicillin. Sometimes, laboratory data can still contain strains ampicillin susceptible ampicillin. antibiogram available identification available, antibiogram re-interpreted based identification (namely, Klebsiella). EUCAST expert rules solve , can applied using eucast_rules(): convenient function mo_is_intrinsic_resistant() uses guideline, allows check one specific microorganisms antibiotics: EUCAST rules can used correction, can also used filling known resistance susceptibility based results antimicrobials drugs. process called interpretive reading, basically form imputation, part eucast_rules() function well:","code":"oops <- data.frame(   mo = c(     \"Klebsiella\",     \"Escherichia\"   ),   ampicillin = \"S\" ) oops #>            mo ampicillin #> 1  Klebsiella          S #> 2 Escherichia          S  eucast_rules(oops, info = FALSE) #>            mo ampicillin #> 1  Klebsiella          R #> 2 Escherichia          S mo_is_intrinsic_resistant(   c(\"Klebsiella\", \"Escherichia\"),   \"ampicillin\" ) #> [1]  TRUE FALSE  mo_is_intrinsic_resistant(   \"Klebsiella\",   c(\"ampicillin\", \"kanamycin\") ) #> [1]  TRUE FALSE data <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE ) data eucast_rules(data)"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"type-of-input","dir":"Articles","previous_headings":"","what":"Type of input","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function takes data set input, regular data.frame. tries automatically determine right columns info isolates, name species columns results antimicrobial agents. See help page info set right settings data command ?mdro. WHONET data (data), settings automatically set correctly.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"guidelines","dir":"Articles","previous_headings":"","what":"Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function support multiple guidelines. can select guideline guideline parameter. Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. “Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.” Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.2\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance Unusual Phenotypes” (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance Exceptional Phenotypes Tables” (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization “Companion handbook guidelines programmatic management drug-resistant tuberculosis” (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"custom-guidelines","dir":"Articles","previous_headings":"Guidelines","what":"Custom Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"can also use custom guideline. Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() dplyr package, recognise input method set rules. Rules must set using R considers ‘formula notation’: row/isolate matches first rule, value first ~ (case ‘Elderly Type ’) set MDRO value. Otherwise, second rule tried . maximum number rules unlimited. can print rules set console overview. Colours help reading console supports colours. outcome function can used guideline argument mdro() function: rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(   CIP == \"R\" & age > 60 ~ \"Elderly Type A\",   ERY == \"R\" & age > 60 ~ \"Elderly Type B\" ) custom #> A set of custom MDRO rules: #>   1. If CIP is \"R\" and age is higher than 60 then: Elderly Type A #>   2. If ERY is \"R\" and age is higher than 60 then: Elderly Type B #>   3. Otherwise: Negative #>  #> Unmatched rows will return NA. #> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B x <- mdro(example_isolates, guideline = custom) table(x) #> x #>       Negative Elderly Type A Elderly Type B  #>           1070            198            732"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function always returns ordered factor predefined guidelines. example, output default guideline Magiorakos et al. returns factor levels ‘Negative’, ‘MDR’, ‘XDR’ ‘PDR’ order. next example uses example_isolates data set. data set included package contains full antibiograms 2,000 microbial isolates. reflects reality can used practise AMR data analysis. test MDR/XDR/PDR guideline data set, get: (16 isolates test results) Frequency table Class: factor > ordered (numeric) Length: 2,000 Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant … Available: 1,729 (86.45%, NA: 271 = 13.55%) Unique: 2 another example, create data set determine multi-drug resistant TB: column names automatically verified valid drug names codes, worked exactly way: data set now looks like : can now add interpretation MDR-TB data set. can use: shortcut mdr_tb(): Create frequency table results: Frequency table Class: factor > ordered (numeric) Length: 5,000 Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <… Available: 5,000 (100%, NA: 0 = 0%) Unique: 5","code":"library(dplyr) # to support pipes: %>% library(cleaner) # to create frequency tables example_isolates %>%   mdro() %>%   freq() # show frequency table of the result #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) # random_sir() is a helper function to generate # a random vector with values S, I and R my_TB_data <- data.frame(   rifampicin = random_sir(5000),   isoniazid = random_sir(5000),   gatifloxacin = random_sir(5000),   ethambutol = random_sir(5000),   pyrazinamide = random_sir(5000),   moxifloxacin = random_sir(5000),   kanamycin = random_sir(5000) ) my_TB_data <- data.frame(   RIF = random_sir(5000),   INH = random_sir(5000),   GAT = random_sir(5000),   ETH = random_sir(5000),   PZA = random_sir(5000),   MFX = random_sir(5000),   KAN = random_sir(5000) ) head(my_TB_data) #>   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin #> 1          S         R            R          R            S            S #> 2          I         I            S          I            R            R #> 3          S         S            S          I            R            I #> 4          I         I            R          R            R            S #> 5          I         I            S          I            R            S #> 6          S         R            I          I            R            S #>   kanamycin #> 1         R #> 2         R #> 3         S #> 4         R #> 5         I #> 6         I mdro(my_TB_data, guideline = \"TB\") my_TB_data$mdr <- mdr_tb(my_TB_data) #> ℹ No column found as input for col_mo, assuming all rows contain #>   Mycobacterium tuberculosis. freq(my_TB_data$mdr)"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"transforming","dir":"Articles","previous_headings":"","what":"Transforming","title":"How to conduct principal component analysis (PCA) for AMR","text":"PCA, need transform AMR data first. example_isolates data set package looks like: Now transform data set resistance percentages per taxonomic order genus:","code":"library(AMR) library(dplyr) glimpse(example_isolates) #> Rows: 2,000 #> Columns: 46 #> $ date    <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2… #> $ patient <chr> \"A77334\", \"A77334\", \"067927\", \"067927\", \"067927\", \"067927\", \"4… #> $ age     <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50… #> $ gender  <chr> \"F\", \"F\", \"F\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\", \"F\", \"M\", \"M\", \"M… #> $ ward    <chr> \"Clinical\", \"Clinical\", \"ICU\", \"ICU\", \"ICU\", \"ICU\", \"Clinical\"… #> $ mo      <mo> \"B_ESCHR_COLI\", \"B_ESCHR_COLI\", \"B_STPHY_EPDR\", \"B_STPHY_EPDR\",… #> $ PEN     <sir> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,… #> $ OXA     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ FLC     <sir> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R… #> $ AMX     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ AMC     <sir> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N… #> $ AMP     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ TZP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CZO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ FEP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CXM     <sir> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S… #> $ FOX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ CTX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ CAZ     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, … #> $ CRO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ GEN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TOB     <sir> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA… #> $ AMK     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ KAN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TMP     <sir> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, … #> $ SXT     <sir> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N… #> $ NIT     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,… #> $ FOS     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ LNZ     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ CIP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S… #> $ MFX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ VAN     <sir> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, … #> $ TEC     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ TCY     <sir> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, … #> $ TGC     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ DOX     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ ERY     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ CLI     <sir> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA… #> $ AZM     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ IPM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ MEM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ MTR     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CHL     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ COL     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, … #> $ MUP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ RIF     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… resistance_data <- example_isolates %>%   group_by(     order = mo_order(mo), # group on anything, like order     genus = mo_genus(mo)   ) %>% #  and genus as we do here   summarise_if(is.sir, resistance) %>% # then get resistance of all drugs   select(     order, genus, AMC, CXM, CTX,     CAZ, GEN, TOB, TMP, SXT   ) # and select only relevant columns  head(resistance_data) #> # A tibble: 6 × 10 #> # Groups:   order [5] #>   order             genus          AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT #>   <chr>             <chr>        <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 (unknown order)   (unknown ge…    NA    NA    NA    NA    NA    NA    NA    NA #> 2 Actinomycetales   Schaalia        NA    NA    NA    NA    NA    NA    NA    NA #> 3 Bacteroidales     Bacteroides     NA    NA    NA    NA    NA    NA    NA    NA #> 4 Campylobacterales Campylobact…    NA    NA    NA    NA    NA    NA    NA    NA #> 5 Caryophanales     Gemella         NA    NA    NA    NA    NA    NA    NA    NA #> 6 Caryophanales     Listeria        NA    NA    NA    NA    NA    NA    NA    NA"},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"perform-principal-component-analysis","dir":"Articles","previous_headings":"","what":"Perform principal component analysis","title":"How to conduct principal component analysis (PCA) for AMR","text":"new pca() function automatically filter rows contain numeric values selected variables, now need : result can reviewed good old summary() function: Good news. first two components explain total 93.3% variance (see PC1 PC2 values Proportion Variance. can create -called biplot base R biplot() function, see antimicrobial resistance per drug explain difference per microorganism.","code":"pca_result <- pca(resistance_data) #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", \"TMP\" #>   and \"TOB\". Total observations available: 7. summary(pca_result) #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\" #> Importance of components: #>                           PC1    PC2    PC3     PC4     PC5     PC6       PC7 #> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\""},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"plotting-the-results","dir":"Articles","previous_headings":"","what":"Plotting the results","title":"How to conduct principal component analysis (PCA) for AMR","text":"can’t see explanation points. Perhaps works better new ggplot_pca() function, automatically adds right labels even groups:  can also print ellipse per group, edit appearance:","code":"biplot(pca_result) ggplot_pca(pca_result) ggplot_pca(pca_result, ellipse = TRUE) +   ggplot2::labs(title = \"An AMR/PCA biplot!\")"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss-sas-stata","dir":"Articles","previous_headings":"","what":"SPSS / SAS / Stata","title":"How to import data from SPSS / SAS / Stata","text":"SPSS (Statistical Package Social Sciences) probably well-known software package statistical analysis. SPSS easier learn R, SPSS click menu run parts analysis. user-friendliness, taught universities particularly useful students new statistics. experience, guess pretty much (bio)medical students know time graduate. SAS Stata comparable statistical packages popular big industries.","code":""},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"compared-to-r","dir":"Articles","previous_headings":"","what":"Compared to R","title":"How to import data from SPSS / SAS / Stata","text":"said, SPSS easier learn R. SPSS, SAS Stata come major downsides comparing R: R highly modular. official R network (CRAN) features 16,000 packages time writing, AMR package one . packages peer-reviewed publication. Aside official channel, also developers choose submit CRAN, rather keep public repository, like GitHub. may even lot 14,000 packages . Bottom line , can really extend ask somebody . Take example AMR package. Among things, adds reliable reference data R help data cleaning analysis. SPSS, SAS Stata never know valid MIC value Gram stain E. coli . species Klebiella resistant amoxicillin Floxapen® trade name flucloxacillin. facts properties often needed clean existing data, inconvenient software package without reliable reference data. See demonstration. R extremely flexible. write syntax , can anything want. flexibility transforming, arranging, grouping summarising data, drawing plots, endless - SPSS, SAS Stata bound algorithms format styles. may bit flexible, can probably never create specific publication-ready plot without using (paid) software. sometimes write syntaxes SPSS run complete analysis ‘automate’ work, lot less time R. notice writing syntaxes R lot nifty clever SPSS. Still, working statistical package, knowledge (statistically) willing accomplish. R can easily automated. last years, R Markdown really made interesting development. R Markdown, can easily produce reports, whether format Word, PowerPoint, website, PDF document just raw data Excel. even allows use reference file containing layout style (e.g. fonts colours) organisation. use lot generate weekly monthly reports automatically. Just write code enjoy automatically updated reports interval like. even professional environment, create Shiny apps: live manipulation data using custom made website. webdesign knowledge needed (JavaScript, CSS, HTML) almost zero. R huge community. Many R users just ask questions websites like StackOverflow.com, largest online community programmers. time writing, 480 788 R-related questions already asked platform (covers questions answers programming language). experience, questions answered within couple minutes. R understands data type, including SPSS/SAS/Stata. ’s vice versa ’m afraid. can import data source R. example SPSS, SAS Stata (link), Minitab, Epi Info EpiData (link), Excel (link), flat files like CSV, TXT TSV (link), directly databases datawarehouses anywhere world (link). can even scrape websites download tables live internet (link) get results API call transform data one command (link). best part - can export R data formats well. can import SPSS file, analysis neatly R export resulting tables Excel files sharing. R completely free open-source. strings attached. created maintained volunteers believe (data) science open publicly available everybody. SPSS, SAS Stata quite expensive. IBM SPSS Staticstics comes subscriptions nowadays, varying USD 1,300 USD 8,500 per user per year. SAS Analytics Pro costs around USD 10,000 per computer. Stata also business model subscription fees, varying USD 600 USD 2,800 per computer per year, lower prices come limitation number variables can work . still offer benefits R. working midsized small company, can save tens thousands dollars using R instead e.g. SPSS - gaining even functions flexibility. R enthousiasts can much PR want (like ), nobody officially associated affiliated R. really free. R (nowadays) preferred analysis software academic papers. present, R among world powerful statistical languages, generally popular science (Bollmann et al., 2017). reasons, number references R analysis method academic papers rising continuously even surpassed SPSS academic use (Muenchen, 2014). believe thing SPSS , always great user interface easy learn use. Back developed , little competition, let alone R. R didn’t even professional user interface last decade (called RStudio, see ). people used R nineties 2010 almost completely incomparable R used now. language restyled completely volunteers dedicated professionals field data science. SPSS great nothing else compete. now 2023, don’t see reason SPSS better use R. demonstrate first point:","code":"# not all values are valid MIC values: as.mic(0.125) #> Class 'mic' #> [1] 0.125 as.mic(\"testvalue\") #> Class 'mic' #> [1] <NA>  # the Gram stain is available for all bacteria: mo_gramstain(\"E. coli\") #> [1] \"Gram-negative\"  # Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST: klebsiella_test <- data.frame(   mo = \"klebsiella\",   amox = \"S\",   stringsAsFactors = FALSE ) klebsiella_test # (our original data) #>           mo amox #> 1 klebsiella    S eucast_rules(klebsiella_test, info = FALSE) # (the edited data by EUCAST rules) #>           mo amox #> 1 klebsiella    R  # hundreds of trade names can be translated to a name, trade name or an ATC code: ab_name(\"floxapen\") #> [1] \"Flucloxacillin\" ab_tradenames(\"floxapen\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\" ab_atc(\"floxapen\") #> [1] \"J01CF05\""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"rstudio","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"RStudio","title":"How to import data from SPSS / SAS / Stata","text":"work R, probably best option use RStudio. open-source free desktop environment allows run R code, also supports project management, version management, package management convenient import menus work data sources. can also install RStudio Server private corporate server, brings nothing less complete RStudio software website (home work). import data file, just click Import Dataset Environment tab:  additional packages needed, RStudio ask installed beforehand. window opens, can define options (parameters) used import ’re ready go:  want named variables imported factors resembles SPSS , use as_factor(). difference :","code":"SPSS_data # # A tibble: 4,203 x 4 #     v001 sex       status    statusage #    <dbl> <dbl+lbl> <dbl+lbl>     <dbl> #  1 10002 1         1              76.6 #  2 10004 0         1              59.1 #  3 10005 1         1              54.5 #  4 10006 1         1              54.1 #  5 10007 1         1              57.7 #  6 10008 1         1              62.8 #  7 10010 0         1              63.7 #  8 10011 1         1              73.1 #  9 10017 1         1              56.7 # 10 10018 0         1              66.6 # # ... with 4,193 more rows  as_factor(SPSS_data) # # A tibble: 4,203 x 4 #     v001 sex    status statusage #    <dbl> <fct>  <fct>      <dbl> #  1 10002 Male   alive       76.6 #  2 10004 Female alive       59.1 #  3 10005 Male   alive       54.5 #  4 10006 Male   alive       54.1 #  5 10007 Male   alive       57.7 #  6 10008 Male   alive       62.8 #  7 10010 Female alive       63.7 #  8 10011 Male   alive       73.1 #  9 10017 Male   alive       56.7 # 10 10018 Female alive       66.6 # # ... with 4,193 more rows"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"base-r","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"Base R","title":"How to import data from SPSS / SAS / Stata","text":"import data SPSS, SAS Stata, can use great haven package : can now import files follows:","code":"# download and install the latest version: install.packages(\"haven\") # load the package you just installed: library(haven)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SPSS","title":"How to import data from SPSS / SAS / Stata","text":"read files SPSS R: forget as_factor(), mentioned . export R objects SPSS file format:","code":"# read any SPSS file based on file extension (best way): read_spss(file = \"path/to/file\")  # read .sav or .zsav file: read_sav(file = \"path/to/file\")  # read .por file: read_por(file = \"path/to/file\") # save as .sav file: write_sav(data = yourdata, path = \"path/to/file\")  # save as compressed .zsav file: write_sav(data = yourdata, path = \"path/to/file\", compress = TRUE)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"sas","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SAS","title":"How to import data from SPSS / SAS / Stata","text":"read files SAS R: export R objects SAS file format:","code":"# read .sas7bdat + .sas7bcat files: read_sas(data_file = \"path/to/file\", catalog_file = NULL)  # read SAS transport files (version 5 and version 8): read_xpt(file = \"path/to/file\") # save as regular SAS file: write_sas(data = yourdata, path = \"path/to/file\")  # the SAS transport format is an open format # (required for submission of the data to the FDA) write_xpt(data = yourdata, path = \"path/to/file\", version = 8)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"stata","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"Stata","title":"How to import data from SPSS / SAS / Stata","text":"read files Stata R: export R objects Stata file format:","code":"# read .dta file: read_stata(file = \"/path/to/file\")  # works exactly the same: read_dta(file = \"/path/to/file\") # save as .dta file, Stata version 14: # (supports Stata v8 until v15 at the time of writing) write_dta(data = yourdata, path = \"/path/to/file\", version = 14)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"import-of-data","dir":"Articles","previous_headings":"","what":"Import of data","title":"How to work with WHONET data","text":"tutorial assumes already imported WHONET data e.g. readxl package. RStudio, can done using menu button ‘Import Dataset’ tab ‘Environment’. Choose option ‘Excel’ select exported file. Make sure date fields imported correctly. example syntax look like : package comes example data set WHONET. use analysis.","code":"library(readxl) data <- read_excel(path = \"path/to/your/file.xlsx\")"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to work with WHONET data","text":"First, load relevant packages yet . use tidyverse analyses. . don’t know yet, suggest read website: https://www.tidyverse.org/. transform variables simplify automate analysis: Microorganisms transformed microorganism codes (called mo) using Catalogue Life reference data set, contains ~70,000 microorganisms taxonomic kingdoms Bacteria, Fungi Protozoa. tranformation .mo(). function also recognises almost WHONET abbreviations microorganisms. Antimicrobial results interpretations clean valid. words, contain values \"S\", \"\" \"R\". exactly .sir() function . errors warnings, values transformed succesfully. also created package dedicated data cleaning checking, called cleaner package. freq() function can used create frequency tables. let’s check data, couple frequency tables: Frequency table Class: character Length: 500 Available: 500 (100%, NA: 0 = 0%) Unique: 38 Shortest: 11 Longest: 40 (omitted 28 entries, n = 57 [11.4%]) Frequency table Class: factor > ordered > sir (numeric) Length: 500 Levels: 3: S < < R Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3 Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) Drug group: Beta-lactams/penicillins %SI: 78.59%","code":"library(dplyr) # part of tidyverse library(ggplot2) # part of tidyverse library(AMR) # this package library(cleaner) # to create frequency tables # transform variables data <- WHONET %>%   # get microbial ID based on given organism   mutate(mo = as.mo(Organism)) %>%   # transform everything from \"AMP_ND10\" to \"CIP_EE\" to the new `sir` class   mutate_at(vars(AMP_ND10:CIP_EE), as.sir) # our newly created `mo` variable, put in the mo_name() function data %>% freq(mo_name(mo), nmax = 10) # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"a-first-glimpse-at-results","dir":"Articles","previous_headings":"","what":"A first glimpse at results","title":"How to work with WHONET data","text":"easy ggplot already give lot information, using included ggplot_sir() function:","code":"data %>%   group_by(Country) %>%   select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%   ggplot_sir(translate_ab = \"ab\", facet = \"Country\", datalabels = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-full-microbial-taxonomy","dir":"Articles","previous_headings":"","what":"microorganisms: Full Microbial Taxonomy","title":"Data sets for download / own use","text":"data set 52 142 rows 22 columns, containing following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, source, lpsn, lpsn_parent, lpsn_renamed_to, gbif, gbif_parent, gbif_renamed_to, prevalence snomed. data set R available microorganisms, load AMR package. last updated 6 February 2023 10:57:22 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (1.2 MB) Download tab-separated text file (11.3 MB) Download Microsoft Excel workbook (5 MB) Download Apache Feather file (5.4 MB) Download Apache Parquet file (2.6 MB) Download SAS data file (50.9 MB) Download IBM SPSS Statistics data file (16.9 MB) Download Stata DTA file (47.1 MB) NOTE: exported files SAS, SPSS Stata contain first 50 SNOMED codes per record, file size otherwise exceed 100 MB; file size limit GitHub. Advice? Use R instead. tab-separated text file Microsoft Excel workbook contain SNOMED codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Source","title":"Data sets for download / own use","text":"data set contains full microbial taxonomy five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF): Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Example content","title":"Data sets for download / own use","text":"Included (sub)species per taxonomic kingdom: Example rows filtering genus Escherichia:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antibiotics-antibiotic-antifungal-drugs","dir":"Articles","previous_headings":"","what":"antibiotics: Antibiotic (+Antifungal) Drugs","title":"Data sets for download / own use","text":"data set 483 rows 14 columns, containing following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units loinc. data set R available antibiotics, load AMR package. last updated 30 October 2022 20:05:46 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (39 kB) Download tab-separated text file (0.1 MB) Download Microsoft Excel workbook (66 kB) Download Apache Feather file (0.1 MB) Download Apache Parquet file (97 kB) Download SAS data file (1.9 MB) Download IBM SPSS Statistics data file (0.3 MB) Download Stata DTA file (0.4 MB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain ATC codes, common abbreviations, trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-1","dir":"Articles","previous_headings":"antibiotics: Antibiotic (+Antifungal) Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains EARS-Net ATC codes gathered WHONET, compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine WHONET software 2019 LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antivirals-antiviral-drugs","dir":"Articles","previous_headings":"","what":"antivirals: Antiviral Drugs","title":"Data sets for download / own use","text":"data set 120 rows 11 columns, containing following column names:av, name, atc, cid, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units loinc. data set R available antivirals, load AMR package. last updated 13 November 2022 07:46:10 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (5 kB) Download tab-separated text file (16 kB) Download Microsoft Excel workbook (16 kB) Download Apache Feather file (15 kB) Download Apache Parquet file (13 kB) Download SAS data file (84 kB) Download IBM SPSS Statistics data file (30 kB) Download Stata DTA file (73 kB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-2","dir":"Articles","previous_headings":"antivirals: Antiviral Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains ATC codes gathered compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir","dir":"Articles","previous_headings":"","what":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","title":"Data sets for download / own use","text":"data set 18 308 rows 11 columns, containing following column names:guideline, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R uti. data set R available clinical_breakpoints, load AMR package. last updated 21 January 2023 22:47:20 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (42 kB) Download tab-separated text file (1.9 MB) Download Microsoft Excel workbook (0.8 MB) Download Apache Feather file (0.7 MB) Download Apache Parquet file (87 kB) Download SAS data file (3.6 MB) Download IBM SPSS Statistics data file (2.3 MB) Download Stata DTA file (3.4 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-3","dir":"Articles","previous_headings":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","what":"Source","title":"Data sets for download / own use","text":"data set contains interpretation rules MIC values disk diffusion diameters. Included guidelines CLSI (2013-2022) EUCAST (2013-2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"intrinsic_resistant-intrinsic-bacterial-resistance","dir":"Articles","previous_headings":"","what":"intrinsic_resistant: Intrinsic Bacterial Resistance","title":"Data sets for download / own use","text":"data set 134 634 rows 2 columns, containing following column names:mo ab. data set R available intrinsic_resistant, load AMR package. last updated 16 December 2022 15:10:43 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (78 kB) Download tab-separated text file (5.1 MB) Download Microsoft Excel workbook (1.3 MB) Download Apache Feather file (1.2 MB) Download Apache Parquet file (0.2 MB) Download SAS data file (9.8 MB) Download IBM SPSS Statistics data file (7.4 MB) Download Stata DTA file (9.5 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Source","title":"Data sets for download / own use","text":"data set contains defined intrinsic resistance EUCAST bug-drug combinations, based ‘EUCAST Expert Rules’ ‘EUCAST Intrinsic Resistance Unusual Phenotypes’ v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Example content","title":"Data sets for download / own use","text":"Example rows filtering Enterobacter cloacae:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"dosage-dosage-guidelines-from-eucast","dir":"Articles","previous_headings":"","what":"dosage: Dosage Guidelines from EUCAST","title":"Data sets for download / own use","text":"data set 336 rows 9 columns, containing following column names:ab, name, type, dose, dose_times, administration, notes, original_txt eucast_version. data set R available dosage, load AMR package. last updated 14 November 2022 14:20:39 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (3 kB) Download tab-separated text file (29 kB) Download Microsoft Excel workbook (19 kB) Download Apache Feather file (16 kB) Download Apache Parquet file (8 kB) Download SAS data file (92 kB) Download IBM SPSS Statistics data file (43 kB) Download Stata DTA file (82 kB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-5","dir":"Articles","previous_headings":"dosage: Dosage Guidelines from EUCAST","what":"Source","title":"Data sets for download / own use","text":"EUCAST breakpoints used package based dosages data set. Currently included dosages data set meant : ‘EUCAST Clinical Breakpoint Tables’ v11.0 (2021) ‘EUCAST Clinical Breakpoint Tables’ v12.0 (2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates: Example Data for Practice","title":"Data sets for download / own use","text":"data set 2 000 rows 46 columns, containing following column names:date, patient, age, gender, ward, mo, PEN, OXA, FLC, AMX, AMC, AMP, TZP, CZO, FEP, CXM, FOX, CTX, CAZ, CRO, GEN, TOB, AMK, KAN, TMP, SXT, NIT, FOS, LNZ, CIP, MFX, VAN, TEC, TCY, TGC, DOX, ERY, CLI, AZM, IPM, MEM, MTR, CHL, COL, MUP RIF. data set R available example_isolates, load AMR package. last updated 21 January 2023 22:47:20 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-6","dir":"Articles","previous_headings":"example_isolates: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates_unclean-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates_unclean: Example Data for Practice","title":"Data sets for download / own use","text":"data set 3 000 rows 8 columns, containing following column names:patient_id, hospital, date, bacteria, AMX, AMC, CIP GEN. data set R available example_isolates_unclean, load AMR package. last updated 27 August 2022 18:49:37 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-7","dir":"Articles","previous_headings":"example_isolates_unclean: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"needed-r-packages","dir":"Articles","previous_headings":"","what":"Needed R packages","title":"How to predict antimicrobial resistance","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. AMR package depends packages even extends use functions.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"tidyverse\", \"AMR\"))"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"prediction-analysis","dir":"Articles","previous_headings":"","what":"Prediction analysis","title":"How to predict antimicrobial resistance","text":"package contains function resistance_predict(), takes input functions AMR data analysis. Based date column, calculates cases per year uses regression model predict antimicrobial resistance. basically easy : function look date column col_date set. running commands, summary regression model printed unless using resistance_predict(..., info = FALSE). text printed summary - actual result (output) function data.frame containing year: number observations, actual observed resistance, estimated resistance standard error estimation: function plot available base R, can extended packages depend output based type input. extended function cope resistance predictions:  fastest way plot result. automatically adds right axes, error bars, titles, number available observations type model. also support ggplot2 package custom function ggplot_sir_predict() create appealing plots:","code":"# resistance prediction of piperacillin/tazobactam (TZP): resistance_predict(tbl = example_isolates, col_date = \"date\", col_ab = \"TZP\", model = \"binomial\")  # or: example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   )  # to bind it to object 'predict_TZP' for example: predict_TZP <- example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   ) predict_TZP #> # A tibble: 32 × 7 #>     year  value se_min se_max observations observed estimated #>  * <dbl>  <dbl>  <dbl>  <dbl>        <int>    <dbl>     <dbl> #>  1  2002 0.2        NA     NA           15   0.2       0.0562 #>  2  2003 0.0625     NA     NA           32   0.0625    0.0616 #>  3  2004 0.0854     NA     NA           82   0.0854    0.0676 #>  4  2005 0.05       NA     NA           60   0.05      0.0741 #>  5  2006 0.0508     NA     NA           59   0.0508    0.0812 #>  6  2007 0.121      NA     NA           66   0.121     0.0889 #>  7  2008 0.0417     NA     NA           72   0.0417    0.0972 #>  8  2009 0.0164     NA     NA           61   0.0164    0.106  #>  9  2010 0.0566     NA     NA           53   0.0566    0.116  #> 10  2011 0.183      NA     NA           93   0.183     0.127  #> # … with 22 more rows plot(predict_TZP) ggplot_sir_predict(predict_TZP) # choose for error bars instead of a ribbon ggplot_sir_predict(predict_TZP, ribbon = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"choosing-the-right-model","dir":"Articles","previous_headings":"Prediction analysis","what":"Choosing the right model","title":"How to predict antimicrobial resistance","text":"Resistance easily predicted; look vancomycin resistance Gram-positive bacteria, spread (.e. standard error) enormous:  Vancomycin resistance 100% ten years, might remain low. can define model model parameter. model chosen generalised linear regression model using binomial distribution, assuming period zero resistance followed period increasing resistance leading slowly resistance. Valid values : vancomycin resistance Gram-positive bacteria, linear model might appropriate:  model also available object, attribute:","code":"example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"binomial\") %>%   ggplot_sir_predict() example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"linear\") %>%   ggplot_sir_predict() model <- attributes(predict_TZP)$model  summary(model)$family #>  #> Family: binomial  #> Link function: logit  summary(model)$coefficients #>                  Estimate  Std. Error   z value     Pr(>|z|) #> (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05 #> year           0.09883005  0.02295317  4.305725 1.664395e-05"},{"path":"https://msberends.github.io/AMR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Matthijs S. Berends. Author, maintainer. Christian F. Luz. Author, contributor. Dennis Souverein. Author, contributor. Erwin E. . Hassing. Author, contributor. Casper J. Albers. Thesis advisor. Peter Dutey-Magni. Contributor. Judith M. Fonville. Contributor. Alex W. Friedrich. Thesis advisor. Corinna Glasner. Thesis advisor. Eric H. L. C. M. Hazenberg. Contributor. Gwen Knight. Contributor. Annick Lenglet. Contributor. Bart C. Meijer. Contributor. Dmytro Mykhailenko. Contributor. Anton Mymrikov. Contributor. Andrew P. Norgan. Contributor. Sofia Ny. Contributor. Jonas Salm. Contributor. Rogier P. Schade. Contributor. Bhanu N. M. Sinha. Thesis advisor. Anthony Underwood. Contributor. Anita Williams. Contributor.","code":""},{"path":"https://msberends.github.io/AMR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). “AMR: R Package Working Antimicrobial Resistance Data.” Journal Statistical Software, 104(3), 1–31. doi:10.18637/jss.v104.i03.","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/index.html","id":"the-amr-package-for-r-","dir":"","previous_headings":"","what":"Antimicrobial Resistance Data Analysis","title":"Antimicrobial Resistance Data Analysis","text":"Generates antibiograms - traditional, combined, syndromic, even WISCA Provides full microbiological taxonomy data antimicrobial drugs Applies recent CLSI EUCAST clinical breakpoints MICs disk zones Corrects duplicate isolates, calculates predicts AMR per antibiotic class Integrates WHONET, ATC, EARS-Net, PubChem, LOINC SNOMED CT Works Windows, macOS Linux versions R since R-3.0 completely dependency-free, highly suitable places limited resources https://msberends.github.io/AMR https://doi.org/10.18637/jss.v104.i03","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Antimicrobial Resistance Data Analysis","text":"AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) formed basis two PhD theses (DOI 10.33612/diss.177417131 DOI 10.33612/diss.192486375). installing package, R knows ~52,000 distinct microbial species (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"used-in-over-175-countries-translated-into-20-languages","dir":"","previous_headings":"Introduction","what":"Used in over 175 countries, translated into 20 languages","title":"Antimicrobial Resistance Data Analysis","text":"Since first public release early 2018, R package used almost countries world. Click map enlarge see country names. help contributors corners world, AMR package available  English,  Czech,  Chinese,  Danish,  Dutch,  Finnish,  French,  German,  Greek,  Italian,  Japanese,  Norwegian,  Polish,  Portuguese,  Romanian,  Russian,  Spanish,  Swedish,  Turkish,  Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"filtering-and-selecting-data","dir":"","previous_headings":"Practical examples","what":"Filtering and selecting data","title":"Antimicrobial Resistance Data Analysis","text":"defined row filter Gram-negative bacteria intrinsic resistance cefotaxime (mo_is_gram_negative() mo_is_intrinsic_resistant()) column selection two antibiotic groups (aminoglycosides() carbapenems()), reference data microorganisms antibiotics AMR package make sure get meant: base R equivalent : base R snippet work version R since April 2013 (R-3.0).","code":"# AMR works great with dplyr, but it's not required or neccesary library(AMR) library(dplyr)  example_isolates %>%   mutate(bacteria = mo_fullname()) %>%   filter(mo_is_gram_negative(),          mo_is_intrinsic_resistant(ab = \"cefotax\")) %>%   select(bacteria,          aminoglycosides(),          carbapenems()) example_isolates$bacteria <- mo_fullname(example_isolates$mo) example_isolates[which(mo_is_gram_negative() &                          mo_is_intrinsic_resistant(ab = \"cefotax\")),                  c(\"bacteria\", aminoglycosides(), carbapenems())]"},{"path":"https://msberends.github.io/AMR/index.html","id":"generating-antibiograms","dir":"","previous_headings":"Practical examples","what":"Generating antibiograms","title":"Antimicrobial Resistance Data Analysis","text":"AMR package supports generating traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). used inside R Markdown Quarto, table printed right output format automatically (markdown, LaTeX, HTML, etc.) using print() antibiogram object. combination antibiograms, clear combined antibiotics yield higher empiric coverage: Like many functions package, antibiogram() comes support 20 languages often detected automatically based system language:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems())) antibiogram(example_isolates,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),             mo_transform = \"gramstain\") antibiogram(example_isolates,             antibiotics = c(\"CIP\", \"TOB\", \"GEN\"),             mo_transform = \"gramstain\",             ab_transform = \"name\",             language = \"uk\") # Ukrainian"},{"path":"https://msberends.github.io/AMR/index.html","id":"calculating-resistance-per-group","dir":"","previous_headings":"Practical examples","what":"Calculating resistance per group","title":"Antimicrobial Resistance Data Analysis","text":"manual approach, can use resistance susceptibility() function:","code":"library(AMR) library(dplyr)  out <- example_isolates %>%   # group by ward:   group_by(ward) %>%   # calculate AMR using resistance(), over all aminoglycosides   # and polymyxins:   summarise(across(c(aminoglycosides(), polymyxins()),             resistance)) out # transform the antibiotic columns to names: out %>% set_ab_names() # transform the antibiotic column to ATC codes: out %>% set_ab_names(property = \"atc\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"what-else-can-you-do-with-this-package","dir":"","previous_headings":"","what":"What else can you do with this package?","title":"Antimicrobial Resistance Data Analysis","text":"package intended comprehensive toolbox integrated AMR data analysis. package can used : Reference taxonomy microorganisms, since package contains microbial (sub)species List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (manual) Interpreting raw MIC disk diffusion values, based CLSI EUCAST guideline last 10 years (manual) Retrieving antimicrobial drug names, doses forms administration clinical health care records (manual) Determining first isolates used AMR data analysis (manual) Calculating antimicrobial resistance (tutorial) Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (tutorial) Calculating (empirical) susceptibility mono therapy combination therapies (tutorial) Predicting future antimicrobial resistance using regression models (tutorial) Getting properties microorganism (like Gram stain, species, genus family) (manual) Getting properties antibiotic (like name, code EARS-Net/ATC/LOINC/PubChem, defined daily dose trade name) (manual) Plotting antimicrobial resistance (tutorial) Applying EUCAST expert rules (manual) Getting SNOMED codes microorganism, getting properties microorganism based SNOMED code (manual) Getting LOINC codes antibiotic, getting properties antibiotic based LOINC code (manual) Machine reading EUCAST CLSI guidelines 2011-2021 translate MIC values disk diffusion diameters SIR (link) Principal component analysis AMR (tutorial)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-official-version","dir":"","previous_headings":"Get this package","what":"Latest official version","title":"Antimicrobial Resistance Data Analysis","text":"package available official R network (CRAN). Install package R CRAN using command: downloaded installed automatically. RStudio, click menu Tools > Install Packages… type “AMR” press Install. Note: functions website may available latest release. use functions data sets mentioned website, install latest development version.","code":"install.packages(\"AMR\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-development-version","dir":"","previous_headings":"Get this package","what":"Latest development version","title":"Antimicrobial Resistance Data Analysis","text":"Please read Developer Guideline . latest unpublished development version can installed GitHub two ways: Manually, using: Automatically, using rOpenSci R-universe platform, adding R-universe address list repositories (‘repos’): , can install update AMR package like official release (e.g., using install.packages(\"AMR\") RStudio via Tools > Check Package Updates…).","code":"install.packages(\"remotes\") # if you haven't already remotes::install_github(\"msberends/AMR\") options(repos = c(getOption(\"repos\"),                   msberends = \"https://msberends.r-universe.dev\"))"},{"path":"https://msberends.github.io/AMR/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Antimicrobial Resistance Data Analysis","text":"find conduct AMR data analysis, please continue reading get started click link ‘’ menu.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"partners","dir":"","previous_headings":"","what":"Partners","title":"Antimicrobial Resistance Data Analysis","text":"development package part , related , made possible following non-profit organisations initiatives:","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"copyright","dir":"","previous_headings":"","what":"Copyright","title":"Antimicrobial Resistance Data Analysis","text":"R package free, open-source software licensed GNU General Public License v2.0 (GPL-2). nutshell, means package: May used commercial purposes May used private purposes May used patent purposes May modified, although: Modifications must released license distributing package Changes made code must documented May distributed, although: Source code must made available package distributed copy license copyright notice must included package. Comes LIMITATION liability Comes warranty","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated Functions — AMR-deprecated","title":"Deprecated Functions — AMR-deprecated","text":"functions -called 'Deprecated'. removed future release. Using functions give warning name function replaced (one).","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated Functions — AMR-deprecated","text":"","code":"NA_rsi_  as.rsi(x, ...)  facet_rsi(...)  geom_rsi(...)  ggplot_rsi(...)  ggplot_rsi_predict(...)  is.rsi(x, ...)  is.rsi.eligible(...)  labels_rsi_count(...)  n_rsi(...)  random_rsi(...)  rsi_df(...)  rsi_predict(...)  scale_rsi_colours(...)  theme_rsi(...)"},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deprecated Functions — AMR-deprecated","text":"object class rsi (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":null,"dir":"Reference","previous_headings":"","what":"Options for the AMR package — AMR-options","title":"Options for the AMR package — AMR-options","text":"overview package-specific options() can set AMR package.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"Options for the AMR package — AMR-options","text":"AMR_custom_ab  Allows use custom antimicrobial drugs package. explained add_custom_antimicrobials(). AMR_custom_mo  Allows use custom microorganisms package. explained add_custom_microorganisms(). AMR_eucastrules  Used setting default types rules eucast_rules() function, must one : \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). AMR_guideline  Used setting default guideline interpreting MIC values disk diffusion diameters .sir(). Can guideline name (e.g., \"CLSI\") name year (e.g. \"CLSI 2019\"). default \"EUCAST 2022\". Supported guideline currently EUCAST (2013-2022) CLSI (2013-2022). AMR_ignore_pattern  regular expression define input must ignored .mo() mo_* functions. AMR_include_PKPD  logical use .sir(), indicate PK/PD clinical breakpoints must applied last resort, defaults TRUE. AMR_include_screening  logical use .sir(), indicate clinical breakpoints screening allowed, defaults FALSE. AMR_keep_synonyms  logical use .mo() mo_* functions, indicate old, previously valid taxonomic names must preserved corrected currently accepted names. AMR_locale  language use AMR package, can one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) Ukrainian (uk). AMR_mo_source  file location manual code list used .mo() mo_* functions. explained set_mo_source().","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"saving-settings-between-sessions","dir":"Reference","previous_headings":"","what":"Saving Settings Between Sessions","title":"Options for the AMR package — AMR-options","text":"Settings R saved globally thus lost R exited. can save options .Rprofile file, user-specific file. can edit using:   file, can set options :   add Portuguese language support antibiotics, allow PK/PD rules interpreting MIC values .sir().","code":"utils::file.edit(\"~/.Rprofile\") options(AMR_locale = \"pt\")  options(AMR_include_PKPD = TRUE)"},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"share-options-within-team","dir":"Reference","previous_headings":"","what":"Share Options Within Team","title":"Options for the AMR package — AMR-options","text":"global approach, e.g. within data team, save options file remote file location, shared network drive. work way: Save plain text file e.g. \"X:/team_folder/R_options.R\" fill preferred settings. user, open .Rprofile file using utils::file.edit(\"~/.Rprofile\") put :   Reload R/RStudio check settings getOption(), e.g. getOption(\"AMR_locale\") set value. Now team settings configured one place, can maintained .","code":"source(\"X:/team_folder/R_options.R\")"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":null,"dir":"Reference","previous_headings":"","what":"The AMR Package — AMR","title":"The AMR Package — AMR","text":"Welcome AMR package. AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) formed basis two PhD theses (DOI 10.33612/diss.177417131 DOI 10.33612/diss.192486375). installing package, R knows ~52 000 (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen. AMR package available English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"The AMR Package — AMR","text":"cite AMR publications use: Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). \"AMR: R Package Working Antimicrobial Resistance Data.\" Journal Statistical Software, 104(3), 1-31. doi:10.18637/jss.v104.i03 . BibTeX entry LaTeX users :","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"The AMR Package — AMR","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The AMR Package — AMR","text":"Maintainer: Matthijs S. Berends m.berends@certe.nl (ORCID) Authors: Christian F. Luz (ORCID) [contributor] Dennis Souverein (ORCID) [contributor] Erwin E. . Hassing [contributor] contributors: Casper J. Albers (ORCID) [thesis advisor] Peter Dutey-Magni (ORCID) [contributor] Judith M. Fonville [contributor] Alex W. Friedrich (ORCID) [thesis advisor] Corinna Glasner (ORCID) [thesis advisor] Eric H. L. C. M. Hazenberg [contributor] Gwen Knight (ORCID) [contributor] Annick Lenglet (ORCID) [contributor] Bart C. Meijer [contributor] Dmytro Mykhailenko [contributor] Anton Mymrikov [contributor] Andrew P. Norgan (ORCID) [contributor] Sofia Ny (ORCID) [contributor] Jonas Salm [contributor] Rogier P. Schade [contributor] Bhanu N. M. Sinha (ORCID) [thesis advisor] Anthony Underwood (ORCID) [contributor] Anita Williams (ORCID) [contributor]","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":null,"dir":"Reference","previous_headings":"","what":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"antimicrobial drugs official names, ATC codes, ATC groups defined daily dose (DDD) included package, using Collaborating Centre Drug Statistics Methodology.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"","code":"as.ab(\"meropenem\") #> Class 'ab' #> [1] MEM ab_name(\"J01DH02\") #> [1] \"Meropenem\"  ab_tradenames(\"flucloxacillin\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 500 Isolates - WHONET Example — WHONET","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"example data set exact structure export file WHONET. files can used package, example data set shows. antibiotic results example_isolates data set. patient names created using online surname generators place practice purposes.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET"},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"tibble 500 observations 53 variables: Identification number ID sample Specimen number ID specimen Organism Name microorganism. analysis, transform valid microbial class, using .mo(). Country Country origin Laboratory Name laboratory Last name Fictitious last name patient First name Fictitious initial patient Sex Fictitious gender patient Age Fictitious age patient Age category Age group, can also looked using age_groups() Date admissionDate hospital admission Specimen dateDate specimen received laboratory Specimen type Specimen type group Specimen type (Numeric) Translation \"Specimen type\" Reason Reason request Differential Diagnosis Isolate number ID isolate Organism type Type microorganism, can also looked using mo_type() Serotype Serotype microorganism Beta-lactamase Microorganism produces beta-lactamase? ESBL Microorganism produces extended spectrum beta-lactamase? Carbapenemase Microorganism produces carbapenemase? MRSA screening test Microorganism possible MRSA? Inducible clindamycin resistance Clindamycin can induced? Comment comments Date data entryDate data entered WHONET AMP_ND10:CIP_EE 0 different antibiotics. can lookup abbreviations antibiotics data set, use e.g. ab_name(\"AMP\") get official name immediately. analysis, transform valid antibiotic class, using .sir().","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> Warning: * The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' #> columns to 'sir' with as.sir(), e.g.: #>   your_data %>% mutate_if(is.rsi, as.sir) #> # A tibble: 500 × 53 #>    Identif…¹ Speci…² Organ…³ Country Labor…⁴ Last …⁵ First…⁶ Sex     Age Age c…⁷ #>    <chr>       <int> <chr>   <chr>   <chr>   <chr>   <chr>   <chr> <dbl> <chr>   #>  1 fe41d7ba…    1748 SPN     Belgium Nation… Abel    B.      F        68 55-74   #>  2 91f175ec…    1767 eco     The Ne… Nation… Delacr… F.      M        89 75+     #>  3 cc401505…    1343 eco     The Ne… Nation… Steens… F.      M        85 75+     #>  4 e864b692…    1894 MAP     Denmark Nation… Beyers… L.      M        62 55-74   #>  5 3d051fe3…    1739 PVU     Belgium Nation… Hummel  W.      M        86 75+     #>  6 c80762a0…    1846 103     The Ne… Nation… Eikenb… J.      F        53 25-54   #>  7 8022d372…    1628 103     Denmark Nation… Leclerc S.      F        77 75+     #>  8 f3dc5f55…    1493 eco     The Ne… Nation… Delacr… W.      M        53 25-54   #>  9 15add38f…    1847 eco     France  Nation… Van La… S.      F        63 55-74   #> 10 fd41248d…    1458 eco     Germany Nation… Moulin  O.      F        75 75+     #> # … with 490 more rows, 43 more variables: `Date of admission` <date>, #> #   `Specimen date` <date>, `Specimen type` <chr>, #> #   `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>, #> #   `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>, #> #   Carbapenemase <lgl>, `MRSA screening test` <lgl>, #> #   `Inducible clindamycin resistance` <lgl>, Comment <chr>, #> #   `Date of data entry` <date>, AMP_ND10 <rsi[!]>, AMC_ED20 <rsi[!]>, …"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Use function e.g. clinical texts health care records. returns list antimicrobial drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"ab_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_ab = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_ab type = \"drug\": column name antibiotics data set translate antibiotic abbreviations , using ab_property(). Defaults FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed, defaults TRUE interactive mode ... arguments passed .ab()","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"function also internally used .ab(), although searches first drug name throw note drug names returned. Note: .ab() function may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"default, function search antimicrobial drug names. text elements searched official names, ATC codes brand names. uses .ab() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(abx = ab_from_text(clinical_text)) returned AB codes can transformed official names, groups, etc. ab_* functions ab_name() ab_group(), using translate_ab argument. using collapse, function return character:df %>% mutate(abx = ab_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"# mind the bad spelling of amoxicillin in this line, # straight from a true health care record: ab_from_text(\"28/03/2020 regular amoxicilliin 500mg po tid\") #> [[1]] #> Class 'ab' #> [1] AMX #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") #> [[1]] #> Class 'ab' #> [1] AMX CIP #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"dose\") #> [[1]] #> [1] 500 400 #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"admin\") #> [[1]] #> [1] \"oral\" \"iv\"   #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", collapse = \", \") #> [1] \"AMX, CIP\" # \\donttest{ # if you want to know which antibiotic groups were administered, do e.g.: abx <- ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") ab_group(abx[[1]]) #> [1] \"Beta-lactams/penicillins\" \"Quinolones\"                if (require(\"dplyr\")) {   tibble(clinical_text = c(     \"given 400mg cipro and 500 mg amox\",     \"started on doxy iv today\"   )) %>%     mutate(       abx_codes = ab_from_text(clinical_text),       abx_doses = ab_from_text(clinical_text, type = \"doses\"),       abx_admin = ab_from_text(clinical_text, type = \"admin\"),       abx_coll = ab_from_text(clinical_text, collapse = \"|\"),       abx_coll_names = ab_from_text(clinical_text,         collapse = \"|\",         translate_ab = \"name\"       ),       abx_coll_doses = ab_from_text(clinical_text,         type = \"doses\",         collapse = \"|\"       ),       abx_coll_admin = ab_from_text(clinical_text,         type = \"admin\",         collapse = \"|\"       )     ) } #> Loading required package: dplyr #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union #> # A tibble: 2 × 8 #>   clinical_text          abx_c…¹ abx_d…² abx_a…³ abx_c…⁴ abx_c…⁵ abx_c…⁶ abx_c…⁷ #>   <chr>                  <list>  <list>  <list>  <chr>   <chr>   <chr>   <chr>   #> 1 given 400mg cipro and… <ab>    <dbl>   <chr>   CIP|AMX Ciprof… 400|500 NA      #> 2 started on doxy iv to… <ab>    <dbl>   <chr>   DOX     Doxycy… NA      iv      #> # … with abbreviated variable names ¹​abx_codes, ²​abx_doses, ³​abx_admin, #> #   ⁴​abx_coll, ⁵​abx_coll_names, ⁶​abx_coll_doses, ⁷​abx_coll_admin # }"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antibiotic — ab_property","title":"Get Properties of an Antibiotic — ab_property","text":"Use functions return specific property antibiotic antibiotics data set. input values evaluated internally .ab().","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  ab_cid(x, ...)  ab_synonyms(x, ...)  ab_tradenames(x, ...)  ab_group(x, language = get_AMR_locale(), ...)  ab_atc(x, only_first = FALSE, ...)  ab_atc_group1(x, language = get_AMR_locale(), ...)  ab_atc_group2(x, language = get_AMR_locale(), ...)  ab_loinc(x, ...)  ab_ddd(x, administration = \"oral\", ...)  ab_ddd_units(x, administration = \"oral\", ...)  ab_info(x, language = get_AMR_locale(), ...)  ab_url(x, open = FALSE, ...)  ab_property(x, property = \"name\", language = get_AMR_locale(), ...)  set_ab_names(   data,   ...,   property = \"name\",   language = get_AMR_locale(),   snake_case = NULL )"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antibiotic — ab_property","text":"x (vector ) text can coerced valid antibiotic drug code .ab() language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. lead e.g. \"polymyxin B\" \"polymyxin b\". ... case set_ab_names() data data.frame: columns select (supports tidy selection column1:column4), otherwise arguments passed .ab() only_first logical indicate whether first ATC code must returned, giving preference J0-codes (.e., antimicrobial drug group) administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antibiotics data set: vector_or(colnames(antibiotics), sort = FALSE). data data.frame columns need renamed, character vector column names snake_case logical indicate whether names -called snake case: lower case spaces/slashes replaced underscore (_)","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antibiotic — ab_property","text":"integer case ab_cid() named list case ab_info() multiple ab_atc()/ab_synonyms()/ab_tradenames() double case ab_ddd() data.frame case set_ab_names() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antibiotic — ab_property","text":"output translated possible. function ab_url() return direct URL official website. warning returned required ATC code available. function set_ab_names() special column renaming function data.frames. renames columns names resemble antimicrobial drugs. always makes sure new column names unique. property = \"atc\" set, preference given ATC codes J-group.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antibiotic — ab_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antibiotic — ab_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"# all properties: ab_name(\"AMX\") #> [1] \"Amoxicillin\" ab_atc(\"AMX\") #> [1] \"J01CA04\" ab_cid(\"AMX\") #> [1] 33613 ab_synonyms(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_tradenames(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_group(\"AMX\") #> [1] \"Beta-lactams/penicillins\" ab_atc_group1(\"AMX\") #> [1] \"Beta-lactam antibacterials, penicillins\" ab_atc_group2(\"AMX\") #> [1] \"Penicillins with extended spectrum\" ab_url(\"AMX\") #>                                                           Amoxicillin  #> \"https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no\"   # smart lowercase tranformation ab_name(x = c(\"AMC\", \"PLB\")) #> [1] \"Amoxicillin/clavulanic acid\" \"Polymyxin B\"                 ab_name(x = c(\"AMC\", \"PLB\"), tolower = TRUE) #> [1] \"amoxicillin/clavulanic acid\" \"polymyxin B\"                  # defined daily doses (DDD) ab_ddd(\"AMX\", \"oral\") #> [1] 1.5 ab_ddd_units(\"AMX\", \"oral\") #> [1] \"g\" ab_ddd(\"AMX\", \"iv\") #> [1] 3 ab_ddd_units(\"AMX\", \"iv\") #> [1] \"g\"  ab_info(\"AMX\") # all properties as a list #> $ab #> [1] \"AMX\" #>  #> $cid #> [1] 33613 #>  #> $name #> [1] \"Amoxicillin\" #>  #> $group #> [1] \"Beta-lactams/penicillins\" #>  #> $atc #> [1] \"J01CA04\" #>  #> $atc_group1 #> [1] \"Beta-lactam antibacterials, penicillins\" #>  #> $atc_group2 #> [1] \"Penicillins with extended spectrum\" #>  #> $tradenames #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            #>  #> $loinc #> [1] \"16365-9\" \"25274-2\" \"3344-9\"  \"80133-2\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 1.5 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 3 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any': ab_atc(\"AMP\") #> [1] \"J01CA01\" \"S01AA19\" ab_group(\"J01CA01\") #> [1] \"Beta-lactams/penicillins\" ab_loinc(\"ampicillin\") #> [1] \"21066-6\" \"3355-5\"  \"33562-0\" \"33919-2\" \"43883-8\" \"43884-6\" \"87604-5\" ab_name(\"21066-6\") #> [1] \"Ampicillin\" ab_name(6249) #> [1] \"Ampicillin\" ab_name(\"J01CA01\") #> [1] \"Ampicillin\"  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") #> [1] \"J01DD04\"  # use set_ab_names() for renaming columns colnames(example_isolates) #>  [1] \"date\"    \"patient\" \"age\"     \"gender\"  \"ward\"    \"mo\"      \"PEN\"     #>  [8] \"OXA\"     \"FLC\"     \"AMX\"     \"AMC\"     \"AMP\"     \"TZP\"     \"CZO\"     #> [15] \"FEP\"     \"CXM\"     \"FOX\"     \"CTX\"     \"CAZ\"     \"CRO\"     \"GEN\"     #> [22] \"TOB\"     \"AMK\"     \"KAN\"     \"TMP\"     \"SXT\"     \"NIT\"     \"FOS\"     #> [29] \"LNZ\"     \"CIP\"     \"MFX\"     \"VAN\"     \"TEC\"     \"TCY\"     \"TGC\"     #> [36] \"DOX\"     \"ERY\"     \"CLI\"     \"AZM\"     \"IPM\"     \"MEM\"     \"MTR\"     #> [43] \"CHL\"     \"COL\"     \"MUP\"     \"RIF\"     colnames(set_ab_names(example_isolates)) #>  [1] \"date\"                          \"patient\"                       #>  [3] \"age\"                           \"gender\"                        #>  [5] \"ward\"                          \"mo\"                            #>  [7] \"benzylpenicillin\"              \"oxacillin\"                     #>  [9] \"flucloxacillin\"                \"amoxicillin\"                   #> [11] \"amoxicillin_clavulanic_acid\"   \"ampicillin\"                    #> [13] \"piperacillin_tazobactam\"       \"cefazolin\"                     #> [15] \"cefepime\"                      \"cefuroxime\"                    #> [17] \"cefoxitin\"                     \"cefotaxime\"                    #> [19] \"ceftazidime\"                   \"ceftriaxone\"                   #> [21] \"gentamicin\"                    \"tobramycin\"                    #> [23] \"amikacin\"                      \"kanamycin\"                     #> [25] \"trimethoprim\"                  \"trimethoprim_sulfamethoxazole\" #> [27] \"nitrofurantoin\"                \"fosfomycin\"                    #> [29] \"linezolid\"                     \"ciprofloxacin\"                 #> [31] \"moxifloxacin\"                  \"vancomycin\"                    #> [33] \"teicoplanin\"                   \"tetracycline\"                  #> [35] \"tigecycline\"                   \"doxycycline\"                   #> [37] \"erythromycin\"                  \"clindamycin\"                   #> [39] \"azithromycin\"                  \"imipenem\"                      #> [41] \"meropenem\"                     \"metronidazole\"                 #> [43] \"chloramphenicol\"               \"colistin\"                      #> [45] \"mupirocin\"                     \"rifampicin\"                    colnames(set_ab_names(example_isolates, NIT:VAN)) #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     set_ab_names()    # this does the same:   example_isolates %>%     rename_with(set_ab_names)    # set_ab_names() works with any AB property:   example_isolates %>%     set_ab_names(property = \"atc\")    example_isolates %>%     set_ab_names(where(is.sir)) %>%     colnames()    example_isolates %>%     set_ab_names(NIT:VAN) %>%     colnames() } #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Antimicrobials — add_custom_antimicrobials","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"add_custom_antimicrobials() can add custom antimicrobial drug names codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"add_custom_antimicrobials(x)  clear_custom_antimicrobials()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"x data.frame resembling antibiotics data set, least containing columns \"ab\" \"name\"","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"Important: Due R works, add_custom_antimicrobials() function run every R session - added antimicrobials stored sessions thus lost R exited. two ways automate process: Method 1: Using option AMR_custom_ab, preferred method. use method: Create data set structure antibiotics data set (containing least columns \"ab\" \"name\") save saveRDS() location choice, e.g. \"~/my_custom_ab.rds\", remote location. Set file location option AMR_custom_ab: options(AMR_custom_ab = \"~/my_custom_ab.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_antimicrobials() function. Method 2: Loading antimicrobial additions directly .Rprofile file. important downside requires AMR package installed else method fail. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_antimicrobials() clear previously added antimicrobials.","code":"# Add custom antimicrobial codes: options(AMR_custom_ab = \"~/my_custom_ab.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_antimicrobials(    data.frame(ab = \"TESTAB\",               name = \"Test Antibiotic\",               group = \"Test Group\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"# \\donttest{  # returns NA and throws a warning (which is suppressed here): suppressWarnings(   as.ab(\"testab\") ) #> Class 'ab' #> [1] <NA>  # now add a custom entry - it will be considered by as.ab() and # all ab_*() functions add_custom_antimicrobials(   data.frame(     ab = \"TESTAB\",     name = \"Test Antibiotic\",     # you can add any property present in the     # 'antibiotics' data set, such as 'group':     group = \"Test Group\"   ) ) #> ℹ Added one record to the internal antibiotics data set.  # \"testab\" is now a new antibiotic: as.ab(\"testab\") #> Class 'ab' #> [1] TESTAB ab_name(\"testab\") #> [1] \"Test Antibiotic\" ab_group(\"testab\") #> [1] \"Test Group\"  ab_info(\"testab\") #> $ab #> [1] \"TESTAB\" #>  #> $cid #> [1] NA #>  #> $name #> [1] \"Test Antibiotic\" #>  #> $group #> [1] \"Test Group\" #>  #> $atc #> [1] NA #>  #> $atc_group1 #> [1] NA #>  #> $atc_group2 #> [1] NA #>  #> $tradenames #> [1] NA #>  #> $loinc #> [1] NA #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] NA #>  #> $ddd$oral$units #> [1] NA #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] NA #>  #> $ddd$iv$units #> [1] NA #>  #>  #>    # Add Co-fluampicil, which is one of the many J01CR50 codes, see # https://www.whocc.no/ddd/list_of_ddds_combined_products/ add_custom_antimicrobials(   data.frame(     ab = \"COFLU\",     name = \"Co-fluampicil\",     atc = \"J01CR50\",     group = \"Beta-lactams/penicillins\"   ) ) #> ℹ Added one record to the internal antibiotics data set. ab_atc(\"Co-fluampicil\") #> [1] \"J01CR50\" ab_name(\"J01CR50\") #> [1] \"Co-fluampicil\"  # even antibiotic selectors work x <- data.frame(   random_column = \"some value\",   coflu = as.sir(\"S\"),   ampicillin = as.sir(\"R\") ) x #>   random_column coflu ampicillin #> 1    some value     S          R x[, betalactams()] #> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and #>   'ampicillin' #>   coflu ampicillin #> 1     S          R # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Microorganisms — add_custom_microorganisms","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"add_custom_microorganisms() can add custom microorganisms, non-taxonomic outcome laboratory analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"add_custom_microorganisms(x)  clear_custom_microorganisms()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"x data.frame resembling microorganisms data set, least containing column \"genus\" (case-insensitive)","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"function fill missing taxonomy , specific taxonomic columns missing, see Examples. Important: Due R works, add_custom_microorganisms() function run every R session - added microorganisms stored sessions thus lost R exited. two ways automate process: Method 1: Using option AMR_custom_mo, preferred method. use method: Create data set structure microorganisms data set (containing least column \"genus\") save saveRDS() location choice, e.g. \"~/my_custom_mo.rds\", remote location. Set file location option AMR_custom_mo: options(AMR_custom_mo = \"~/my_custom_mo.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_microorganisms() function. Method 2: Loading microorganism directly .Rprofile file. important downside requires AMR package installed else method fail. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_microorganisms() clear previously added antimicrobials.","code":"# Add custom microorganism codes: options(AMR_custom_mo = \"~/my_custom_mo.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_microorganisms(    data.frame(genus = \"Enterobacter\",               species = \"asburiae/cloacae\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"# \\donttest{ # a combination of species is not formal taxonomy, so # this will result in only \"Enterobacter asburiae\": mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae\"  # now add a custom entry - it will be considered by as.mo() and # all mo_*() functions add_custom_microorganisms(   data.frame(     genus = \"Enterobacter\",     species = \"asburiae/cloacae\"   ) ) #> ℹ Added Enterobacter asburiae/cloacae to the internal microorganisms data #>   set.  # E. asburiae/cloacae is now a new microorganism: mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # its code: as.mo(\"Enterobacter asburiae/cloacae\") #> Class 'mo' #> [1] CUSTOM1_ENTRBC_A_C  # all internal algorithms will work as well: mo_name(\"Ent asburia cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # and even the taxonomy was added based on the genus! mo_family(\"E. asburiae/cloacae\") #> [1] \"Enterobacteriaceae\" mo_gramstain(\"Enterobacter asburiae/cloacae\") #> [1] \"Gram-negative\"  mo_info(\"Enterobacter asburiae/cloacae\") #> $mo #> [1] \"CUSTOM1_ENTRBC_A_C\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Enterobacter\" #>  #> $species #> [1] \"asburiae/cloacae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $url #> [1] \"\" #>  #> $ref #> [1] \"Self-added, 2023\" #>  #> $snomed #> [1] NA #>    # the function tries to be forgiving: add_custom_microorganisms(   data.frame(     GENUS = \"BACTEROIDES / PARABACTEROIDES SLASHLINE\",     SPECIES = \"SPECIES\"   ) ) #> ℹ Added Bacteroides/Parabacteroides to the internal microorganisms data #>   set. mo_name(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"Bacteroides/Parabacteroides\" mo_rank(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"genus\"  # taxonomy still works, although a slashline genus was given as input: mo_family(\"Bacteroides/Parabacteroides\") #> [1] \"Bacteroidaceae\"   # for groups and complexes, set them as species or subspecies: add_custom_microorganisms(   data.frame(     genus = \"Citrobacter\",     species = c(\"freundii\", \"braakii complex\"),     subspecies = c(\"complex\", \"\")   ) ) #> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the #>   internal microorganisms data set. mo_name(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Citrobacter freundii complex\" \"Citrobacter braakii complex\"  mo_species(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"freundii complex\" \"braakii complex\"  mo_gramstain(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Gram-negative\" \"Gram-negative\" # }"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":null,"dir":"Reference","previous_headings":"","what":"Age in Years of Individuals — age","title":"Age in Years of Individuals — age","text":"Calculates age years based reference date, system date default.","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Age in Years of Individuals — age","text":"","code":"age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Age in Years of Individuals — age","text":"x date(s), character (vectors) coerced .POSIXlt() reference reference date(s) (defaults today), character (vectors) coerced .POSIXlt() exact logical indicate whether age calculation exact, .e. decimals. divides number days year--date (YTD) x number days year reference (either 365 366). na.rm logical indicate whether missing values removed ... arguments passed .POSIXlt(), origin","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Age in Years of Individuals — age","text":"integer (decimals) exact = FALSE, double (decimals) otherwise","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Age in Years of Individuals — age","text":"Ages 0 returned NA warning. Ages 120 give warning. function vectorises x reference, meaning either can length 1 argument larger length.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Age in Years of Individuals — age","text":"","code":"# 10 random pre-Y2K birth dates df <- data.frame(birth_date = as.Date(\"2000-01-01\") - runif(10) * 25000)  # add ages df$age <- age(df$birth_date)  # add exact ages df$age_exact <- age(df$birth_date, exact = TRUE)  # add age at millenium switch df$age_at_y2k <- age(df$birth_date, \"2000-01-01\")  df #>    birth_date age age_exact age_at_y2k #> 1  1939-01-24  84  84.06849         60 #> 2  1951-10-09  71  71.36164         48 #> 3  1932-05-25  90  90.73699         67 #> 4  1968-09-21  54  54.41096         31 #> 5  1953-07-06  69  69.62192         46 #> 6  1991-10-10  31  31.35890          8 #> 7  1995-02-19  27  27.99726          4 #> 8  1961-04-11  61  61.85753         38 #> 9  1952-03-22  70  70.91233         47 #> 10 1967-09-04  55  55.45753         32"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split Ages into Age Groups — age_groups","title":"Split Ages into Age Groups — age_groups","text":"Split ages age groups defined split argument. allows easier demographic (antimicrobial resistance) analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split Ages into Age Groups — age_groups","text":"","code":"age_groups(x, split_at = c(12, 25, 55, 75), na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split Ages into Age Groups — age_groups","text":"x age, e.g. calculated age() split_at values split x , defaults age groups 0-11, 12-24, 25-54, 55-74 75+. See Details. na.rm logical indicate whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split Ages into Age Groups — age_groups","text":"Ordered factor","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split Ages into Age Groups — age_groups","text":"split ages, input split_at argument can : numeric vector. value e.g. c(10, 20) split x 0-9, 10-19 20+. value 50 split x 0-49 50+. default split young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) elderly (75+). character: \"children\" \"kids\", equivalent : c(0, 1, 2, 4, 6, 13, 18). split 0, 1, 2-3, 4-5, 6-12, 13-17 18+. \"elderly\" \"seniors\", equivalent : c(65, 75, 85). split 0-64, 65-74, 75-84, 85+. \"fives\", equivalent : 1:20 * 5. split 0-4, 5-9, ..., 95-99, 100+. \"tens\", equivalent : 1:10 * 10. split 0-9, 10-19, ..., 90-99, 100+.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split Ages into Age Groups — age_groups","text":"","code":"ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)  # split into 0-49 and 50+ age_groups(ages, 50) #> [1] 0-49 0-49 0-49 50+  0-49 50+  50+  0-49 0-49 #> Levels: 0-49 < 50+  # split into 0-19, 20-49 and 50+ age_groups(ages, c(20, 50)) #> [1] 0-19  0-19  0-19  50+   20-49 50+   50+   20-49 20-49 #> Levels: 0-19 < 20-49 < 50+  # split into groups of ten years age_groups(ages, 1:10 * 10) #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+ age_groups(ages, split_at = \"tens\") #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+  # split into groups of five years age_groups(ages, 1:20 * 5) #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+ age_groups(ages, split_at = \"fives\") #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+  # split specifically for children age_groups(ages, c(1, 2, 4, 6, 13, 18)) #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+ age_groups(ages, \"children\") #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+  # \\donttest{ # resistance of ciprofloxacin per age group if (require(\"dplyr\") && require(\"ggplot2\")) {   example_isolates %>%     filter_first_isolate() %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(       x = \"age_group\",       minimum = 0,       x.title = \"Age Group\",       title = \"Ciprofloxacin resistance per age group\"     ) } #> Loading required package: ggplot2  # }"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Generate antibiogram, communicate results plots tables. functions follow logic Klinker et al. Barbieri et al. (see Source), allow reporting e.g. R Markdown Quarto well.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"antibiogram(   x,   antibiotics = where(is.sir),   mo_transform = \"shortname\",   ab_transform = NULL,   syndromic_group = NULL,   add_total_n = TRUE,   only_all_tested = FALSE,   digits = 0,   col_mo = NULL,   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   sep = \" + \",   info = interactive() )  # S3 method for antibiogram plot(x, ...)  # S3 method for antibiogram autoplot(object, ...)  # S3 method for antibiogram print(x, as_kable = !interactive(), italicise = TRUE, ...)"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Klinker KP et al. (2021). Antimicrobial stewardship antibiograms: importance moving beyond traditional antibiograms. Therapeutic Advances Infectious Disease, May 5;8:20499361211011373; doi:10.1177/20499361211011373 Barbieri E et al. (2021). Development Weighted-Incidence Syndromic Combination Antibiogram (WISCA) guide choice empiric antibiotic treatment urinary tract infection paediatric patients: Bayesian approach Antimicrobial Resistance & Infection Control May 1;10(1):74; doi:10.1186/s13756-021-00939-2 M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"x data.frame containing least column microorganisms columns antibiotic results (class 'sir', see .sir()) antibiotics vector column names, (combinations ) antibiotic selectors aminoglycosides() carbapenems(). combination antibiograms, can also column names separated \"+\", \"TZP+TOB\" given data set contains columns \"TZP\" \"TOB\". See Examples. mo_transform character transform microorganism input - must \"name\", \"shortname\", \"gramstain\", one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\" \"snomed\". Can also NULL transform input. ab_transform character transform antibiotic input - must one column names antibiotics data set: \"ab\", \"cid\", \"name\", \"group\", \"atc\", \"atc_group1\", \"atc_group2\", \"abbreviations\", \"synonyms\", \"oral_ddd\", \"oral_units\", \"iv_ddd\", \"iv_units\" \"loinc\". Can also NULL transform input. syndromic_group column name x, values calculated split rows x, e.g. using ifelse() case_when(). See Examples. add_total_n logical indicate whether total available numbers per pathogen added table (defaults TRUE). add lowest highest number available isolate per antibiotic (e.g, E. coli 200 isolates available ciprofloxacin 150 amoxicillin, returned number \"150-200\"). only_all_tested (combination antibiograms): logical indicate isolates must tested antibiotics, see Details digits number digits use rounding col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). language language translate text, defaults system language (see get_AMR_locale()) minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether susceptibility determined results either S , instead S (defaults TRUE) sep separating character antibiotic columns combination antibiograms info logical indicate info printed, defaults TRUE interactive mode ... used print(): arguments passed knitr::kable() (otherwise, use) object antibiogram() object as_kable logical indicate whether printing done using knitr::kable() (default non-interactive sessions) italicise logical indicate whether microorganism names output table made italic, using italicise_taxonomy(). works output format markdown, HTML output.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"function returns table values 0 100 susceptibility, resistance. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. four antibiogram types, proposed Klinker et al. (2021, doi:10.1177/20499361211011373 ), supported antibiogram(): Traditional Antibiogram Case example: Susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Code example:   Combination Antibiogram Case example: Additional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Code example:   Syndromic Antibiogram Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Code example:   Weighted-Incidence Syndromic Combination Antibiogram (WISCA) Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure Code example:   types antibiograms can generated functions described page, can plotted (using ggplot2::autoplot() base R plot()/barplot()) printed R Markdown / Quarto formats reports using print(). Use functions specific 'table reporting' packages transform output antibiogram() needs, e.g. flextable::as_flextable() gt::gt(). Note combination antibiograms, important realise susceptibility can calculated two ways, can set only_all_tested argument (defaults FALSE). See example two antibiotics, Drug Drug B, antibiogram() works calculate %SI:   Printing antibiogram non-interactive sessions done knitr::kable(), support implemented formats, \"markdown\". knitr format automatically determined printed inside knitr document (LaTeX, HTML, etc.).","code":"antibiogram(your_data,             antibiotics = \"TZP\") antibiogram(your_data,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\")) antibiogram(your_data,             antibiotics = penicillins(),             syndromic_group = \"ward\") library(dplyr) your_data %>%    filter(ward == \"ICU\" & specimen_type == \"Respiratory\") %>%    antibiogram(antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),               syndromic_group = ifelse(.$age >= 65 &                                          .$gender == \"Male\" &                                          .$condition == \"Heart Disease\",                                        \"Study Group\", \"Control Group\")) --------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - --------------------------------------------------------------------"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>  # \\donttest{ # Traditional antibiogram ----------------------------------------------  antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()) ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 10 × 7 #>    `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 CoNS (43-309)              0    86    52     0    52    22 #>  2 E. coli (0-462)          100    98   100    NA   100    97 #>  3 E. faecalis (0-39)         0     0   100     0    NA     0 #>  4 K. pneumoniae (0-58)      NA    90   100    NA   100    90 #>  5 P. aeruginosa (17-30)     NA   100    NA     0    NA   100 #>  6 P. mirabilis (0-34)       NA    94    94    NA    NA    94 #>  7 S. aureus (2-233)         NA    99    NA    NA    NA    98 #>  8 S. epidermidis (8-163)     0    79    NA     0    NA    51 #>  9 S. hominis (3-80)         NA    92    NA    NA    NA    85 #> 10 S. pneumoniae (11-117)     0     0    NA     0    NA     0  antibiogram(example_isolates,   antibiotics = aminoglycosides(),   ab_transform = \"atc\",   mo_transform = \"gramstain\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Pathogen (N min-max)`   J01GB01 J01GB03 J01GB04 J01GB06 #> * <chr>                      <dbl>   <dbl>   <dbl>   <dbl> #> 1 Gram-negative (35-686)        96      96       0      98 #> 2 Gram-positive (436-1170)      34      63       0       0  antibiogram(example_isolates,   antibiotics = carbapenems(),   ab_transform = \"name\",   mo_transform = \"name\" ) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 5 × 3 #>   `Pathogen (N min-max)`                           Imipenem Meropenem #> * <chr>                                               <dbl>     <dbl> #> 1 Coagulase-negative Staphylococcus (CoNS) (48-48)       52        52 #> 2 Enterococcus faecalis (0-38)                          100        NA #> 3 Escherichia coli (418-422)                            100       100 #> 4 Klebsiella pneumoniae (51-53)                         100       100 #> 5 Proteus mirabilis (27-32)                              94        NA   # Combined antibiogram -------------------------------------------------  # combined antibiotics yield higher empiric coverage antibiogram(example_isolates,   antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),   mo_transform = \"gramstain\" ) #> # A tibble: 2 × 4 #>   `Pathogen (N min-max)`     TZP `TZP + GEN` `TZP + TOB` #> * <chr>                    <dbl>       <dbl>       <dbl> #> 1 Gram-negative (641-693)     88          99          98 #> 2 Gram-positive (345-1044)    86          98          95  antibiogram(example_isolates,   antibiotics = c(\"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   ab_transform = \"name\",   sep = \" & \" ) #> # A tibble: 2 × 3 #>   `Pathogen (N min-max)`  `Piperacillin/tazobactam` Piperacillin/tazobactam & …¹ #> * <chr>                                       <dbl>                        <dbl> #> 1 Gram-negative (641-693)                        88                           98 #> 2 Gram-positive (345-550)                        86                           95 #> # … with abbreviated variable name ¹​`Piperacillin/tazobactam & Tobramycin`   # Syndromic antibiogram ------------------------------------------------  # the data set could contain a filter for e.g. respiratory specimens antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()),   syndromic_group = \"ward\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 14 × 8 #>    `Syndromic Group` `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>             <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 Clinical          CoNS (23-205)             NA    89    57    NA    57    26 #>  2 ICU               CoNS (10-73)              NA    79    NA    NA    NA    NA #>  3 Outpatient        CoNS (3-31)               NA    84    NA    NA    NA    NA #>  4 Clinical          E. coli (0-299)          100    98   100    NA   100    98 #>  5 ICU               E. coli (0-137)          100    99   100    NA   100    96 #>  6 Clinical          K. pneumoniae (0-51)      NA    92   100    NA   100    92 #>  7 Clinical          P. mirabilis (0-30)       NA   100    NA    NA    NA   100 #>  8 Clinical          S. aureus (2-150)         NA    99    NA    NA    NA    97 #>  9 ICU               S. aureus (0-66)          NA   100    NA    NA    NA    NA #> 10 Clinical          S. epidermidis (4-79)     NA    82    NA    NA    NA    55 #> 11 ICU               S. epidermidis (4-75)     NA    72    NA    NA    NA    41 #> 12 Clinical          S. hominis (1-45)         NA    96    NA    NA    NA    94 #> 13 Clinical          S. pneumoniae (5-78)       0     0    NA     0    NA     0 #> 14 ICU               S. pneumoniae (5-30)       0     0    NA     0    NA     0  # now define a data set with only E. coli ex1 <- example_isolates[which(mo_genus() == \"Escherichia\"), ] #> ℹ Using column 'mo' as input for mo_genus()  # with a custom language, though this will be determined automatically # (i.e., this table will be in Spanish on Spanish systems) antibiogram(ex1,   antibiotics = aminoglycosides(),   ab_transform = \"name\",   syndromic_group = ifelse(ex1$ward == \"ICU\",     \"UCI\", \"No UCI\"   ),   language = \"es\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina #> * <chr>              <chr>                      <dbl>       <dbl>       <dbl> #> 1 No UCI             E. coli (0-325)              100          98          98 #> 2 UCI                E. coli (0-137)              100          99          96   # Weighted-incidence syndromic combination antibiogram (WISCA) ---------  # the data set could contain a filter for e.g. respiratory specimens/ICU antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   minimum = 10, # this should be >=30, but now just as example   syndromic_group = ifelse(example_isolates$age >= 65 &     example_isolates$gender == \"M\",   \"WISCA Group 1\", \"WISCA Group 2\"   ) ) #> # A tibble: 4 × 6 #>   `Syndromic Group` `Pathogen (N min-max)`    AMC `AMC + CIP`   TZP `TZP + TOB` #> * <chr>             <chr>                   <dbl>       <dbl> <dbl>       <dbl> #> 1 WISCA Group 1     Gram-negative (261-285)    76          95    89          99 #> 2 WISCA Group 2     Gram-negative (380-442)    76          98    88          98 #> 3 WISCA Group 1     Gram-positive (123-406)    76          89    81          95 #> 4 WISCA Group 2     Gram-positive (222-732)    76          89    88          95  # Print the output for R Markdown / Quarto -----------------------------  ureido <- antibiogram(example_isolates,                       antibiotics = ureidopenicillins(),                       ab_transform = \"name\") #> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)  # in an Rmd file, you would just need print(ureido), but to be explicit: print(ureido, as_kable = TRUE, format = \"markdown\", italicise = TRUE) #>  #>  #> | Pathogen (N min-max)      | Piperacillin/tazobactam| #> |:--------------------------|-----------------------:| #> | CoNS (33-33)              |                      30| #> | *E. coli* (416-416)       |                      94| #> | *K. pneumoniae* (53-53)   |                      89| #> | *S. pneumoniae* (112-112) |                     100|   # Generate plots with ggplot2 or base R --------------------------------  ab1 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\" ) ab2 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   syndromic_group = \"ward\" )  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab1) }  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab2) }   plot(ab1)  plot(ab2)   # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Antibiotic Selectors — antibiotic_class_selectors","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions allow filtering rows selecting columns based antibiotic test results specific antibiotic class group, without need define columns antibiotic abbreviations. short, column name resembles antimicrobial drug, picked functions matches pharmaceutical class: \"cefazolin\", \"CZO\" \"J01DB04\" picked cephalosporins().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"ab_class(ab_class, only_sir_columns = FALSE, only_treatable = TRUE, ...)  ab_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminopenicillins(only_sir_columns = FALSE, ...)  antifungals(only_sir_columns = FALSE, ...)  antimycobacterials(only_sir_columns = FALSE, ...)  betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)  carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)  cephalosporins(only_sir_columns = FALSE, ...)  cephalosporins_1st(only_sir_columns = FALSE, ...)  cephalosporins_2nd(only_sir_columns = FALSE, ...)  cephalosporins_3rd(only_sir_columns = FALSE, ...)  cephalosporins_4th(only_sir_columns = FALSE, ...)  cephalosporins_5th(only_sir_columns = FALSE, ...)  fluoroquinolones(only_sir_columns = FALSE, ...)  glycopeptides(only_sir_columns = FALSE, ...)  lincosamides(only_sir_columns = FALSE, ...)  lipoglycopeptides(only_sir_columns = FALSE, ...)  macrolides(only_sir_columns = FALSE, ...)  oxazolidinones(only_sir_columns = FALSE, ...)  penicillins(only_sir_columns = FALSE, ...)  polymyxins(only_sir_columns = FALSE, only_treatable = TRUE, ...)  streptogramins(only_sir_columns = FALSE, ...)  quinolones(only_sir_columns = FALSE, ...)  tetracyclines(only_sir_columns = FALSE, ...)  trimethoprims(only_sir_columns = FALSE, ...)  ureidopenicillins(only_sir_columns = FALSE, ...)  administrable_per_os(only_sir_columns = FALSE, ...)  administrable_iv(only_sir_columns = FALSE, ...)  not_intrinsic_resistant(   only_sir_columns = FALSE,   col_mo = NULL,   version_expertrules = 3.3,   ... )"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"ab_class antimicrobial class part , \"carba\" \"carbapenems\". columns group, atc_group1 atc_group2 antibiotics data set searched (case-insensitive) value. only_sir_columns logical indicate whether columns class sir must selected (defaults FALSE), see .sir() only_treatable logical indicate whether antimicrobial drugs excluded laboratory tests (defaults TRUE), gentamicin-high (GEH) imipenem/EDTA (IPE) ... ignored, place allow future extensions filter expression evaluated antibiotics data set, name %like% \"trim\" col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\" \"3.1\".","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"(internally) character vector column names, additional class \"ab_selector\"","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions can used data set calls selecting columns filtering rows. heavily inspired Tidyverse selection helpers everything(), also work base R dplyr verbs. Nonetheless, convenient use dplyr functions select(), filter() summarise(), see Examples. columns data functions called searched known antibiotic names, abbreviations, brand names, codes (ATC, EARS-Net, , etc.) according antibiotics data set. means selector aminoglycosides() pick column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. ab_class() function can used filter/select manually defined antibiotic class. searches results antibiotics data set within columns group, atc_group1 atc_group2. ab_selector() function can used internally filter antibiotics data set results, see Examples. allows filtering (part ) certain name, /group name even minimum DDDs oral treatment. function yields highest flexibility, also least user-friendly, since requires hard-coded filter set. administrable_per_os() administrable_iv() functions also rely antibiotics data set - antibiotic columns matched DDD (defined daily dose) resp. oral IV treatment available antibiotics data set. not_intrinsic_resistant() function can used select antibiotic columns pose intrinsic resistance microorganisms data set. example, data set contains microorganism codes names E. coli K. pneumoniae contains column \"vancomycin\", column removed (rather, unselected) using function. currently applies 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021) determine intrinsic resistance, using eucast_rules() function internally. determination, function quite slow terms performance.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"full-list-of-supported-antibiotic-classes","dir":"Reference","previous_headings":"","what":"Full list of supported (antibiotic) classes","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"aminoglycosides() can select:  amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) tobramycin-high (TOH) aminopenicillins() can select:  amoxicillin (AMX) ampicillin (AMP) antifungals() can select:  amphotericin B (AMB), anidulafungin (ANI), butoconazole (), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) voriconazole (VOR) antimycobacterials() can select:  4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR) viomycin (VIO) betalactams() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) ticarcillin/clavulanic acid (TCC) carbapenems() can select:  biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) tebipenem (TBP) cephalosporins() can select:  cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM) loracarbef (LOR) cephalosporins_1st() can select:  cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL) cephradine (CED) cephalosporins_2nd() can select:  cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) loracarbef (LOR) cephalosporins_3rd() can select:  cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB) latamoxef (LTM) cephalosporins_4th() can select:  cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) cefquinome (CEQ) cephalosporins_5th() can select:  ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1) ceftolozane/tazobactam (CZT) fluoroquinolones() can select:  besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) trovafloxacin (TVA) glycopeptides() can select:  avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) vancomycin-macromethod (VAM) lincosamides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) tylvalosin (TYL1) lipoglycopeptides() can select:  dalbavancin (DAL), oritavancin (ORI) telavancin (TLV) macrolides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) tylvalosin (TYL1) oxazolidinones() can select:  cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) thiacetazone (THA) penicillins() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) ticarcillin/clavulanic acid (TCC) polymyxins() can select:  colistin (COL), polymyxin B (PLB) polymyxin B/polysorbate 80 (POP) quinolones() can select:  besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) trovafloxacin (TVA) streptogramins() can select:  pristinamycin (PRI) quinupristin/dalfopristin (QDA) tetracyclines() can select:  cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY) tigecycline (TGC) trimethoprims() can select:  brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP) trimethoprim/sulfamethoxazole (SXT) ureidopenicillins() can select:  azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) piperacillin/tazobactam (TZP)","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>  # base R ------------------------------------------------------------------  # select columns 'IPM' (imipenem) and 'MEM' (meropenem) example_isolates[, carbapenems()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # … with 1,990 more rows  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' example_isolates[, c(\"mo\", aminoglycosides())] #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # … with 1,990 more rows  # select only antibiotic columns with DDDs for oral treatment example_isolates[, administrable_per_os()] #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 23 #>    OXA   FLC   AMX   AMC   AMP   CXM   KAN   TMP   NIT   FOS   LNZ   CIP   MFX   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  2 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  3 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  4 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  5 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  6 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  7 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  8 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  9 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    S     NA    #> 10 NA    S     NA    NA    NA    S     NA    S     NA    NA    NA    S     NA    #> # … with 1,990 more rows, and 10 more variables: VAN <sir>, TCY <sir>, #> #   DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, RIF <sir>  # filter using any() or all() example_isolates[any(carbapenems() == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> subset(example_isolates, any(carbapenems() == \"R\")) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir>  # filter on any or all results in the carbapenem columns (i.e., IPM, MEM): example_isolates[any(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 962 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  7 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  8 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  9 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #> 10 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #> # … with 952 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> example_isolates[all(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 756 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-04-14 F30196     73 M      Outpat… B_STRPT_GRPB  S     NA    S     S     #>  2 2003-04-08 114570     74 M      ICU     B_STRPT_PYGN  S     NA    S     S     #>  3 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  4 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  5 2003-08-14 F71508      0 F      Clinic… B_STRPT_GRPB  S     NA    S     S     #>  6 2003-10-16 650870     63 F      ICU     B_ESCHR_COLI  R     NA    NA    R     #>  7 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  9 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> 10 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> # … with 746 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir>  # filter with multiple antibiotic selectors using c() example_isolates[all(c(carbapenems(), aminoglycosides()) == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 26 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  2 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  4 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  5 2008-12-06 501361     43 F      Clinical B_STNTR_MLTP R     NA    NA    R     #>  6 2011-05-09 207325     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2012-03-12 582258     80 M      ICU      B_STPHY_CONS R     R     R     R     #>  8 2012-05-19 C25552     89 F      Outpati… B_STPHY_CONS R     R     R     R     #>  9 2012-07-17 F05015     83 M      ICU      B_STPHY_CONS R     R     R     R     #> 10 2012-07-20 404299     66 F      Clinical B_STPHY_CONS R     R     R     R     #> # … with 16 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir>  # filter + select in one go: get penicillins in carbapenems-resistant strains example_isolates[any(carbapenems() == \"R\"), penicillins()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP' #>   (piperacillin/tazobactam) #> # A tibble: 55 × 7 #>    PEN   OXA   FLC   AMX   AMC   AMP   TZP   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    NA    NA    NA    NA    #>  2 NA    NA    NA    NA    NA    NA    NA    #>  3 R     NA    NA    R     R     R     R     #>  4 NA    NA    NA    NA    NA    NA    R     #>  5 NA    NA    NA    NA    NA    NA    R     #>  6 NA    NA    NA    NA    NA    NA    R     #>  7 NA    NA    NA    NA    NA    NA    R     #>  8 NA    NA    NA    NA    NA    NA    R     #>  9 R     NA    NA    NA    S     NA    S     #> 10 R     NA    NA    NA    S     NA    S     #> # … with 45 more rows  # You can combine selectors with '&' to be more specific. For example, # penicillins() would select benzylpenicillin ('peni G') and # administrable_per_os() would select erythromycin. Yet, when combined these # drugs are both omitted since benzylpenicillin is not administrable per os # and erythromycin is not a penicillin: example_isolates[, penicillins() & administrable_per_os()] #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # … with 1,990 more rows  # ab_selector() applies a filter in the `antibiotics` data set and is thus very # flexible. For instance, to select antibiotic columns with an oral DDD of at # least 1 gram: example_isolates[, ab_selector(oral_ddd > 1 & oral_units == \"g\")] #> ℹ For ab_selector(oral_ddd > 1 & oral_units == \"g\") using columns 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS' #>   (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin), #>   'CLI' (clindamycin), 'MTR' (metronidazole) and 'CHL' (chloramphenicol) #> # A tibble: 2,000 × 13 #>    OXA   FLC   AMX   AMC   AMP   KAN   FOS   LNZ   VAN   ERY   CLI   MTR   CHL   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  2 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  3 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    NA    NA    NA    S     R     R     NA    NA    #>  7 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  8 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  9 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    NA    NA    NA    S     S     NA    NA    NA    #> # … with 1,990 more rows  # dplyr ------------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   # get AMR for all aminoglycosides e.g., per ward:   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), resistance)) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `across(aminoglycosides(), resistance)`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 5 #>   ward         GEN   TOB   AMK   KAN #>   <chr>      <dbl> <dbl> <dbl> <dbl> #> 1 Clinical   0.229 0.315 0.626     1 #> 2 ICU        0.290 0.400 0.662     1 #> 3 Outpatient 0.2   0.368 0.605    NA if (require(\"dplyr\")) {   # You can combine selectors with '&' to be more specific:   example_isolates %>%     select(penicillins() & administrable_per_os()) } #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin) and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin) and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # … with 1,990 more rows if (require(\"dplyr\")) {   # get AMR for only drugs that matter - no intrinsic resistance:   example_isolates %>%     filter(mo_genus() %in% c(\"Escherichia\", \"Klebsiella\")) %>%     group_by(ward) %>%     summarise(across(not_intrinsic_resistant(), resistance)) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ For not_intrinsic_resistant() removing columns 'PEN' #>   (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC' #>   (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM' #>   (azithromycin) and 'RIF' (rifampicin) #> Warning: There were 52 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `across(not_intrinsic_resistant(), resistance)`. #> ℹ In group 1: `ward = \"Clinical\"`. #> Caused by warning: #> ! Introducing NA: no results available for OXA in group: ward = \"Clinical\" #> (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 51 remaining warnings. #> # A tibble: 3 × 33 #>   ward    OXA   FLC    AMX    AMC    AMP     TZP     CZO     FEP     CXM     FOX #>   <chr> <dbl> <dbl>  <dbl>  <dbl>  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl> #> 1 Clin…    NA    NA  0.606  0.121  0.606  0.0504  0.0656  0.0159  0.0622  0.0648 #> 2 ICU      NA    NA  0.535  0.172  0.535  0.119  NA       0.0722  0.0828  0.0992 #> 3 Outp…    NA    NA NA     NA     NA     NA      NA      NA      NA      NA      #> # … with 22 more variables: CTX <dbl>, CAZ <dbl>, CRO <dbl>, GEN <dbl>, #> #   TOB <dbl>, AMK <dbl>, KAN <dbl>, TMP <dbl>, SXT <dbl>, NIT <dbl>, #> #   FOS <dbl>, CIP <dbl>, MFX <dbl>, TCY <dbl>, TGC <dbl>, DOX <dbl>, #> #   IPM <dbl>, MEM <dbl>, MTR <dbl>, CHL <dbl>, COL <dbl>, MUP <dbl> if (require(\"dplyr\")) {   # get susceptibility for antibiotics whose name contains \"trim\":   example_isolates %>%     filter(first_isolate()) %>%     group_by(ward) %>%     summarise(across(ab_selector(name %like% \"trim\"), susceptibility)) } #> ℹ For ab_selector(name %like% \"trim\") using columns 'TMP' (trimethoprim) #>   and 'SXT' (trimethoprim/sulfamethoxazole) #> # A tibble: 3 × 3 #>   ward         TMP   SXT #>   <chr>      <dbl> <dbl> #> 1 Clinical   0.627 0.808 #> 2 ICU        0.549 0.778 #> 3 Outpatient 0.667 0.821 if (require(\"dplyr\")) {   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):   example_isolates %>%     select(carbapenems()) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # … with 1,990 more rows if (require(\"dplyr\")) {   # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':   example_isolates %>%     select(mo, aminoglycosides()) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # … with 1,990 more rows if (require(\"dplyr\")) {   # any() and all() work in dplyr's filter() too:   example_isolates %>%     filter(       any(aminoglycosides() == \"R\"),       all(cephalosporins_2nd() == \"R\")     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> ℹ For cephalosporins_2nd() using columns 'CXM' (cefuroxime) and 'FOX' #>   (cefoxitin) #> # A tibble: 112 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  7 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #> 10 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #> # … with 102 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> if (require(\"dplyr\")) {   # also works with c():   example_isolates %>%     filter(any(c(carbapenems(), aminoglycosides()) == \"R\")) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 531 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  4 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  5 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> # … with 521 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> if (require(\"dplyr\")) {   # not setting any/all will automatically apply all():   example_isolates %>%     filter(aminoglycosides() == \"R\") } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around all() or #>   any() to prevent this note. #> # A tibble: 427 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  3 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  4 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  6 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-16 D25302     65 F      ICU      B_STRPT_ANGN S     NA    NA    S     #> # … with 417 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> if (require(\"dplyr\")) {   # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):   example_isolates %>%     select(mo, ab_class(\"mycobact\")) } #> ℹ For ab_class(\"mycobact\") using column 'RIF' (rifampicin) #> # A tibble: 2,000 × 2 #>    mo           RIF   #>    <mo>         <sir> #>  1 B_ESCHR_COLI R     #>  2 B_ESCHR_COLI R     #>  3 B_STPHY_EPDR NA    #>  4 B_STPHY_EPDR NA    #>  5 B_STPHY_EPDR NA    #>  6 B_STPHY_EPDR NA    #>  7 B_STPHY_AURS NA    #>  8 B_STPHY_AURS NA    #>  9 B_STPHY_EPDR NA    #> 10 B_STPHY_EPDR NA    #> # … with 1,990 more rows if (require(\"dplyr\")) {   # get bug/drug combinations for only glycopeptides in Gram-positives:   example_isolates %>%     filter(mo_is_gram_positive()) %>%     select(mo, glycopeptides()) %>%     bug_drug_combinations() %>%     format() } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC' #>   (teicoplanin) #> # A tibble: 2 × 8 #>   Group           Drug             CoNS  E. fa…¹ S. au…² S. ep…³ S. ho…⁴ S. pn…⁵ #>   <chr>           <chr>            <chr> <chr>   <chr>   <chr>   <chr>   <chr>   #> 1 \"Glycopeptides\" Teicoplanin (TE… \"\"    \"\"      \" 0.0%… \"64.1%… \" 6.8%… \"\"      #> 2 \"\"              Vancomycin (VAN… \" 0.… \" 0.0%… \" 0.0%… \" 0.0%… \" 0.0%… \" 0.0%… #> # … with abbreviated variable names ¹​`E. faecalis`, ²​`S. aureus`, #> #   ³​`S. epidermidis`, ⁴​`S. hominis`, ⁵​`S. pneumoniae` if (require(\"dplyr\")) {   data.frame(     some_column = \"some_value\",     J01CA01 = \"S\"   ) %>% # ATC code of ampicillin     select(penicillins()) # only the 'J01CA01' column will be selected } #> ℹ For penicillins() using column 'J01CA01' (ampicillin) #>   J01CA01 #> 1       S if (require(\"dplyr\")) {   # with recent versions of dplyr this is all equal:   x <- example_isolates[carbapenems() == \"R\", ]   y <- example_isolates %>% filter(carbapenems() == \"R\")   z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == \"R\"))   identical(x, y) && identical(y, z) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> [1] TRUE # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Sets with 603 Antimicrobial Drugs — antibiotics","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Two data sets containing antibiotics/antimycotics antivirals. Use .ab() one ab_* functions retrieve values antibiotics data set. Three identifiers included data set: antibiotic ID (ab, primarily used package) defined WHONET/EARS-Net, ATC code (atc) defined , Compound ID (cid) found PubChem. properties data set derived one codes. Note drugs multiple ATC codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics  antivirals"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"object class tbl_df (inherits tbl, data.frame) 120 rows 11 columns.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antibiotics data set: a tibble with 483 observations and 14 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available cid Compound ID found PubChem name Official name used WHONET/EARS-Net group short concise group name, based WHONET WHOCC definitions atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC, like J01CR02 atc_group1 Official pharmacological subgroup (3rd level ATC code) defined WHOCC, like \"Macrolides, lincosamides streptogramins\" atc_group2 Official chemical subgroup (4th level ATC code) defined WHOCC, like \"Macrolides\" abbr List abbreviations used many countries, also antibiotic susceptibility testing (AST) synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment, currently available 174 drugs oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available 146 drugs iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug. Use ab_loinc() retrieve quickly, see ab_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antivirals-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antivirals data set: a tibble with 120 observations and 11 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"av Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name used WHONET/EARS-Net atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC cid Compound ID found PubChem atc_group Official pharmacological subgroup (3rd level ATC code) defined WHOCC synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral treatment iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology (WHOCC): https://www.whocc./atc_ddd_index/ Logical Observation Identifiers Names Codes (LOINC), Version 2.73 (8 August, 2022). Accessed https://loinc.org 30 October, 2022. European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Properties based ATC code available ATC available. properties : atc_group1, atc_group2, oral_ddd, oral_units, iv_ddd iv_units. Synonyms (.e. trade names) derived PubChem Compound ID (column cid) consequently available CID available.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Like data sets package, data sets publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics #> # A tibble: 483 × 14 #>    ab        cid name        group atc   atc_g…¹ atc_g…² abbre…³ synon…⁴ oral_…⁵ #>    <ab>    <dbl> <chr>       <chr> <lis> <chr>   <chr>   <list>  <named>   <dbl> #>  1 AMA      4649 4-aminosal… Anti… <chr> Drugs … Aminos… <chr>   <chr>     12    #>  2 ACM   6450012 Acetylmide… Macr… <chr> NA      NA      <chr>   <chr>     NA    #>  3 ASP  49787020 Acetylspir… Macr… <chr> NA      NA      <chr>   <chr>     NA    #>  4 ALS      8954 Aldesulfon… Othe… <chr> Drugs … Drugs … <chr>   <chr>      0.33 #>  5 AMK     37768 Amikacin    Amin… <chr> Aminog… Other … <chr>   <chr>     NA    #>  6 AKF        NA Amikacin/f… Amin… <chr> NA      NA      <chr>   <chr>     NA    #>  7 AMX     33613 Amoxicillin Beta… <chr> Beta-l… Penici… <chr>   <chr>      1.5  #>  8 AMC  23665637 Amoxicilli… Beta… <chr> Beta-l… Combin… <chr>   <chr>      1.5  #>  9 AXS    465441 Amoxicilli… Beta… <chr> NA      NA      <chr>   <chr>     NA    #> 10 AMB   5280965 Amphoteric… Anti… <chr> Antimy… Antibi… <chr>   <chr>     40    #> # … with 473 more rows, 4 more variables: oral_units <chr>, iv_ddd <dbl>, #> #   iv_units <chr>, loinc <list>, and abbreviated variable names ¹​atc_group1, #> #   ²​atc_group2, ³​abbreviations, ⁴​synonyms, ⁵​oral_ddd antivirals #> # A tibble: 120 × 11 #>    av    name  atc      cid atc_g…¹ synon…² oral_…³ oral_…⁴ iv_ddd iv_un…⁵ loinc #>    <av>  <chr> <chr>  <dbl> <chr>   <list>    <dbl> <chr>    <dbl> <chr>   <lis> #>  1 ABA   Abac… J05A… 4.41e5 Nucleo… <chr>       0.6 g           NA NA      <chr> #>  2 ACI   Acic… J05A… 1.35e8 Nucleo… <chr>       4   g            4 g       <chr> #>  3 ADD   Adef… J05A… 6.09e4 Nucleo… <chr>      10   mg          NA NA      <chr> #>  4 AME   Amen… J05A… 1.14e7 Other … <chr>       0.4 g           NA NA      <chr> #>  5 AMP   Ampr… J05A… 6.50e4 Protea… <chr>       1.2 g           NA NA      <chr> #>  6 ASU   Asun… J05A… 1.61e7 Antivi… <chr>       0.2 g           NA NA      <chr> #>  7 ATA   Ataz… J05A… 1.48e5 Protea… <chr>       0.3 g           NA NA      <chr> #>  8 ATA+… Ataz… J05A… 8.66e7 Antivi… <chr>      NA   NA          NA NA      <chr> #>  9 ATA+… Ataz… J05A… 2.51e7 Antivi… <chr>       0.3 g           NA NA      <chr> #> 10 BAM   Balo… J05A… 1.24e8 Other … <chr>      40   mg          NA NA      <chr> #> # … with 110 more rows, and abbreviated variable names ¹​atc_group, ²​synonyms, #> #   ³​oral_ddd, ⁴​oral_units, ⁵​iv_units"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antibiotic ID — as.ab","title":"Transform Input to an Antibiotic ID — as.ab","text":"Use function determine antibiotic drug code one antibiotics. data set antibiotics searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.ab(x)"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antibiotic ID — as.ab","text":"x character vector determine antibiotic ID flag_multiple_results logical indicate whether note printed console probably one antibiotic drug code name can retrieved single input value. info logical indicate whether progress bar printed, defaults TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antibiotic ID — as.ab","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antibiotic ID — as.ab","text":"entries antibiotics data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .ab() can correct different forms misspelling: Wrong spelling drug names (\"tobramicin\" \"gentamycin\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"mreopenem\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use ab_* functions get properties based returned antibiotic ID, see Examples. Note: .ab() ab_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems. can add manual codes considered .ab() ab_* functions, see add_custom_antimicrobials().","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antibiotic ID — as.ab","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antibiotic ID — as.ab","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antibiotic ID — as.ab","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"# these examples all return \"ERY\", the ID of erythromycin: as.ab(\"J01FA01\") #> Class 'ab' #> [1] ERY as.ab(\"J 01 FA 01\") #> Class 'ab' #> [1] ERY as.ab(\"Erythromycin\") #> Class 'ab' #> [1] ERY as.ab(\"eryt\") #> Class 'ab' #> [1] ERY as.ab(\"   eryt 123\") #> Class 'ab' #> [1] ERY as.ab(\"ERYT\") #> Class 'ab' #> [1] ERY as.ab(\"ERY\") #> Class 'ab' #> [1] ERY as.ab(\"eritromicine\") # spelled wrong, yet works #> Class 'ab' #> [1] ERY as.ab(\"Erythrocin\") # trade name #> Class 'ab' #> [1] ERY as.ab(\"Romycin\") # trade name #> Class 'ab' #> [1] ERY  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") # small spelling error #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") # or a bit more severe #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") # and even this works #> [1] \"J01DD04\"  # use ab_* functions to get a specific properties (see ?ab_property); # they use as.ab() internally: ab_name(\"J01FA01\") #> [1] \"Erythromycin\" ab_name(\"eryt\") #> [1] \"Erythromycin\"  # \\donttest{ if (require(\"dplyr\")) {   # you can quickly rename 'sir' columns using set_ab_names() with dplyr:   example_isolates %>%     set_ab_names(where(is.sir), property = \"atc\") } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           J01CE01 J01CF04 J01CF05 #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir>   <sir>   <sir>   #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R       NA      S       #> # … with 1,990 more rows, and 37 more variables: J01CA04 <sir>, J01CR02 <sir>, #> #   J01CA01 <sir>, J01CR05 <sir>, J01DB04 <sir>, J01DE01 <sir>, J01DC02 <sir>, #> #   J01DC01 <sir>, J01DD01 <sir>, J01DD02 <sir>, J01DD04 <sir>, J01GB03 <sir>, #> #   J01GB01 <sir>, J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, J01EE01 <sir>, #> #   J01XE01 <sir>, J01XX01 <sir>, J01XX08 <sir>, J01MA02 <sir>, J01MA14 <sir>, #> #   J01XA01 <sir>, J01XA02 <sir>, J01AA07 <sir>, J01AA12 <sir>, J01AA02 <sir>, #> #   J01FA01 <sir>, J01FF01 <sir>, J01FA10 <sir>, J01DH51 <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antiviral Drug ID — as.av","title":"Transform Input to an Antiviral Drug ID — as.av","text":"Use function determine antiviral drug code one antiviral drugs. data set antivirals searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.av(x)"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antiviral Drug ID — as.av","text":"x character vector determine antiviral drug ID flag_multiple_results logical indicate whether note printed console probably one antiviral drug code name can retrieved single input value. info logical indicate whether progress bar printed, defaults TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antiviral Drug ID — as.av","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antiviral Drug ID — as.av","text":"entries antivirals data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .av() can correct different forms misspelling: Wrong spelling drug names (\"acyclovir\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"aycclovir\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use av_* functions get properties based returned antiviral drug ID, see Examples. Note: .av() av_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antiviral Drug ID — as.av","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antiviral Drug ID — as.av","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antiviral Drug ID — as.av","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"# these examples all return \"ACI\", the ID of aciclovir: as.av(\"J05AB01\") #> Class 'av' #> [1] ACI as.av(\"J 05 AB 01\") #> Class 'av' #> [1] ACI as.av(\"Aciclovir\") #> Class 'av' #> [1] ACI as.av(\"aciclo\") #> Class 'av' #> [1] ACI as.av(\"   aciclo 123\") #> Class 'av' #> [1] ACI as.av(\"ACICL\") #> Class 'av' #> [1] ACI as.av(\"ACI\") #> Class 'av' #> [1] ACI as.av(\"Virorax\") # trade name #> Class 'av' #> [1] ACI as.av(\"Zovirax\") # trade name #> Class 'av' #> [1] ACI  as.av(\"acyklofir\") # severe spelling error, yet works #> Class 'av' #> [1] ACI  # use av_* functions to get a specific properties (see ?av_property); # they use as.av() internally: av_name(\"J05AB01\") #> [1] \"Aciclovir\" av_name(\"acicl\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Disk Diffusion Diameters — as.disk","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"transforms vector new class disk, disk diffusion growth zone size (around antibiotic disk) millimetres 6 50.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"as.disk(x, na.rm = FALSE)  NA_disk_  is.disk(x)"},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"object class disk (inherits integer) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"x vector na.rm logical indicating whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"integer additional class disk","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"Interpret disk values SIR values .sir(). supports guidelines EUCAST CLSI. Disk diffusion growth zone sizes must 6 50 millimetres. Values higher 50 lower 100 maximised 50. others input values outside 6-50 range return NA. NA_disk_ missing value new disk class.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"# transform existing disk zones to the `disk` class (using base R) df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = 20,   CIP = 14,   GEN = 18,   TOB = 16 ) df[, 2:5] <- lapply(df[, 2:5], as.disk) str(df) #> 'data.frame':\t1 obs. of  5 variables: #>  $ microorganism: chr \"Escherichia coli\" #>  $ AMP          : 'disk' int 20 #>  $ CIP          : 'disk' int 14 #>  $ GEN          : 'disk' int 18 #>  $ TOB          : 'disk' int 16  # \\donttest{ # transforming is easier with dplyr: if (require(\"dplyr\")) {   df %>% mutate(across(AMP:TOB, as.disk)) } #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli  20  14  18  16 # }  # interpret disk values, see ?as.sir as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # interpret whole data set, pretend to be all from urinary tract infections: as.sir(df, uti = TRUE) #> => Interpreting disk diffusion zones of column 'AMP' (ampicillin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'CIP' (ciprofloxacin) #>    according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli   S   R   S   S"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"transforms vectors new class mic, treats input decimal numbers, maintaining operators (\">=\") allowing valid MIC values known field (medical) microbiology.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"as.mic(x, na.rm = FALSE)  NA_mic_  is.mic(x)  # S3 method for mic droplevels(x, as.mic = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"x character numeric vector na.rm logical indicating whether missing values removed .mic logical indicate whether mic class kept, defaults FALSE ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"Ordered factor additional class mic, mathematical operations acts decimal numbers. Bare mind outcome mathematical operation MICs return numeric value.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"interpret MIC values SIR values, use .sir() MIC values. supports guidelines EUCAST (2013-2022) CLSI (2013-2022). class MIC values quite special data type: formally ordered factor valid MIC values factor levels (make sure valid MIC values retained), mathematical operation acts decimal numbers:   makes possible maintain operators often come MIC values, \">=\" \"<=\", even filtering using numeric values data analysis, e.g.:   following generic functions implemented MIC class: !, !=, %%, %/%, &, *, +, -, /, <, <=, ==, >, >=, ^, |, abs(), acos(), acosh(), (), (), asin(), asinh(), atan(), atanh(), ceiling(), cos(), cosh(), cospi(), cummax(), cummin(), cumprod(), cumsum(), digamma(), exp(), expm1(), floor(), gamma(), lgamma(), log(), log1p(), log2(), log10(), max(), mean(), min(), prod(), range(), round(), sign(), signif(), sin(), sinh(), sinpi(), sqrt(), sum(), tan(), tanh(), tanpi(), trigamma() trunc(). functions stats package also implemented: median(), quantile(), mad(), IQR(), fivenum(). Also, boxplot.stats() supported. Since sd() var() non-generic functions, extended. Use mad() alternative, use e.g. sd(.numeric(x)) x vector MIC values. Using .double() .numeric() MIC values remove operators return numeric vector. use .integer() MIC values R convention factors, return index factor levels (often useless regular users). Use droplevels() drop unused levels. default, return plain factor. Use droplevels(..., .mic = TRUE) maintain mic class. NA_mic_ missing value new mic class, analogous e.g. base R's NA_character_.","code":"x <- random_mic(10) x #> Class 'mic' #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16  is.factor(x) #> [1] TRUE  x[1] * 2 #> [1] 32  median(x) #> [1] 26 x[x > 4] #> Class 'mic' #> [1] 16    8     8     64    >=128 32    32    16  df <- data.frame(x, hospital = \"A\") subset(df, x > 4) # or with dplyr: df %>% filter(x > 4) #>        x hospital #> 1     16        A #> 5     64        A #> 6  >=128        A #> 8     32        A #> 9     32        A #> 10    16        A"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"mic_data <- as.mic(c(\">=32\", \"1.0\", \"1\", \"1.00\", 8, \"<=0.128\", \"8\", \"16\", \"16\")) mic_data #> Class 'mic' #> [1] >=32    1       1       1       8       <=0.128 8       16      16      is.mic(mic_data) #> [1] TRUE  # this can also coerce combined MIC/SIR values: as.mic(\"<=0.002; S\") #> Class 'mic' #> [1] <=0.002  # mathematical processing treats MICs as numeric values fivenum(mic_data) #> [1]  0.128  1.000  8.000 16.000 32.000 quantile(mic_data) #>     0%    25%    50%    75%   100%  #>  0.128  1.000  8.000 16.000 32.000  all(mic_data < 512) #> [1] TRUE  # interpret MIC values as.sir(   x = as.mic(2),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] R as.sir(   x = as.mic(c(0.01, 2, 4, 8)),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] S R R R  # plot MIC values, see ?plot plot(mic_data)  plot(mic_data, mo = \"E. coli\", ab = \"cipro\")   if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"nl\") # Dutch }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"uk\") # Ukrainian }"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to a Microorganism Code — as.mo","title":"Transform Input to a Microorganism Code — as.mo","text":"Use function determine valid microorganism code (mo). Determination done using intelligent rules complete taxonomic kingdoms Animalia, Archaea, Bacteria Protozoa, microbial species kingdom Fungi (see Source). input can almost anything: full name (like \"Staphylococcus aureus\"), abbreviated name (\"S. aureus\"), abbreviation known field (\"MRSA\"), just genus. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to a Microorganism Code — as.mo","text":"","code":"as.mo(   x,   Becker = FALSE,   Lancefield = FALSE,   minimum_matching_score = NULL,   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   reference_df = get_mo_source(),   ignore_pattern = getOption(\"AMR_ignore_pattern\", NULL),   remove_from_input = mo_cleaning_regex(),   language = get_AMR_locale(),   info = interactive(),   ... )  is.mo(x)  mo_uncertainties()  mo_renamed()  mo_failures()  mo_reset_session()  mo_cleaning_regex()"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to a Microorganism Code — as.mo","text":"x character vector data.frame one two columns Becker logical indicate whether staphylococci categorised coagulase-negative staphylococci (\"CoNS\") coagulase-positive staphylococci (\"CoPS\") instead species, according Karsten Becker et al. (see Source). excludes Staphylococcus aureus default, use Becker = \"\" also categorise S. aureus \"CoPS\". Lancefield logical indicate whether beta-haemolytic Streptococcus categorised Lancefield groups instead species, according Rebecca C. Lancefield (see Source). streptococci categorised first group, e.g. Streptococcus dysgalactiae group C, although officially also categorised groups G L. excludes enterococci default (group D), use Lancefield = \"\" also categorise enterococci group D. minimum_matching_score numeric value set lower limit MO matching score. left blank, determined automatically based character length x, taxonomic kingdom human pathogenicity. keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). reference_df data.frame used extra reference translating x valid mo. See set_mo_source() get_mo_source() automate usage codes (e.g. used analysis organisation). ignore_pattern regular expression (case-insensitive) matches x must return NA. can convenient exclude known non-relevant input can also set option AMR_ignore_pattern, e.g. options(AMR_ignore_pattern = \"(reported|contaminated flora)\"). remove_from_input regular expression (case-insensitive) clean input x. Everything matched x removed. default, outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". language language translate text like \"growth\", defaults system language (see get_AMR_locale()) info logical indicate progress bar printed 25 items coerced, defaults TRUE interactive mode ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to a Microorganism Code — as.mo","text":"character  vector additional class mo","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to a Microorganism Code — as.mo","text":"microorganism (MO) code package (class: mo) human readable typically looks like examples:   Values coerced considered 'unknown' returned MO code UNKNOWN warning. Use mo_* functions get properties based returned code, see Examples. .mo() function uses novel matching score algorithm (see Matching Score Microorganisms ) match input available microbial taxonomy package. lead effect e.g. \"E. coli\" (microorganism highly prevalent humans) return microbial ID Escherichia coli Entamoeba coli (microorganism less prevalent humans), although latter alphabetically come first. algorithm uses data List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (see microorganisms).","code":"Code               Full name   ---------------    --------------------------------------   B_KLBSL            Klebsiella   B_KLBSL_PNMN       Klebsiella pneumoniae   B_KLBSL_PNMN_RHNS  Klebsiella pneumoniae rhinoscleromatis   |   |    |    |   |   |    |    |   |   |    |    \\---> subspecies, a 3-5 letter acronym   |   |    \\----> species, a 3-6 letter acronym   |   \\----> genus, a 4-8 letter acronym   \\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),                             F (Fungi), PL (Plantae), P (Protozoa)"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"coping-with-uncertain-results","dir":"Reference","previous_headings":"","what":"Coping with Uncertain Results","title":"Transform Input to a Microorganism Code — as.mo","text":"Results non-exact taxonomic input based matching score. lowest allowed score can set minimum_matching_score argument. default determined based character length input, taxonomic kingdom human pathogenicity taxonomic outcome. values matched uncertainty, message shown suggest user evaluate results mo_uncertainties(), returns data.frame specifications. increase quality matching, remove_from_input argument can used clean input (.e., x). must regular expression matches parts input removed input matched available microbial taxonomy. matched Perl-compatible case-insensitive. default value remove_from_input outcome helper function mo_cleaning_regex(). three helper functions can run using .mo() function: Use mo_uncertainties() get data.frame prints pretty format taxonomic names guessed. output contains matching score matches (see Matching Score Microorganisms ). Use mo_failures() get character vector values coerced valid value. Use mo_renamed() get data.frame values coerced based old, previously accepted taxonomic names.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"microbial-prevalence-of-pathogens-in-humans","dir":"Reference","previous_headings":"","what":"Microbial Prevalence of Pathogens in Humans","title":"Transform Input to a Microorganism Code — as.mo","text":"coercion rules consider prevalence microorganisms humans, available prevalence column microorganisms data set. grouping human pathogenic prevalence explained section Matching Score Microorganisms .","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to a Microorganism Code — as.mo","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019 Microorganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Transform Input to a Microorganism Code — as.mo","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to a Microorganism Code — as.mo","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to a Microorganism Code — as.mo","text":"","code":"# \\donttest{ # These examples all return \"B_STPHY_AURS\", the ID of S. aureus: as.mo(c(   \"sau\", # WHONET code   \"stau\",   \"STAU\",   \"staaur\",   \"S. aureus\",   \"S aureus\",   \"Sthafilokkockus aureus\", # handles incorrect spelling   \"Staphylococcus aureus (MRSA)\",   \"MRSA\", # Methicillin Resistant S. aureus   \"VISA\", # Vancomycin Intermediate S. aureus   \"VRSA\", # Vancomycin Resistant S. aureus   115329001 # SNOMED CT code )) #> Class 'mo' #>  [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #>  [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #> [11] B_STPHY_AURS B_STPHY_AURS  # Dyslexia is no problem - these all work: as.mo(c(   \"Ureaplasma urealyticum\",   \"Ureaplasma urealyticus\",   \"Ureaplasmium urealytica\",   \"Ureaplazma urealitycium\" )) #> Class 'mo' #> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY  as.mo(\"Streptococcus group A\") #> Class 'mo' #> [1] B_STRPT_GRPA  as.mo(\"S. epidermidis\") # will remain species: B_STPHY_EPDR #> Class 'mo' #> [1] B_STPHY_EPDR as.mo(\"S. epidermidis\", Becker = TRUE) # will not remain species: B_STPHY_CONS #> Class 'mo' #> [1] B_STPHY_CONS  as.mo(\"S. pyogenes\") # will remain species: B_STRPT_PYGN #> Class 'mo' #> [1] B_STRPT_PYGN as.mo(\"S. pyogenes\", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA #> Class 'mo' #> [1] B_STRPT_GRPA  # All mo_* functions use as.mo() internally too (see ?mo_property): mo_genus(\"E. coli\") #> [1] \"Escherichia\" mo_gramstain(\"ESCO\") #> [1] \"Gram-negative\" mo_is_intrinsic_resistant(\"ESCCOL\", ab = \"vanco\") #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and #>   'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note #>   will be shown once per session. #> [1] TRUE # }"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Interpret minimum inhibitory concentration (MIC) values disk diffusion diameters according EUCAST CLSI, clean existing SIR values. transforms input new class sir, ordered factor levels S < < R. breakpoints used interpretation publicly available clinical_breakpoints data set.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"as.sir(x, ...)  NA_sir_  is.sir(x)  is_sir_eligible(x, threshold = 0.05)  # S3 method for mic as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for disk as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for data.frame as.sir(   x,   ...,   col_mo = NULL,   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE) )  sir_interpretation_history(clean = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"object class sir (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpretations minimum inhibitory concentration (MIC) values disk diffusion diameters: M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. M100 Performance Standard Antimicrobial Susceptibility Testing, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m100/. Breakpoint tables interpretation MICs zone diameters, 2013-2022, European Committee Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"x vector values (class mic: MIC values mg/L, class disk: disk diffusion radius millimetres) ... using data.frame: names columns apply .sir() (supports tidy selection column1:column4). Otherwise: arguments passed methods. threshold maximum fraction invalid antimicrobial interpretations x, see Examples mo (vector ) text can coerced valid microorganism codes .mo(), can left empty determine automatically ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline defaults EUCAST 2022 (latest implemented EUCAST guideline clinical_breakpoints data set), can set option AMR_guideline. Currently supports EUCAST (2013-2022) CLSI (2013-2022), see Details. uti (Urinary Tract Infection) vector logicals (TRUE FALSE) specify whether UTI specific interpretation guideline chosen. using .sir() data.frame, can also column containing logicals left blank, data set searched column 'specimen', rows within column containing 'urin' ('urine', 'urina') regarded isolates UTI. See Examples. conserve_capped_values logical indicate MIC values starting \">\" (\">=\") must always return \"R\" , MIC values starting \"<\" (\"<=\") must always return \"S\" add_intrinsic_resistance (useful using EUCAST guideline) logical indicate whether intrinsic antibiotic resistance must also considered applicable bug-drug combinations, meaning e.g. ampicillin always return \"R\" Klebsiella species. Determination based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). reference_data data.frame used interpretation, defaults clinical_breakpoints data set. Changing argument allows using interpretation guidelines. argument must contain data set equal structure clinical_breakpoints data set (column names column types). Please note guideline argument ignored reference_data manually set. include_screening logical indicate clinical breakpoints screening allowed, defaults FALSE. Can also set option AMR_include_screening. include_PKPD logical indicate PK/PD clinical breakpoints must applied last resort, defaults TRUE. Can also set option AMR_include_PKPD. col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). clean logical indicate whether previously stored results forgotten returning 'logbook' results","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Ordered factor new class sir","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"NA_sir_ missing value new sir class, analogous e.g. base R's NA_character_.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"how-it-works","dir":"Reference","previous_headings":"","what":"How it Works","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":".sir() function works four ways: cleaning raw / untransformed data. data cleaned contain values S, R try best determine intelligence. example, mixed values SIR interpretations MIC values \"<0.25; S\" coerced \"S\". Combined interpretations multiple test methods (seen laboratory records) \"S; S\" coerced \"S\", value like \"S; \" return NA warning input unclear. interpreting minimum inhibitory concentration (MIC) values according EUCAST CLSI. must clean MIC values first using .mic(), also gives columns new data class mic. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   Operators like \"<=\" stripped interpretation. using conserve_capped_values = TRUE, MIC value e.g. \">2\" always return \"R\", even breakpoint according chosen guideline \">=4\". prevent capped values raw laboratory data treated conservatively. default behaviour (conserve_capped_values = FALSE) considers \">2\" lower \">=4\" might case return \"S\" \"\". interpreting disk diffusion diameters according EUCAST CLSI. must clean disk zones first using .disk(), also gives columns new data class disk. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   interpreting complete data set, automatic determination MIC values, disk diffusion diameters, microorganism names codes, antimicrobial test results. done simply running .sir(your_data). points 2, 3 4: Use sir_interpretation_history() retrieve data.frame (tibble tibble package installed) results last .sir() call.","code":"your_data %>% mutate_if(is.mic, as.sir) your_data %>% mutate(across(where(is.mic), as.sir)) your_data %>% mutate_if(is.disk, as.sir) your_data %>% mutate(across(where(is.disk), as.sir))"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"supported-guidelines","dir":"Reference","previous_headings":"","what":"Supported Guidelines","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpreting MIC values well disk diffusion diameters, currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Thus, guideline argument must set e.g., \"EUCAST 2022\" \"CLSI 2022\". simply using \"EUCAST\" (default) \"CLSI\" input, latest included version guideline automatically selected. can set data set using reference_data argument. guideline argument ignored. can set default guideline option AMR_guideline (e.g. .Rprofile file), :","code":"options(AMR_guideline = \"CLSI\")   options(AMR_guideline = \"CLSI 2018\")   options(AMR_guideline = \"EUCAST 2020\")   # or to reset:   options(AMR_guideline = NULL)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"after-interpretation","dir":"Reference","previous_headings":"","what":"After Interpretation","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"using .sir(), can use eucast_rules() defined EUCAST (1) apply inferred susceptibility resistance based results antimicrobials (2) apply intrinsic resistance based taxonomic properties microorganism.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"machine-readable-clinical-breakpoints","dir":"Reference","previous_headings":"","what":"Machine-Readable Clinical Breakpoints","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"repository package contains machine-readable version guidelines. CSV file consisting 18 308 rows 11 columns. file machine-readable, since contains one row every unique combination test method (MIC disk diffusion), antimicrobial drug microorganism. allows easy implementation rules laboratory information systems (LIS). Note contains interpretation guidelines humans - interpretation guidelines CLSI animals removed.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"other","dir":"Reference","previous_headings":"","what":"Other","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"function .sir() detects input contains class sir. input data.frame, iterates columns returns logical vector. function is_sir_eligible() returns TRUE columns contains 5% invalid antimicrobial interpretations (S //R), FALSE otherwise. threshold 5% can set threshold argument. input data.frame, iterates columns returns logical vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir> summary(example_isolates) # see all SIR results at a glance #>       date              patient               age           gender          #>  Min.   :2002-01-02   Length:2000        Min.   : 0.00   Length:2000        #>  1st Qu.:2005-07-31   Class :character   1st Qu.:63.00   Class :character   #>  Median :2009-07-31   Mode  :character   Median :74.00   Mode  :character   #>  Mean   :2009-11-20                      Mean   :70.69                      #>  3rd Qu.:2014-05-30                      3rd Qu.:82.00                      #>  Max.   :2017-12-28                      Max.   :97.00                      #>      ward                mo                  PEN                 #>  Length:2000        Class :mo             Class:sir              #>  Class :character   <NA>  :0              %R   :73.7% (n=1201)   #>  Mode  :character   Unique:90             %SI  :26.3% (n=428)    #>                     #1    :B_ESCHR_COLI   - %S :25.6% (n=417)    #>                     #2    :B_STPHY_CONS   - %I : 0.7% (n=11)     #>                     #3    :B_STPHY_AURS                          #>     OXA                   FLC                   AMX                #>  Class:sir             Class:sir             Class:sir             #>  %R   :31.2% (n=114)   %R   :29.5% (n=278)   %R   :59.6% (n=804)   #>  %SI  :68.8% (n=251)   %SI  :70.5% (n=665)   %SI  :40.4% (n=546)   #>  - %S :68.8% (n=251)   - %S :70.5% (n=665)   - %S :40.2% (n=543)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)     - %I : 0.2% (n=3)     #>                                                                    #>     AMC                    AMP                   TZP                #>  Class:sir              Class:sir             Class:sir             #>  %R   :23.7% (n=446)    %R   :59.6% (n=804)   %R   :12.6% (n=126)   #>  %SI  :76.3% (n=1433)   %SI  :40.4% (n=546)   %SI  :87.4% (n=875)   #>  - %S :71.4% (n=1342)   - %S :40.2% (n=543)   - %S :86.1% (n=862)   #>  - %I : 4.8% (n=91)     - %I : 0.2% (n=3)     - %I : 1.3% (n=13)    #>                                                                     #>     CZO                   FEP                   CXM                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :44.6% (n=199)   %R   :14.2% (n=103)   %R   :26.3% (n=470)    #>  %SI  :55.4% (n=247)   %SI  :85.8% (n=621)   %SI  :73.7% (n=1319)   #>  - %S :54.9% (n=245)   - %S :85.6% (n=620)   - %S :72.5% (n=1297)   #>  - %I : 0.4% (n=2)     - %I : 0.1% (n=1)     - %I : 1.2% (n=22)     #>                                                                     #>     FOX                   CTX                   CAZ                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :27.4% (n=224)   %R   :15.5% (n=146)   %R   :66.5% (n=1204)   #>  %SI  :72.6% (n=594)   %SI  :84.5% (n=797)   %SI  :33.5% (n=607)    #>  - %S :71.6% (n=586)   - %S :84.4% (n=796)   - %S :33.5% (n=607)    #>  - %I : 1.0% (n=8)     - %I : 0.1% (n=1)     - %I : 0.0% (n=0)      #>                                                                     #>     CRO                   GEN                    TOB                #>  Class:sir             Class:sir              Class:sir             #>  %R   :15.5% (n=146)   %R   :24.6% (n=456)    %R   :34.4% (n=465)   #>  %SI  :84.5% (n=797)   %SI  :75.4% (n=1399)   %SI  :65.6% (n=886)   #>  - %S :84.4% (n=796)   - %S :74.0% (n=1372)   - %S :65.1% (n=879)   #>  - %I : 0.1% (n=1)     - %I : 1.5% (n=27)     - %I : 0.5% (n=7)     #>                                                                     #>     AMK                   KAN                    TMP                #>  Class:sir             Class:sir              Class:sir             #>  %R   :63.7% (n=441)   %R   :100.0% (n=471)   %R   :38.1% (n=571)   #>  %SI  :36.3% (n=251)   %SI  : 0.0% (n=0)      %SI  :61.9% (n=928)   #>  - %S :36.3% (n=251)   - %S : 0.0% (n=0)      - %S :61.2% (n=918)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)      - %I : 0.7% (n=10)    #>                                                                     #>     SXT                    NIT                   FOS                #>  Class:sir              Class:sir             Class:sir             #>  %R   :20.5% (n=361)    %R   :17.1% (n=127)   %R   :42.2% (n=148)   #>  %SI  :79.5% (n=1398)   %SI  :82.9% (n=616)   %SI  :57.8% (n=203)   #>  - %S :79.1% (n=1392)   - %S :76.0% (n=565)   - %S :57.8% (n=203)   #>  - %I : 0.3% (n=6)      - %I : 6.9% (n=51)    - %I : 0.0% (n=0)     #>                                                                     #>     LNZ                   CIP                    MFX                #>  Class:sir             Class:sir              Class:sir             #>  %R   :69.3% (n=709)   %R   :16.2% (n=228)    %R   :33.6% (n=71)    #>  %SI  :30.7% (n=314)   %SI  :83.8% (n=1181)   %SI  :66.4% (n=140)   #>  - %S :30.7% (n=314)   - %S :78.9% (n=1112)   - %S :64.5% (n=136)   #>  - %I : 0.0% (n=0)     - %I : 4.9% (n=69)     - %I : 1.9% (n=4)     #>                                                                     #>     VAN                    TEC                   TCY                #>  Class:sir              Class:sir             Class:sir             #>  %R   :38.3% (n=712)    %R   :75.7% (n=739)   %R   :29.8% (n=357)   #>  %SI  :61.7% (n=1149)   %SI  :24.3% (n=237)   %SI  :70.3% (n=843)   #>  - %S :61.7% (n=1149)   - %S :24.3% (n=237)   - %S :68.3% (n=820)   #>  - %I : 0.0% (n=0)      - %I : 0.0% (n=0)     - %I : 1.9% (n=23)    #>                                                                     #>     TGC                   DOX                   ERY                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :12.7% (n=101)   %R   :27.7% (n=315)   %R   :57.2% (n=1084)   #>  %SI  :87.3% (n=697)   %SI  :72.3% (n=821)   %SI  :42.8% (n=810)    #>  - %S :87.3% (n=697)   - %S :71.7% (n=814)   - %S :42.3% (n=801)    #>  - %I : 0.0% (n=0)     - %I : 0.6% (n=7)     - %I : 0.5% (n=9)      #>                                                                     #>     CLI                   AZM                    IPM                #>  Class:sir             Class:sir              Class:sir             #>  %R   :61.2% (n=930)   %R   :57.2% (n=1084)   %R   : 6.2% (n=55)    #>  %SI  :38.8% (n=590)   %SI  :42.8% (n=810)    %SI  :93.8% (n=834)   #>  - %S :38.6% (n=586)   - %S :42.3% (n=801)    - %S :92.7% (n=824)   #>  - %I : 0.3% (n=4)     - %I : 0.5% (n=9)      - %I : 1.1% (n=10)    #>                                                                     #>     MEM                   MTR                  CHL                #>  Class:sir             Class:sir            Class:sir             #>  %R   : 5.9% (n=49)    %R   :14.7% (n=5)    %R   :21.4% (n=33)    #>  %SI  :94.1% (n=780)   %SI  :85.3% (n=29)   %SI  :78.6% (n=121)   #>  - %S :94.1% (n=780)   - %S :85.3% (n=29)   - %S :78.6% (n=121)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)    - %I : 0.0% (n=0)     #>                                                                   #>     COL                    MUP                   RIF                #>  Class:sir              Class:sir             Class:sir             #>  %R   :81.2% (n=1331)   %R   : 5.9% (n=16)    %R   :69.6% (n=698)   #>  %SI  :18.8% (n=309)    %SI  :94.1% (n=254)   %SI  :30.4% (n=305)   #>  - %S :18.8% (n=309)    - %S :93.0% (n=251)   - %S :30.2% (n=303)   #>  - %I : 0.0% (n=0)      - %I : 1.1% (n=3)     - %I : 0.2% (n=2)     #>                                                                      # For INTERPRETING disk diffusion and MIC values -----------------------  # a whole data set, even with combined MIC values and disk zones df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = as.mic(8),   CIP = as.mic(0.256),   GEN = as.disk(18),   TOB = as.disk(16),   ERY = \"R\" ) as.sir(df) #> => Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of column 'CIP' (ciprofloxacin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Assigning class 'sir' to already clean column 'ERY' (erythromycin)... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # return a 'logbook' about the results: sir_interpretation_history() #> # A tibble: 50 × 17 #>    datetime            index ab_input ab_guid…¹ mo_in…² mo_guideline     guide…³ #>    <dttm>              <int> <chr>    <ab>      <chr>   <mo>             <chr>   #>  1 2023-02-18 14:03:27     1 TOB      TOB       Escher… B_[ORD]_ENTRBCTR EUCAST… #>  2 2023-02-18 14:03:26     1 GEN      GEN       Escher… B_[ORD]_ENTRBCTR EUCAST… #>  3 2023-02-18 14:03:26     1 CIP      CIP       Escher… B_[ORD]_ENTRBCTR EUCAST… #>  4 2023-02-18 14:03:25     1 AMP      AMP       Escher… B_[ORD]_ENTRBCTR EUCAST… #>  5 2023-02-18 14:03:20     1 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #>  6 2023-02-18 14:03:20     2 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #>  7 2023-02-18 14:03:20     3 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #>  8 2023-02-18 14:03:20     4 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #>  9 2023-02-18 14:03:20     5 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #> 10 2023-02-18 14:03:20     6 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST… #> # … with 40 more rows, 10 more variables: ref_table <chr>, method <chr>, #> #   input <dbl>, outcome <sir>, breakpoint_S_R <chr>, ab_considered <lgl>, #> #   mo_considered <lgl>, breakpoint_S <lgl>, breakpoint_R <lgl>, #> #   interpretation <lgl>, and abbreviated variable names ¹​ab_guideline, #> #   ²​mo_input, ³​guideline  # for single values as.sir(   x = as.mic(2),   mo = as.mo(\"S. pneumoniae\"),   ab = \"AMP\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for ampicillin (AMP) in Streptococcus #>      pneumoniae - assuming body site 'Non-meningitis'. #> Class 'sir' #> [1] R  as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # \\donttest{ # the dplyr way if (require(\"dplyr\")) {   df %>% mutate_if(is.mic, as.sir)   df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)   df %>% mutate(across(where(is.mic), as.sir))   df %>% mutate_at(vars(AMP:TOB), as.sir)   df %>% mutate(across(AMP:TOB, as.sir))    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = .$microorganism)    # to include information about urinary tract infections (UTI)   data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     from_the_bladder = c(TRUE, FALSE)   ) %>%     as.sir(uti = \"from_the_bladder\")    data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     specimen = c(\"urine\", \"blood\")   ) %>%     as.sir() # automatically determines urine isolates    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = \"E. coli\", uti = TRUE) } #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> ℹ Assuming value \"urine\" in column 'specimen' reflects a urinary tract #>   infection. #>   Use as.sir(uti = FALSE) to prevent this. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # For CLEANING existing SIR values ------------------------------------  as.sir(c(\"S\", \"I\", \"R\", \"A\", \"B\", \"C\")) #> Warning: in as.sir(): 3 results in column '24' truncated (50%) that were invalid #> antimicrobial interpretations: \"A\", \"B\" and \"C\" #> Class 'sir' #> [1] S    I    R    <NA> <NA> <NA> as.sir(\"<= 0.002; S\") # will return \"S\" #> Class 'sir' #> [1] S sir_data <- as.sir(c(rep(\"S\", 474), rep(\"I\", 36), rep(\"R\", 370))) is.sir(sir_data) #> [1] TRUE plot(sir_data) # for percentages  barplot(sir_data) # for frequencies   # the dplyr way if (require(\"dplyr\")) {   example_isolates %>%     mutate_at(vars(PEN:RIF), as.sir)   # same:   example_isolates %>%     as.sir(PEN:RIF)    # fastest way to transform all columns with already valid AMR results to class `sir`:   example_isolates %>%     mutate_if(is_sir_eligible, as.sir)    # since dplyr 1.0.0, this can also be:   # example_isolates %>%   #   mutate(across(where(is_sir_eligible), as.sir)) } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir> # }"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":null,"dir":"Reference","previous_headings":"","what":"Get ATC Properties from WHOCC Website — atc_online_property","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Gets data WHOCC website determine properties Anatomical Therapeutic Chemical (ATC) (e.g. antibiotic), name, defined daily dose (DDD) standard unit.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"atc_online_property(   atc_code,   property,   administration = \"O\",   url = \"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no\",   url_vet = \"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no\" )  atc_online_groups(atc_code, ...)  atc_online_ddd(atc_code, ...)  atc_online_ddd_units(atc_code, ...)"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"https://www.whocc./atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"atc_code character (vector) ATC code(s) antibiotics, coerced .ab() ab_atc() internally valid ATC code property property ATC code. Valid values \"ATC\", \"Name\", \"DDD\", \"U\" (\"unit\"), \"Adm.R\", \"Note\" groups. last option, hierarchical groups ATC code returned, see Examples. administration type administration using property = \"Adm.R\", see Details url url website WHOCC. sign %s can used placeholder ATC codes. url_vet url website WHOCC veterinary medicine. sign %s can used placeholder ATC_vet codes (start \"Q\"). ... arguments pass atc_property","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Options argument administration: \"Implant\" = Implant \"Inhal\" = Inhalation \"Instill\" = Instillation \"N\" = nasal \"O\" = oral \"P\" = parenteral \"R\" = rectal \"SL\" = sublingual/buccal \"TD\" = transdermal \"V\" = vaginal Abbreviations return values using property = \"U\" (unit): \"g\" = gram \"mg\" = milligram \"mcg\" = microgram \"U\" = unit \"TU\" = thousand units \"MU\" = million units \"mmol\" = millimole \"ml\" = millilitre (e.g. eyedrops) N.B. function requires internet connection works following packages installed: curl, rvest, xml2.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"# \\donttest{ if (requireNamespace(\"curl\") && requireNamespace(\"rvest\") && requireNamespace(\"xml2\")) {   # oral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"O\")   atc_online_ddd(ab_atc(\"amox\"))    # parenteral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"P\")    atc_online_property(\"J01CA04\", property = \"groups\") # search hierarchical groups of amoxicillin } #> Loading required namespace: rvest #> [1] \"ANTIINFECTIVES FOR SYSTEMIC USE\"         #> [2] \"ANTIBACTERIALS FOR SYSTEMIC USE\"         #> [3] \"BETA-LACTAM ANTIBACTERIALS, PENICILLINS\" #> [4] \"Penicillins with extended spectrum\"      # }"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Use function e.g. clinical texts health care records. returns list antiviral drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_av = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_av type = \"drug\": column name antivirals data set translate antibiotic abbreviations , using av_property(). Defaults FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed, defaults TRUE interactive mode ... arguments passed .av()","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"function also internally used .av(), although searches first drug name throw note drug names returned. Note: .av() function may use long regular expression match brand names antiviral drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"default, function search antiviral drug names. text elements searched official names, ATC codes brand names. uses .av() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(avx = av_from_text(clinical_text)) returned AV codes can transformed official names, groups, etc. av_* functions av_name() av_group(), using translate_av argument. using collapse, function return character:df %>% mutate(avx = av_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(\"28/03/2020 valaciclovir po tid\") #> [[1]] #> Class 'av' #> [1] VALA #>  av_from_text(\"28/03/2020 valaciclovir po tid\", type = \"admin\") #> [[1]] #> [1] \"oral\" #>"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antiviral Drug — av_property","title":"Get Properties of an Antiviral Drug — av_property","text":"Use functions return specific property antiviral drug antivirals data set. input values evaluated internally .av().","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  av_cid(x, ...)  av_synonyms(x, ...)  av_tradenames(x, ...)  av_group(x, language = get_AMR_locale(), ...)  av_atc(x, ...)  av_loinc(x, ...)  av_ddd(x, administration = \"oral\", ...)  av_ddd_units(x, administration = \"oral\", ...)  av_info(x, language = get_AMR_locale(), ...)  av_url(x, open = FALSE, ...)  av_property(x, property = \"name\", language = get_AMR_locale(), ...)"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antiviral Drug — av_property","text":"x (vector ) text can coerced valid antiviral drug code .av() language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. ... arguments passed .av() administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antivirals data set: vector_or(colnames(antivirals), sort = FALSE).","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antiviral Drug — av_property","text":"integer case av_cid() named list case av_info() multiple av_atc()/av_synonyms()/av_tradenames() double case av_ddd() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antiviral Drug — av_property","text":"output translated possible. function av_url() return direct URL official website. warning returned required ATC code available.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antiviral Drug — av_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antiviral Drug — av_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"# all properties: av_name(\"ACI\") #> [1] \"Aciclovir\" av_atc(\"ACI\") #> [1] \"J05AB01\" av_cid(\"ACI\") #> [1] 135398513 av_synonyms(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_tradenames(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_group(\"ACI\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_url(\"ACI\") #>                                                             Aciclovir  #> \"https://www.whocc.no/atc_ddd_index/?code=J05AB01&showdescription=no\"   # smart lowercase tranformation av_name(x = c(\"ACI\", \"VALA\")) #> [1] \"Aciclovir\"    \"Valaciclovir\" av_name(x = c(\"ACI\", \"VALA\"), tolower = TRUE) #> [1] \"aciclovir\"    \"valaciclovir\"  # defined daily doses (DDD) av_ddd(\"ACI\", \"oral\") #> [1] 4 av_ddd_units(\"ACI\", \"oral\") #> [1] \"g\" av_ddd(\"ACI\", \"iv\") #> [1] 4 av_ddd_units(\"ACI\", \"iv\") #> [1] \"g\"  av_info(\"ACI\") # all properties as a list #> $av #> [1] \"ACI\" #>  #> $cid #> [1] 135398513 #>  #> $name #> [1] \"Aciclovir\" #>  #> $group #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" #>  #> $atc #> [1] \"J05AB01\" #>  #> $tradenames #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            #>  #> $loinc #> [1] \"\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 4 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 4 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all av_* functions use as.av() internally, so you can go from 'any' to 'any': av_atc(\"ACI\") #> [1] \"J05AB01\" av_group(\"J05AB01\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_loinc(\"abacavir\") #> [1] \"29113-8\" \"78772-1\" \"78773-9\" \"79134-3\" \"80118-3\" av_name(\"29113-8\") #> [1] \"Abacavir\" av_name(135398513) #> [1] \"Aciclovir\" av_name(\"J05AB01\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Availability of Columns — availability","title":"Check Availability of Columns — availability","text":"Easy check data availability columns data set. makes easy get idea antimicrobial combinations can used calculation e.g. susceptibility() resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Availability of Columns — availability","text":"","code":"availability(tbl, width = NULL)"},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Availability of Columns — availability","text":"tbl data.frame list width number characters present visual availability, defaults filling width console","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Availability of Columns — availability","text":"data.frame column names tbl row names","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check Availability of Columns — availability","text":"function returns data.frame columns \"resistant\" \"visual_resistance\". values columns calculated resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Availability of Columns — availability","text":"","code":"availability(example_isolates) #>         count available     visual_availabilty resistant      visual_resistance #> date     2000    100.0% |####################|                                  #> patient  2000    100.0% |####################|                                  #> age      2000    100.0% |####################|                                  #> gender   2000    100.0% |####################|                                  #> ward     2000    100.0% |####################|                                  #> mo       2000    100.0% |####################|                                  #> PEN      1629     81.5% |################----|     73.7% |##############------| #> OXA       365     18.3% |###-----------------|     31.2% |######--------------| #> FLC       943     47.2% |#########-----------|     29.5% |#####---------------| #> AMX      1350     67.5% |#############-------|     59.6% |###########---------| #> AMC      1879     94.0% |##################--|     23.7% |####----------------| #> AMP      1350     67.5% |#############-------|     59.6% |###########---------| #> TZP      1001     50.0% |##########----------|     12.6% |##------------------| #> CZO       446     22.3% |####----------------|     44.6% |########------------| #> FEP       724     36.2% |#######-------------|     14.2% |##------------------| #> CXM      1789     89.5% |#################---|     26.3% |#####---------------| #> FOX       818     40.9% |########------------|     27.4% |#####---------------| #> CTX       943     47.2% |#########-----------|     15.5% |###-----------------| #> CAZ      1811     90.6% |##################--|     66.5% |#############-------| #> CRO       943     47.2% |#########-----------|     15.5% |###-----------------| #> GEN      1855     92.8% |##################--|     24.6% |####----------------| #> TOB      1351     67.6% |#############-------|     34.4% |######--------------| #> AMK       692     34.6% |######--------------|     63.7% |############--------| #> KAN       471     23.6% |####----------------|    100.0% |####################| #> TMP      1499     75.0% |###############-----|     38.1% |#######-------------| #> SXT      1759     88.0% |#################---|     20.5% |####----------------| #> NIT       743     37.2% |#######-------------|     17.1% |###-----------------| #> FOS       351     17.6% |###-----------------|     42.2% |########------------| #> LNZ      1023     51.2% |##########----------|     69.3% |#############-------| #> CIP      1409     70.5% |#############-------|     16.2% |###-----------------| #> MFX       211     10.6% |##------------------|     33.6% |######--------------| #> VAN      1861     93.1% |##################--|     38.3% |#######-------------| #> TEC       976     48.8% |#########-----------|     75.7% |###############-----| #> TCY      1200     60.0% |###########---------|     29.8% |#####---------------| #> TGC       798     39.9% |########------------|     12.7% |##------------------| #> DOX      1136     56.8% |###########---------|     27.7% |#####---------------| #> ERY      1894     94.7% |##################--|     57.2% |###########---------| #> CLI      1520     76.0% |###############-----|     61.2% |############--------| #> AZM      1894     94.7% |##################--|     57.2% |###########---------| #> IPM       889     44.5% |########------------|      6.2% |#-------------------| #> MEM       829     41.5% |########------------|      5.9% |#-------------------| #> MTR        34      1.7% |--------------------|     14.7% |##------------------| #> CHL       154      7.7% |#-------------------|     21.4% |####----------------| #> COL      1640     82.0% |################----|     81.2% |################----| #> MUP       270     13.5% |##------------------|      5.9% |#-------------------| #> RIF      1003     50.2% |##########----------|     69.6% |#############-------| # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     select_if(is.sir) %>%     availability() } #>     count available       visual_availabilty resistant        visual_resistance #> PEN   467    100.0% |######################|    100.0% |######################| #> OXA     0      0.0% |----------------------|                                    #> FLC     0      0.0% |----------------------|                                    #> AMX   392     83.9% |##################----|     50.0% |###########-----------| #> AMC   467    100.0% |######################|     13.1% |##--------------------| #> AMP   392     83.9% |##################----|     50.0% |###########-----------| #> TZP   416     89.1% |###################---|      5.5% |#---------------------| #> CZO    82     17.6% |###-------------------|      2.4% |----------------------| #> FEP   317     67.9% |##############--------|      2.8% |----------------------| #> CXM   465     99.6% |######################|      5.4% |#---------------------| #> FOX   377     80.7% |#################-----|      6.9% |#---------------------| #> CTX   459     98.3% |#####################-|      2.4% |----------------------| #> CAZ   460     98.5% |#####################-|      2.4% |----------------------| #> CRO   459     98.3% |#####################-|      2.4% |----------------------| #> GEN   460     98.5% |#####################-|      2.0% |----------------------| #> TOB   462     98.9% |#####################-|      2.6% |----------------------| #> AMK   171     36.6% |########--------------|      0.0% |----------------------| #> KAN     0      0.0% |----------------------|                                    #> TMP   396     84.8% |##################----|     39.1% |########--------------| #> SXT   465     99.6% |######################|     31.6% |######----------------| #> NIT   458     98.1% |#####################-|      2.8% |----------------------| #> FOS    61     13.1% |##--------------------|      0.0% |----------------------| #> LNZ   467    100.0% |######################|    100.0% |######################| #> CIP   456     97.6% |#####################-|     12.5% |##--------------------| #> MFX    57     12.2% |##--------------------|    100.0% |######################| #> VAN   467    100.0% |######################|    100.0% |######################| #> TEC   467    100.0% |######################|    100.0% |######################| #> TCY     3      0.6% |----------------------|     66.7% |##############--------| #> TGC    68     14.6% |###-------------------|      0.0% |----------------------| #> DOX     0      0.0% |----------------------|                                    #> ERY   467    100.0% |######################|    100.0% |######################| #> CLI   467    100.0% |######################|    100.0% |######################| #> AZM   467    100.0% |######################|    100.0% |######################| #> IPM   422     90.4% |###################---|      0.0% |----------------------| #> MEM   418     89.5% |###################---|      0.0% |----------------------| #> MTR     2      0.4% |----------------------|      0.0% |----------------------| #> CHL     0      0.0% |----------------------|                                    #> COL   240     51.4% |###########-----------|      0.0% |----------------------| #> MUP     0      0.0% |----------------------|                                    #> RIF   467    100.0% |######################|    100.0% |######################| # }"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Bug-Drug Combinations — bug_drug_combinations","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"Determine antimicrobial resistance (AMR) bug-drug combinations data set least 30 (default) isolates available per species. Use format() result prettify publishable/printable format, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)  # S3 method for bug_drug_combinations format(   x,   translate_ab = \"name (ab, atc)\",   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   add_ab_group = TRUE,   remove_intrinsic_resistant = FALSE,   decimal.mark = getOption(\"OutDec\"),   big.mark = ifelse(decimal.mark == \",\", \".\", \",\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). FUN function call mo column transform microorganism codes, defaults mo_shortname() ... arguments passed FUN translate_ab character length 1 containing column names antibiotics data set language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether values S summed, resistance based R, defaults TRUE add_ab_group logical indicate group antimicrobials must included first column remove_intrinsic_resistant logical indicate rows columns 100% resistance tested antimicrobials must removed table decimal.mark character used indicate numeric     decimal point. big.mark character; empty used mark every     big.interval decimals (hence big)     decimal point.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function bug_drug_combinations() returns data.frame columns \"mo\", \"ab\", \"S\", \"\", \"R\" \"total\".","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function format() calculates resistance per bug-drug combination. Use combine_SI = TRUE (default) test R vs. S+combine_SI = FALSE test R+vs. S.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>  # \\donttest{ x <- bug_drug_combinations(example_isolates) head(x) #> # A tibble: 6 × 6 #>   mo                ab        S     I     R total #>   <chr>             <chr> <int> <int> <int> <int> #> 1 (unknown species) AMC      15     0     0    15 #> 2 (unknown species) AMK       0     0     0     0 #> 3 (unknown species) AMP      15     0     1    16 #> 4 (unknown species) AMX      15     0     1    16 #> 5 (unknown species) AZM       3     0     3     6 #> 6 (unknown species) CAZ       0     0     0     0 #> Use 'format()' on this result to get a publishable/printable format. format(x, translate_ab = \"name (atc)\") #> # A tibble: 39 × 12 #>    Group     Drug  CoNS  E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷ #>    <chr>     <chr> <chr> <chr>   <chr>   <chr>   <chr>   <chr>   <chr>   <chr>   #>  1 \"Aminogl… Amik… \"100… \"  0.0… \"100.0… \"\"      \"\"      \"\"      \"\"      \"100.0… #>  2 \"\"        Gent… \" 13… \"  2.0… \"100.0… \" 10.3… \"  0.0… \"  5.9… \"  0.9… \" 21.5… #>  3 \"\"        Kana… \"100… \"\"      \"100.0… \"\"      \"100.0… \"\"      \"\"      \"100.0… #>  4 \"\"        Tobr… \" 78… \"  2.6… \"100.0… \" 10.3… \"  0.0… \"  5.9… \"  2.3… \" 49.4… #>  5 \"Ampheni… Chlo… \"\"    \"\"      \"\"      \"\"      \"100.0… \"\"      \"  0.0… \"  3.1… #>  6 \"Antimyc… Rifa… \"\"    \"100.0… \"\"      \"100.0… \"100.0… \"100.0… \"  0.0… \"  2.7… #>  7 \"Beta-la… Amox… \" 93… \" 50.0… \"\"      \"100.0… \"100.0… \"\"      \" 93.9… \" 98.9… #>  8 \"\"        Amox… \" 42… \" 13.1… \"\"      \" 10.3… \"100.0… \"  2.8… \"  0.4… \" 54.5… #>  9 \"\"        Ampi… \" 93… \" 50.0… \"\"      \"100.0… \"100.0… \"\"      \" 93.9… \" 98.9… #> 10 \"\"        Benz… \" 77… \"100.0… \"\"      \"100.0… \"100.0… \"100.0… \" 80.9… \" 89.4… #> # … with 29 more rows, 2 more variables: `S. hominis` <chr>, #> #   `S. pneumoniae` <chr>, and abbreviated variable names ¹​`E. coli`, #> #   ²​`E. faecalis`, ³​`K. pneumoniae`, ⁴​`P. aeruginosa`, ⁵​`P. mirabilis`, #> #   ⁶​`S. aureus`, ⁷​`S. epidermidis`  # Use FUN to change to transformation of microorganism codes bug_drug_combinations(example_isolates,   FUN = mo_gramstain ) #> # A tibble: 80 × 6 #>    mo            ab        S     I     R total #>  * <chr>         <chr> <int> <int> <int> <int> #>  1 Gram-negative AMC     463    89   174   726 #>  2 Gram-negative AMK     251     0     5   256 #>  3 Gram-negative AMP     226     0   405   631 #>  4 Gram-negative AMX     226     0   405   631 #>  5 Gram-negative AZM       1     2   696   699 #>  6 Gram-negative CAZ     607     0    27   634 #>  7 Gram-negative CHL       1     0    30    31 #>  8 Gram-negative CIP     610    11    63   684 #>  9 Gram-negative CLI      18     1   709   728 #> 10 Gram-negative COL     309     0    78   387 #> # … with 70 more rows #> Use 'format()' on this result to get a publishable/printable format.  bug_drug_combinations(example_isolates,   FUN = function(x) {     ifelse(x == as.mo(\"Escherichia coli\"),       \"E. coli\",       \"Others\"     )   } ) #> # A tibble: 80 × 6 #>    mo      ab        S     I     R total #>  * <chr>   <chr> <int> <int> <int> <int> #>  1 E. coli AMC     332    74    61   467 #>  2 E. coli AMK     171     0     0   171 #>  3 E. coli AMP     196     0   196   392 #>  4 E. coli AMX     196     0   196   392 #>  5 E. coli AZM       0     0   467   467 #>  6 E. coli CAZ     449     0    11   460 #>  7 E. coli CHL       0     0     0     0 #>  8 E. coli CIP     398     1    57   456 #>  9 E. coli CLI       0     0   467   467 #> 10 E. coli COL     240     0     0   240 #> # … with 70 more rows #> Use 'format()' on this result to get a publishable/printable format. # }"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Data set containing clinical breakpoints interpret MIC disk diffusion SIR values, according international guidelines. Currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Use .sir() transform MICs disks measurements SIR values.","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"tibble 18 308 observations 11 variables: guideline Name guideline method Either \"DISK\" \"MIC\" site Body site, e.g. \"Oral\" \"Respiratory\" mo Microbial ID, see .mo() rank_index Taxonomic rank index mo 1 (subspecies/infraspecies) 5 (unknown microorganism) ab Antibiotic ID, see .ab() ref_tbl Info guideline rule can found disk_dose Dose used disk diffusion method breakpoint_S Lowest MIC value highest number millimetres leads \"S\" breakpoint_R Highest MIC value lowest number millimetres leads \"R\" uti logical value (TRUE/FALSE) indicate whether rule applies urinary tract infection (UTI)","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints #> # A tibble: 18,308 × 11 #>    guideline method site  mo               rank_…¹ ab   ref_tbl  disk_…² break…³ #>    <chr>     <chr>  <chr> <mo>               <dbl> <ab> <chr>    <chr>     <dbl> #>  1 EUCAST 2… MIC    NA    F_ASPRG_MGTS           2 AMB  Aspergi… NA            1 #>  2 EUCAST 2… MIC    NA    F_ASPRG_NIGR           2 AMB  Aspergi… NA            1 #>  3 EUCAST 2… MIC    NA    F_CANDD_ALBC           2 AMB  Candida  NA            1 #>  4 EUCAST 2… MIC    NA    F_CANDD_DBLN           2 AMB  Candida  NA            1 #>  5 EUCAST 2… MIC    NA    F_CANDD_GLBR           2 AMB  Candida  NA            1 #>  6 EUCAST 2… MIC    NA    F_CANDD_KRUS           2 AMB  Candida  NA            1 #>  7 EUCAST 2… MIC    NA    F_CANDD_PRPS           2 AMB  Candida  NA            1 #>  8 EUCAST 2… MIC    NA    F_CANDD_TRPC           2 AMB  Candida  NA            1 #>  9 EUCAST 2… MIC    NA    F_CRYPT_NFRM           2 AMB  Candida  NA            1 #> 10 EUCAST 2… DISK   NA    B_[ORD]_ENTRBCTR       5 AMC  Enterob… 20ug/1…      19 #> # … with 18,298 more rows, 2 more variables: breakpoint_R <dbl>, uti <lgl>, and #> #   abbreviated variable names ¹​rank_index, ²​disk_dose, ³​breakpoint_S"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":null,"dir":"Reference","previous_headings":"","what":"Count Available Isolates — count","title":"Count Available Isolates — count","text":"functions can used count resistant/susceptible microbial isolates. functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. count_resistant() used count resistant isolates, count_susceptible() used count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count Available Isolates — count","text":"","code":"count_resistant(..., only_all_tested = FALSE)  count_susceptible(..., only_all_tested = FALSE)  count_R(..., only_all_tested = FALSE)  count_IR(..., only_all_tested = FALSE)  count_I(..., only_all_tested = FALSE)  count_SI(..., only_all_tested = FALSE)  count_S(..., only_all_tested = FALSE)  count_all(..., only_all_tested = FALSE)  n_sir(..., only_all_tested = FALSE)  count_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   combine_SI = TRUE )"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count Available Isolates — count","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant), defaults TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count Available Isolates — count","text":"integer","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count Available Isolates — count","text":"functions meant count isolates. Use resistance()/susceptibility() functions calculate microbial resistance/susceptibility. function count_resistant() equal function count_R(). function count_susceptible() equal function count_SI(). function n_sir() alias count_all(). can used count available isolates, .e. input antibiotics available result (S, R). use equal n_distinct(). function equal count_susceptible(...) + count_resistant(...). function count_df() takes variable data sir class (created .sir()) counts number S's, 's R's. also supports grouped variables. function sir_df() works exactly like count_df(), adds percentage S, R.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Count Available Isolates — count","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Count Available Isolates — count","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count Available Isolates — count","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info.  # base R ------------------------------------------------------------ count_resistant(example_isolates$AMX) # counts \"R\" #> [1] 804 count_susceptible(example_isolates$AMX) # counts \"S\" and \"I\" #> [1] 546 count_all(example_isolates$AMX) # counts \"S\", \"I\" and \"R\" #> [1] 1350  # be more specific count_S(example_isolates$AMX) #> Using count_S() is discouraged; use count_susceptible() instead to also #> consider \"I\" being susceptible. This note will be shown once for this #> session. #> [1] 543 count_SI(example_isolates$AMX) #> [1] 546 count_I(example_isolates$AMX) #> [1] 3 count_IR(example_isolates$AMX) #> Using count_IR() is discouraged; use count_resistant() instead to not #> consider \"I\" being resistant. This note will be shown once for this #> session. #> [1] 807 count_R(example_isolates$AMX) #> [1] 804  # Count all available isolates count_all(example_isolates$AMX) #> [1] 1350 n_sir(example_isolates$AMX) #> [1] 1350  # n_sir() is an alias of count_all(). # Since it counts all available isolates, you can # calculate back to count e.g. susceptible isolates. # These results are the same: count_susceptible(example_isolates$AMX) #> [1] 546 susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX) #> [1] 546  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = count_R(CIP),       I = count_I(CIP),       S = count_S(CIP),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Number of available isolates for a whole antibiotic class   # (i.e., in this data set columns GEN, TOB, AMK, KAN)   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), n_sir))    # Count co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy.   # Please mind that `susceptibility()` calculates percentages right away instead.   example_isolates %>% count_susceptible(AMC) # 1433   example_isolates %>% count_all(AMC) # 1879    example_isolates %>% count_susceptible(GEN) # 1399   example_isolates %>% count_all(GEN) # 1855    example_isolates %>% count_susceptible(AMC, GEN) # 1764   example_isolates %>% count_all(AMC, GEN) # 1936    # Get number of S+I vs. R immediately of selected columns   example_isolates %>%     select(AMX, CIP) %>%     count_df(translate = FALSE)    # It also supports grouping variables   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     count_df(translate = FALSE) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> # A tibble: 12 × 4 #>    ward       antibiotic interpretation value #>  * <chr>      <chr>      <ord>          <int> #>  1 Clinical   AMX        SI               357 #>  2 Clinical   AMX        R                487 #>  3 Clinical   CIP        SI               741 #>  4 Clinical   CIP        R                128 #>  5 ICU        AMX        SI               158 #>  6 ICU        AMX        R                270 #>  7 ICU        CIP        SI               362 #>  8 ICU        CIP        R                 85 #>  9 Outpatient AMX        SI                31 #> 10 Outpatient AMX        R                 47 #> 11 Outpatient CIP        SI                78 #> 12 Outpatient CIP        R                 15 # }"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Define Custom EUCAST Rules — custom_eucast_rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"Define custom EUCAST rules organisation specific analysis use output function eucast_rules().","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"custom_eucast_rules(...)"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"... rules formula notation, see Examples","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"list containing custom rules","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"organisations adoption EUCAST rules. function can used define custom EUCAST rules used eucast_rules() function.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"basics","dir":"Reference","previous_headings":"","what":"Basics","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   two custom EUCAST rules: TZP (piperacillin/tazobactam) \"S\", aminopenicillins (ampicillin amoxicillin) must made \"S\", TZP \"R\", aminopenicillins must made \"R\". rules can also printed console, immediately clear work:   rules (part tilde, example TZP == \"S\" TZP == \"R\") must evaluable data set: able run filter data set without errors. means example column TZP must exist. create sample data set test rules set:","code":"x <- custom_eucast_rules(TZP == \"S\" ~ aminopenicillins == \"S\",                          TZP == \"R\" ~ aminopenicillins == \"R\") x #> A set of custom EUCAST rules: #> #>   1. If TZP is \"S\" then set to  S : #>      amoxicillin (AMX), ampicillin (AMP) #> #>   2. If TZP is \"R\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) df <- data.frame(mo = c(\"Escherichia coli\", \"Klebsiella pneumoniae\"),                  TZP = as.sir(\"R\"),                  ampi = as.sir(\"S\"),                  cipro = as.sir(\"S\")) df #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    S     S  eucast_rules(df, rules = \"custom\", custom_rules = x, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    R     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"using-taxonomic-properties-in-rules","dir":"Reference","previous_headings":"","what":"Using taxonomic properties in rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"one exception columns used rules: column names microorganisms data set can also used, exist data set. column names : \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\" \"snomed\". Thus, next example work well, despite fact df data set contain column genus:","code":"y <- custom_eucast_rules(TZP == \"S\" & genus == \"Klebsiella\" ~ aminopenicillins == \"S\",                          TZP == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\")  eucast_rules(df, rules = \"custom\", custom_rules = y, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"usage-of-antibiotic-group-names","dir":"Reference","previous_headings":"","what":"Usage of antibiotic group names","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"possible define antibiotic groups instead single antibiotics rule consequence, part tilde. examples, antibiotic group aminopenicillins used include ampicillin amoxicillin. following groups allowed (case-insensitive). Within parentheses drugs matched running rule. \"aminoglycosides\"(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin tobramycin-high) \"aminopenicillins\"(amoxicillin ampicillin) \"antifungals\"(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole voriconazole) \"antimycobacterials\"(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide viomycin) \"betalactams\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin ticarcillin/clavulanic acid) \"carbapenems\"(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil tebipenem) \"cephalosporins\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef loracarbef) \"cephalosporins_1st\"(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole cephradine) \"cephalosporins_2nd\"(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil loracarbef) \"cephalosporins_3rd\"(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor latamoxef) \"cephalosporins_4th\"(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome cefquinome) \"cephalosporins_5th\"(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril ceftolozane/tazobactam) \"cephalosporins_except_caz\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef loracarbef) \"fluoroquinolones\"(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin trovafloxacin) \"glycopeptides\"(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin vancomycin-macromethod) \"glycopeptides_except_lipo\"(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin vancomycin-macromethod) \"lincosamides\"(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin tylvalosin) \"lipoglycopeptides\"(dalbavancin, oritavancin telavancin) \"macrolides\"(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin tylvalosin) \"oxazolidinones\"(cadazolid, cycloserine, linezolid, tedizolid thiacetazone) \"penicillins\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin ticarcillin/clavulanic acid) \"polymyxins\"(colistin, polymyxin B polymyxin B/polysorbate 80) \"quinolones\"(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin trovafloxacin) \"streptogramins\"(pristinamycin quinupristin/dalfopristin) \"tetracyclines\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline tigecycline) \"tetracyclines_except_tgc\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline tetracycline) \"trimethoprims\"(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim trimethoprim/sulfamethoxazole) \"ureidopenicillins\"(azlocillin, mezlocillin, piperacillin piperacillin/tazobactam)","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"x <- custom_eucast_rules(   AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",   AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\" ) x #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP)  # run the custom rule set (verbose = TRUE will return a logbook instead of the data set): eucast_rules(example_isolates,   rules = \"custom\",   custom_rules = x,   info = FALSE,   verbose = TRUE ) #> # A tibble: 8 × 9 #>     row col   mo_fullname           old   new   rule     rule_…¹ rule_…² rule_…³ #>   <int> <chr> <chr>                 <ord> <chr> <chr>    <chr>   <chr>   <chr>   #> 1    33 AMP   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 2    33 AMX   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 3    34 AMP   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 4    34 AMX   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 5   531 AMP   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 6   531 AMX   Klebsiella pneumoniae R     I     \"report… Custom… Custom… Object… #> 7  1485 AMP   Klebsiella oxytoca    R     I     \"report… Custom… Custom… Object… #> 8  1485 AMX   Klebsiella oxytoca    R     I     \"report… Custom… Custom… Object… #> # … with abbreviated variable names ¹​rule_group, ²​rule_name, ³​rule_source  # combine rule sets x2 <- c(   x,   custom_eucast_rules(TZP == \"R\" ~ carbapenems == \"R\") ) x2 #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   3. If TZP is \"R\" then set to  R : #>      biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), #>      imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), #>      meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), #>      razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"EUCAST breakpoints used package based dosages data set. can retrieved eucast_dosage().","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"tibble 336 observations 9 variables: ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name antimicrobial drug used WHONET/EARS-Net type Type dosage, either \"high_dosage\", \"standard_dosage\" \"uncomplicated_uti\" dose Dose, \"2 g\" \"25 mg/kg\" dose_times Number times dose must administered administration Route administration, either \"im\", \"iv\" \"oral\" notes Additional dosage notes original_txt Original text PDF file EUCAST eucast_version Version number EUCAST Clinical Breakpoints guideline dosages apply","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"data set based 'EUCAST Clinical Breakpoint Tables' v12.0 (2022) 'EUCAST Clinical Breakpoint Tables' v11.0 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage #> # A tibble: 336 × 9 #>    ab   name                   type  dose  dose_…¹ admin…² notes origi…³ eucas…⁴ #>    <ab> <chr>                  <chr> <chr>   <int> <chr>   <chr> <chr>     <dbl> #>  1 AMK  Amikacin               stan… 25-3…       1 iv      \"\"    25-30 …      12 #>  2 AMX  Amoxicillin            high… 2 g         6 iv      \"\"    2 g x …      12 #>  3 AMX  Amoxicillin            stan… 1 g         3 iv      \"\"    1 g x …      12 #>  4 AMX  Amoxicillin            high… 0.75…       3 oral    \"\"    0.75-1…      12 #>  5 AMX  Amoxicillin            stan… 0.5 g       3 oral    \"\"    0.5 g …      12 #>  6 AMX  Amoxicillin            unco… 0.5 g       3 oral    \"\"    0.5 g …      12 #>  7 AMC  Amoxicillin/clavulani… high… 2 g …       3 iv      \"\"    (2 g a…      12 #>  8 AMC  Amoxicillin/clavulani… stan… 1 g …       3 iv      \"\"    (1 g a…      12 #>  9 AMC  Amoxicillin/clavulani… high… 0.87…       3 oral    \"\"    (0.875…      12 #> 10 AMC  Amoxicillin/clavulani… stan… 0.5 …       3 oral    \"\"    (0.5 g…      12 #> # … with 326 more rows, and abbreviated variable names ¹​dose_times, #> #   ²​administration, ³​original_txt, ⁴​eucast_version"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply EUCAST Rules — eucast_rules","title":"Apply EUCAST Rules — eucast_rules","text":"Apply rules clinical breakpoints intrinsic resistance defined European Committee Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() get data.frame advised dosages certain bug-drug combination, based dosage data set. improve interpretation antibiogram EUCAST rules applied, non-EUCAST rules can applied default, see Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"eucast_rules(   x,   col_mo = NULL,   info = interactive(),   rules = getOption(\"AMR_eucastrules\", default = c(\"breakpoints\", \"expert\")),   verbose = FALSE,   version_breakpoints = 12,   version_expertrules = 3.3,   ampc_cephalosporin_resistance = NA,   only_sir_columns = FALSE,   custom_rules = NULL,   ... )  eucast_dosage(ab, administration = \"iv\", version_breakpoints = 12)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Apply EUCAST Rules — eucast_rules","text":"EUCAST Expert Rules. Version 2.0, 2012. Leclercq et al. EUCAST expert rules antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60; doi:10.1111/j.1469-0691.2011.03703.x EUCAST Expert Rules, Intrinsic Resistance Exceptional Phenotypes Tables. Version 3.1, 2016. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.2, 2020. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.3, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 9.0, 2019. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 10.0, 2020. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 11.0, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 12.0, 2022. (link)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply EUCAST Rules — eucast_rules","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console, defaults print interactive sessions rules character vector specifies rules applied. Must one \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). default value can set another value using option AMR_eucastrules: options(AMR_eucastrules = \"\"). using \"custom\", sure fill argument custom_rules . Custom rules can created custom_eucast_rules(). verbose logical turn Verbose mode (default ). Verbose mode, function apply rules data, instead returns data set logbook form extensive info rows columns effected way. Using Verbose mode takes lot time. version_breakpoints version number use EUCAST Clinical Breakpoints guideline. Can either \"12.0\", \"11.0\" \"10.0\". version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\" \"3.1\". ampc_cephalosporin_resistance character value applied cefotaxime, ceftriaxone ceftazidime AmpC de-repressed cephalosporin-resistant mutants, defaults NA. Currently works version_expertrules 3.2 higher; version 'EUCAST Expert Rules Enterobacterales' state results cefotaxime, ceftriaxone ceftazidime reported note, results suppressed (emptied) three drugs. value NA (default) argument remove results three drugs, e.g. value \"R\" make results drugs resistant. Use NULL FALSE alter results three drugs AmpC de-repressed cephalosporin-resistant mutants. Using TRUE equal using \"R\".  EUCAST Expert Rules v3.2, rule applies : Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia Serratia. only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (defaults FALSE) custom_rules custom rules apply, created custom_eucast_rules() ... column name antibiotic, see section Antibiotics ab (vector ) text can coerced valid antibiotic drug code .ab() administration route administration, either \"im\", \"iv\" \"oral\"","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply EUCAST Rules — eucast_rules","text":"input x, possibly edited values antibiotics. , verbose = TRUE, data.frame original new values affected bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Apply EUCAST Rules — eucast_rules","text":"Note: function translate MIC values SIR values. Use .sir() . Note: ampicillin (AMP, J01CA01) available amoxicillin (AMX, J01CA04) , latter used rules dependency ampicillin. drugs interchangeable comes expression antimicrobial resistance. file containing EUCAST rules located : https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv.  Note: Old taxonomic names replaced current taxonomy applicable. example, Ochrobactrum anthropi renamed Brucella anthropi 2020; original EUCAST rules v3.1 v3.2 yet contain new taxonomic name. AMR package contains full microbial taxonomy updated 11 December, 2022, see microorganisms.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"custom-rules","dir":"Reference","previous_headings":"","what":"Custom Rules","title":"Apply EUCAST Rules — eucast_rules","text":"Custom rules can created using custom_eucast_rules(), e.g.:","code":"x <- custom_eucast_rules(AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",                          AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\")  eucast_rules(example_isolates, rules = \"custom\", custom_rules = x)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"-other-rules","dir":"Reference","previous_headings":"","what":"'Other' Rules","title":"Apply EUCAST Rules — eucast_rules","text":"processing, two non-EUCAST rules drug combinations can applied improve efficacy EUCAST rules, reliability data (analysis). rules : drug enzyme inhibitor set S drug without enzyme inhibitor S drug without enzyme inhibitor set R drug enzyme inhibitor R Important examples include amoxicillin amoxicillin/clavulanic acid, trimethoprim trimethoprim/sulfamethoxazole. Needless say, rules work, drugs must available data set. Since rules officially approved EUCAST, applied default. use rules, include \"\" rules argument, use eucast_rules(..., rules = \"\"). can also set option AMR_eucastrules, .e. run options(AMR_eucastrules = \"\").","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Apply EUCAST Rules — eucast_rules","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, S01AE08), amoxicillin (AMX, J01MA02), amoxicillin/clavulanic acid (AMC, J01MA23), ampicillin (AMP, J01MA04), ampicillin/sulbactam (SAM, J01MA08), arbekacin (ARB, J01MA19), aspoxicillin (APX, J01MA16), azidocillin (AZD, J01MA15), azithromycin (AZM, J01MA11), azlocillin (AZL, J01MA25), aztreonam (ATM, J01MA12), bacampicillin (BAM, J01MA24), bekanamycin (BEK, J01MA07), benzathine benzylpenicillin (BNB, J01MA14), benzathine phenoxymethylpenicillin (BNP, D10AF05), benzylpenicillin (PEN, J01MA06), besifloxacin (BES, J01MA01), biapenem (BIA, J01MA18), carbenicillin (CRB, J01MA03), carindacillin (CRN, J01MA17), cefacetrile (CAC, J01MA10), cefaclor (CEC, J01MA21), cefadroxil (CFR, J01MA09), cefalexin (LEX, J01MA05), cefaloridine (RID, P01AA05), cefalotin (CEP, J01MA22), cefamandole (MAN, J01MA13), cefapirin (HAP, J01CA01), cefatrizine (CTZ, J01CA04), cefazedone (CZD, J01CA12), cefazolin (CZO, J01CR05), cefcapene (CCP, J01CA13), cefdinir (CDR, J01AA02), cefditoren (DIT, J01FA10), cefepime (FEP, J01FA09), cefetamet (CAT, J01CR02), cefixime (CFM, J01AA08), cefmenoxime (CMX, J01FA06), cefmetazole (CMZ, J01CF04), cefodizime (DIZ, J01CF05), cefonicid (CID, J01CR01), cefoperazone (CFP, J01CA19), cefoperazone/sulbactam (CSL, J01CE04), ceforanide (CND, J01CA09), cefotaxime (CTX, J01DF01), cefotaxime/clavulanic acid (CTC, J01CA06), cefotetan (CTT, J01CE08), cefotiam (CTF, J01CE10), cefoxitin (FOX, J01CE01), cefozopran (ZOP, J01CA03), cefpiramide (CPM, J01CA05), cefpirome (CPO, J01CE07), cefpodoxime (CPD, J01CF02), cefprozil (CPR, J01CF01), cefroxadine (CRD, J01CA07), cefsulodin (CFS, J01CA18), ceftaroline (CPT, J01CA11), ceftazidime (CAZ, J01CA14), ceftazidime/clavulanic acid (CCV, J01CF03), cefteram (CEM, J01CA10), ceftezole (CTL, J01CF06), ceftibuten (CTB, J01CE06), ceftizoxime (CZX, J01CE05), ceftobiprole medocaril (CFM1, J01CE02), ceftolozane/tazobactam (CZT, J01CA02), ceftriaxone (CRO, J01CA08), ceftriaxone/beta-lactamase inhibitor (CEB, J01CE09), cefuroxime (CXM, J01CE03), cephradine (CED, J01CG01), chloramphenicol (CHL, J01CA16), ciprofloxacin (CIP, J01CR04), clarithromycin (CLR, J01CA15), clindamycin (CLI, J01CG02), clometocillin (CLM, J01CA17), cloxacillin (CLO, J01CR03), colistin (COL, J01DB10), cycloserine (CYC, J01DC04), dalbavancin (DAL, J01DB05), daptomycin (DAP, J01DB01), delafloxacin (DFX, J01DB02), dibekacin (DKB, J01DB03), dicloxacillin (DIC, J01DC03), dirithromycin (DIR, J01DB08), doripenem (DOR, J01DB07), doxycycline (DOX, J01DB06), enoxacin (ENX, J01DB04), epicillin (EPC, J01DD17), ertapenem (ETP, J01DD15), erythromycin (ERY, J01DD16), fleroxacin (FLE, J01DE01), flucloxacillin (FLC, J01DD10), flurithromycin (FLR1, J01DD08), fosfomycin (FOS, J01DD05), framycetin (FRM, J01DC09), fusidic acid (FUS, J01DD09), garenoxacin (GRN, J01DC06), gatifloxacin (GAT, J01DD12), gemifloxacin (GEM, J01DD62), gentamicin (GEN, J01DC11), grepafloxacin (GRX, J01DD01), hetacillin (HET, J01DD51), imipenem (IPM, J01DC05), imipenem/relebactam (IMR, J01DC07), isepamicin (ISE, J01DC01), josamycin (JOS, J01DE03), kanamycin (KAN, J01DD11), lascufloxacin (LSC, J01DE02), latamoxef (LTM, J01DD13), levofloxacin (LVX, J01DC10), levonadifloxacin (LND, J01DB11), lincomycin (LIN, J01DD03), linezolid (LNZ, J01DI02), lomefloxacin (LOM, J01DD02), loracarbef (LOR, J01DD52), mecillinam (MEC, J01DD18), meropenem (MEM, J01DB12), meropenem/vaborbactam (MEV, J01DD14), metampicillin (MTM, J01DD07), meticillin (MET, J01DI01), mezlocillin (MEZ, J01DI54), micronomicin (MCR, J01DD04), midecamycin (MID, J01DD63), minocycline (MNO, J01DC02), miocamycin (MCM, J01DB09), moxifloxacin (MFX, J01DD06), nadifloxacin (NAD, J01DC08), nafcillin (NAF, J01DH05), nalidixic acid (NAL, J01DH04), neomycin (NEO, J01DH03), netilmicin (NET, J01DH51), nitrofurantoin (NIT, J01DH56), norfloxacin (, J01DH02), ofloxacin (OFX, J01DH52), oleandomycin (OLE, J01DH55), oritavancin (ORI, J01DH06), oxacillin (OXA, J01XA02), panipenem (PAN, J01XA01), pazufloxacin (PAZ, J01XC01), pefloxacin (PEF, J01FA13), penamecillin (PNM, J01FA01), pheneticillin (PHE, J01FA14), phenoxymethylpenicillin (PHN, J01FA07), piperacillin (PIP, J01FA03), piperacillin/tazobactam (TZP, J01FA11), pivampicillin (PVM, J01FA05), pivmecillinam (PME, J01FA12), plazomicin (PLZ, J01FA16), polymyxin B (PLB, J01FA02), pristinamycin (PRI, J01FA15), procaine benzylpenicillin (PRB, J01FA08), propicillin (PRP, J01FF02), prulifloxacin (PRU, J01FG01), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J04AB02), rifampicin (RIF, J01XX09), rokitamycin (ROK, J01XX08), roxithromycin (RXT, J01AA07), rufloxacin (RFL, J01XB01), sisomicin (SIS, J01XB02), sitafloxacin (SIT, J01XE01), solithromycin (SOL, J01AA12), sparfloxacin (SPX, J01EA01), spiramycin (SPI, J01XX01), streptoduocin (STR, J01BA01), streptomycin (STR1, J01GB06), sulbactam (SUL, J01GB12), sulbenicillin (SBC, J01GB13), sulfadiazine (SDI, J01GB09), sulfadiazine/trimethoprim (SLT1, D09AA01), sulfadimethoxine (SUD, J01GB03), sulfadimidine (SDM, J01GB11), sulfadimidine/trimethoprim (SLT2, J01GB04), sulfafurazole (SLF, S01AA22), sulfaisodimidine (SLF1, J01GB05), sulfalene (SLF2, J01GB07), sulfamazone (SZO, J01GB14), sulfamerazine (SLF3, J01GB10), sulfamerazine/trimethoprim (SLT3, J01GB08), sulfamethizole (SLF4, J01GA02), sulfamethoxazole (SMX, J01GA01), sulfamethoxypyridazine (SLF5, J01GB01), sulfametomidine (SLF6, J01EE01), sulfametoxydiazine (SLF7, J01MB02), sulfametrole/trimethoprim (SLT4, J01FF01), sulfamoxole (SLF8, J01XA04), sulfamoxole/trimethoprim (SLT5, J01XA05), sulfanilamide (SLF9, J01XA03), sulfaperin (SLF10, J04AB01), sulfaphenazole (SLF11, J01XX11), sulfapyridine (SLF12, J01EC02), sulfathiazole (SUT, J01ED01), sulfathiourea (SLF13, J01EB03), sultamicillin (SLT6, J01EB05), talampicillin (TAL, J01EB01), tazobactam (TAZ, J01ED02), tebipenem (TBP, J01ED09), tedizolid (TZD, J01ED07), teicoplanin (TEC, J01EB02), telavancin (TLV, J01EC01), telithromycin (TLT, J01ED05), temafloxacin (TMX, J01ED03), temocillin (TEM, J01ED04), tetracycline (TCY, J01EC03), ticarcillin (TIC, J01EB06), ticarcillin/clavulanic acid (TCC, J01ED06), tigecycline (TGC, J01ED08), tilbroquinol (TBQ, J01EB04), tobramycin (TOB, J01EB07), tosufloxacin (TFX, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Apply EUCAST Rules — eucast_rules","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"# \\donttest{ a <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylpenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE )  head(a) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   -   -   -   -   S   S #> 2  Enterococcus faecalis   -   -   -   -   -   S   S #> 3       Escherichia coli   -   -   -   -   -   S   S #> 4  Klebsiella pneumoniae   -   -   -   -   -   S   S #> 5 Pseudomonas aeruginosa   -   -   -   -   -   S   S   # apply EUCAST rules: some results wil be changed b <- eucast_rules(a) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir))  head(b) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   S   R   S   S   S   S #> 2  Enterococcus faecalis   -   -   R   R   R   S   R #> 3       Escherichia coli   R   -   -   -   -   R   S #> 4  Klebsiella pneumoniae   R   R   -   -   -   R   S #> 5 Pseudomonas aeruginosa   R   R   -   -   R   R   R   # do not apply EUCAST rules, but rather get a data.frame # containing all details about the transformations: c <- eucast_rules(a, verbose = TRUE) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir)) head(c) #>   row col           mo_fullname old new rule   rule_group #> 1   1 AMX Staphylococcus aureus   -   S       Breakpoints #> 2   1 CXM Staphylococcus aureus   -   S       Breakpoints #> 3   1 CAZ Staphylococcus aureus   R   S      Expert Rules #> 4   1 CAZ Staphylococcus aureus   -   R      Expert Rules #> 5   1 COL Staphylococcus aureus   -   R      Expert Rules #> 6   2 CAZ Enterococcus faecalis   -   R      Expert Rules #>                                                 rule_name #> 1                                          Staphylococcus #> 2                                          Staphylococcus #> 3                          Expert Rules on Staphylococcus #> 4 Table 4: Intrinsic resistance in gram-positive bacteria #> 5 Table 4: Intrinsic resistance in gram-positive bacteria #> 6 Table 4: Intrinsic resistance in gram-positive bacteria #>                                                                                 rule_source #> 1                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 2                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 3 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 4 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 5 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 6 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 # }  # Dosage guidelines:  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\") #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v12.0 (2022). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\", version_breakpoints = 10) #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v10.0 (2020). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 2 000 Example Isolates — example_isolates","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"data set containing 2 000 microbial isolates full antibiograms. data set contains randomised fictitious data, reflects reality can used practise AMR data analysis. examples, please read tutorial website.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"tibble 2 000 observations 46 variables: date Date receipt laboratory patient ID patient age Age patient gender Gender patient, either \"F\" \"M\" ward Ward type patient admitted, either \"Clinical\", \"ICU\" \"Outpatient\" mo ID microorganism created .mo(), see also microorganisms data set PEN:RIF 40 different antibiotics class sir (see .sir()); column names occur antibiotics data set can translated set_ab_names() ab_name()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Unclean Data — example_isolates_unclean","title":"Data Set with Unclean Data — example_isolates_unclean","text":"data set containing 3 000 microbial isolates cleaned consequently ready AMR data analysis. data set can used practice.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Unclean Data — example_isolates_unclean","text":"tibble 3 000 observations 8 variables: patient_id ID patient date date receipt laboratory hospital ID hospital, C bacteria info microorganism can transformed .mo(), see also microorganisms AMX:GEN 4 different antibiotics transformed .sir()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Unclean Data — example_isolates_unclean","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # … with 2,990 more rows"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine First Isolates — first_isolate","title":"Determine First Isolates — first_isolate","text":"Determine first isolates microorganisms every patient per episode (needed) per specimen type. functions support four methods summarised Hindler et al. 2007 (doi:10.1086/511864 ). determine patient episodes necessarily based microorganisms, use is_new_episode() also supports grouping dplyr package.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine First Isolates — first_isolate","text":"","code":"first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   col_testcode = NULL,   col_specimen = NULL,   col_icu = NULL,   col_keyantimicrobials = NULL,   episode_days = 365,   testcodes_exclude = NULL,   icu_exclude = FALSE,   specimen_group = NULL,   type = \"points\",   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ignore_I = TRUE,   points_threshold = 2,   info = interactive(),   include_unknown = FALSE,   include_untested_sir = TRUE,   ... )  filter_first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   episode_days = 365,   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine First Isolates — first_isolate","text":"Methodology function strictly based : M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. Hindler JF Stelling J (2007). Analysis Presentation Cumulative Antibiograms: New Consensus Guideline Clinical Laboratory Standards Institute. Clinical Infectious Diseases, 44(6), 867-873. doi:10.1086/511864","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine First Isolates — first_isolate","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_date column name result date (date received lab), defaults first column date class col_patient_id column name unique IDs patients, defaults first column starts 'patient' 'patid' (case insensitive) col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). col_testcode column name test codes. Use col_testcode = NULL exclude certain test codes (test codes screening). case testcodes_exclude ignored. col_specimen column name specimen type group col_icu column name logicals (TRUE/FALSE) whether ward department Intensive Care Unit (ICU). can also logical vector length rows x. col_keyantimicrobials (useful method = \"phenotype-based\") column name key antimicrobials determine first isolates, see key_antimicrobials(). Defaults first column starts 'key' followed 'ab' 'antibiotics' 'antimicrobials' (case insensitive). Use col_keyantimicrobials = FALSE prevent . Can also output key_antimicrobials(). episode_days episode days genus/species combination determined 'first isolate' . default 365 days based guideline CLSI, see Source. testcodes_exclude character vector test codes excluded (case-insensitive) icu_exclude logical indicate whether ICU isolates excluded (rows value TRUE column set col_icu) specimen_group value column set col_specimen filter type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details method method apply, either \"phenotype-based\", \"episode-based\", \"patient-based\" \"isolate-based\" (can abbreviated), see Details. default \"phenotype-based\" antimicrobial test results present data, \"episode-based\" otherwise. ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details info logical indicate info printed, defaults TRUE interactive mode include_unknown logical indicate whether 'unknown' microorganisms included , .e. microbial code \"UNKNOWN\", defaults FALSE. WHONET users, means records organism code \"con\" (contamination) excluded default. Isolates microbial ID NA always excluded first isolate. include_untested_sir logical indicate whether also rows without antibiotic results still eligible becoming first isolate. Use include_untested_sir = FALSE always return FALSE rows. checks data set columns class sir consequently requires transforming columns antibiotic results using .sir() first. ... arguments passed first_isolate() using filter_first_isolate(), otherwise arguments passed key_antimicrobials() (universal, gram_negative, gram_positive)","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine First Isolates — first_isolate","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine First Isolates — first_isolate","text":"conduct epidemiological analyses antimicrobial resistance data, -called first isolates included prevent overestimation underestimation antimicrobial resistance. Different methods can used , see . functions context-aware. means x argument can left blank used inside data.frame call, see Examples. first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names. isolates microbial ID NA excluded first isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"different-methods","dir":"Reference","previous_headings":"","what":"Different methods","title":"Determine First Isolates — first_isolate","text":"According Hindler et al. (2007, doi:10.1086/511864 ), different methods (algorithms) select first isolates increasing reliability: isolate-based, patient-based, episode-based phenotype-based. methods select combination taxonomic genus species (subspecies). mentioned methods covered first_isolate() function:","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"isolate-based","dir":"Reference","previous_headings":"","what":"Isolate-based","title":"Determine First Isolates — first_isolate","text":"method require selection, isolates included. , however, respect arguments set first_isolate() function. example, default setting include_unknown (FALSE) omit selection rows without microbial ID.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"patient-based","dir":"Reference","previous_headings":"","what":"Patient-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient , set episode_days Inf. Although often inappropriate, method makes sure duplicate isolates selected patient. large longitudinal data set, mean isolates excluded found years initial isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"episode-based","dir":"Reference","previous_headings":"","what":"Episode-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient episode , set episode_days sensible number days. Depending type analysis, 14, 30, 60 365. Short episodes common analysing specific hospital ward data, long episodes common analysing regional national data. common method correct duplicate isolates. Patients categorised episodes based ID dates (e.g., date specimen receipt laboratory result). common method, take account antimicrobial test results. means e.g. methicillin-resistant Staphylococcus aureus (MRSA) isolate differentiated wildtype Staphylococcus aureus isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"phenotype-based","dir":"Reference","previous_headings":"","what":"Phenotype-based","title":"Determine First Isolates — first_isolate","text":"reliable method, since also weighs antibiogram (antimicrobial test results) yielding -called 'first weighted isolates'. two different methods weigh antibiogram: Using type = \"points\" argument points_threshold (default) method weighs antimicrobial drugs available data set. difference S R (vice versa) counts 0.5 points, difference S R (vice versa) counts 1 point. sum points exceeds points_threshold, defaults 2, isolate selected first weighted isolate. antimicrobials internally selected using all_antimicrobials() function. output function need passed first_isolate() function. Using type = \"keyantimicrobials\" argument ignore_I method weighs specific antimicrobial drugs, called key antimicrobials. difference S R (vice versa) key antimicrobials select isolate first weighted isolate. ignore_I = FALSE, also differences S R (vice versa) lead . Key antimicrobials internally selected using key_antimicrobials() function, can also added manually variable data set col_keyantimicrobials argument. Another option pass output key_antimicrobials() function directly col_keyantimicrobials argument. default method phenotype-based (using type = \"points\") episode-based (using episode_days = 365). makes sure every genus-species combination selected per patient per year, taking account antimicrobial test results. antimicrobial test results available data set, episode-based method applied default.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine First Isolates — first_isolate","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  example_isolates[first_isolate(info = TRUE), ] #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # … with 1,369 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir> # \\donttest{ # get all first Gram-negatives example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ] #> ℹ Using column 'mo' as input for mo_is_gram_negative() #> # A tibble: 437 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  7 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #>  8 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  9 2002-04-01 496896     46 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> 10 2002-04-23 EE2510     69 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> # … with 427 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir>  if (require(\"dplyr\")) {   # filter on first isolates using dplyr:   example_isolates %>%     filter(first_isolate(info = TRUE)) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # … with 1,369 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir> if (require(\"dplyr\")) {   # short-hand version:   example_isolates %>%     filter_first_isolate(info = FALSE) } #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # … with 1,369 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir> if (require(\"dplyr\")) {   # flag the first isolates per group:   example_isolates %>%     group_by(ward) %>%     mutate(first = first_isolate(info = TRUE)) %>%     select(ward, date, patient, mo, first) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #>  #> Group: ward = \"Clinical\" #> ℹ Excluded 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 861 'phenotype-based' first isolates (69.8% of total where a #>    microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"ICU\" #> ℹ Excluded 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5% #>    of total where a microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"Outpatient\" #> ℹ Excluded 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7% #>    of total where a microbial ID was available) #> # A tibble: 2,000 × 5 #> # Groups:   ward [3] #>    ward     date       patient mo           first #>    <chr>    <date>     <chr>   <mo>         <lgl> #>  1 Clinical 2002-01-02 A77334  B_ESCHR_COLI TRUE  #>  2 Clinical 2002-01-03 A77334  B_ESCHR_COLI FALSE #>  3 ICU      2002-01-07 067927  B_STPHY_EPDR TRUE  #>  4 ICU      2002-01-07 067927  B_STPHY_EPDR FALSE #>  5 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  6 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  7 Clinical 2002-01-14 462729  B_STPHY_AURS TRUE  #>  8 Clinical 2002-01-14 462729  B_STPHY_AURS FALSE #>  9 ICU      2002-01-16 067927  B_STPHY_EPDR FALSE #> 10 ICU      2002-01-17 858515  B_STPHY_EPDR TRUE  #> # … with 1,990 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":null,"dir":"Reference","previous_headings":"","what":"G-test for Count Data — g.test","title":"G-test for Count Data — g.test","text":"g.test() performs chi-squared contingency table tests goodness--fit tests, just like chisq.test() reliable (1). G-test can used see whether number observations category fits theoretical expectation (called G-test goodness--fit), see whether proportions one variable different different values variable (called G-test independence).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"G-test for Count Data — g.test","text":"","code":"g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"G-test for Count Data — g.test","text":"code function identical chisq.test(), except : calculation statistic changed \\(2 * sum(x * log(x / E))\\) Yates' continuity correction removed apply G-test possibility simulate p values simulate.p.value removed","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"G-test for Count Data — g.test","text":"x numeric vector matrix. x y can also     factors. y numeric vector; ignored x matrix.      x factor, y factor length. p vector probabilities length x.     error given entry p negative. rescale.p logical scalar; TRUE p rescaled     (necessary) sum 1.  rescale.p FALSE,     p sum 1, error given.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"G-test for Count Data — g.test","text":"list class \"htest\" containing following   components: statistic value chi-squared test statistic. parameter degrees freedom approximate     chi-squared distribution test statistic, NA     p-value computed Monte Carlo simulation. p.value p-value test. method character string indicating type test     performed, whether Monte Carlo simulation continuity     correction used. data.name character string giving name(s) data. observed observed counts. expected expected counts null hypothesis. residuals Pearson residuals,     (observed - expected) / sqrt(expected). stdres standardized residuals,     (observed - expected) / sqrt(V), V residual cell variance (Agresti, 2007,     section 2.4.5 case x matrix, n * p * (1 - p) otherwise).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"G-test for Count Data — g.test","text":"x matrix one row column, x vector y given, goodness--fit test performed (x treated one-dimensional contingency table). entries x must non-negative integers. case, hypothesis tested whether population probabilities equal p, equal p given. x matrix least two rows columns, taken two-dimensional contingency table: entries x must non-negative integers.  Otherwise, x y must vectors factors length; cases missing values removed, objects coerced factors, contingency table computed .  Pearson's chi-squared test performed null hypothesis joint distribution cell counts 2-dimensional contingency table product row column marginals. p-value computed asymptotic chi-squared distribution test statistic. contingency table case simulation done random sampling set contingency tables given marginals, works marginals strictly positive. Note usual sampling situation assumed chi-squared test (G-test) rather Fisher's exact test. goodness--fit case simulation done random sampling discrete distribution specified p, sample size n = sum(x). simulation done R may slow.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-goodness-of-fit-likelihood-ratio-test-","dir":"Reference","previous_headings":"","what":"G-test Of Goodness-of-Fit (Likelihood Ratio Test)","title":"G-test for Count Data — g.test","text":"Use G-test goodness--fit one nominal variable two values (male female, red, pink white flowers). compare observed counts numbers observations category expected counts, calculate using kind theoretical expectation (1:1 sex ratio 1:2:1 ratio genetic cross). expected number observations category small, G-test may give inaccurate results, use exact test instead (fisher.test()). G-test goodness--fit alternative chi-square test goodness--fit (chisq.test()); tests advantages disadvantages, results two tests usually similar.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-independence","dir":"Reference","previous_headings":"","what":"G-test of Independence","title":"G-test for Count Data — g.test","text":"Use G-test independence two nominal variables, two possible values. want know whether proportions one variable different among values variable. also possible G-test independence two nominal variables. example, Jackson et al. (2013) also data children 3, analysis old vs. young, thigh vs. arm, reaction vs. reaction, analyzed together. Fisher's exact test (fisher.test()) exact test, G-test still approximation. 2x2 table, Fisher's Exact test may slower still run seconds, even sum observations multiple millions. G-test independence alternative chi-square test independence (chisq.test()), give approximately results.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"how-the-test-works","dir":"Reference","previous_headings":"","what":"How the Test Works","title":"G-test for Count Data — g.test","text":"Unlike exact test goodness--fit (fisher.test()), G-test directly calculate probability obtaining observed results something extreme. Instead, like almost statistical tests, G-test intermediate step; uses data calculate test statistic measures far observed data null expectation. use mathematical relationship, case chi-square distribution, estimate probability obtaining value test statistic. G-test uses log ratio two likelihoods test statistic, also called likelihood ratio test log-likelihood ratio test. formula calculate G-statistic : \\(G = 2 * sum(x * log(x / E))\\) E expected values. Since chi-square distributed, p value can calculated R :   df degrees freedom. two categories want find ones significantly different null expectation, can use method testing category vs. sum categories, Bonferroni correction. use G-tests category, course.","code":"p <- stats::pchisq(G, df, lower.tail = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"G-test for Count Data — g.test","text":"McDonald, J.H. 2014. Handbook Biological Statistics (3rd ed.). Sparky House Publishing, Baltimore, Maryland. http://www.biostathandbook.com/gtestgof.html.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"G-test for Count Data — g.test","text":"","code":"# = EXAMPLE 1 = # Shivrain et al. (2006) crossed clearfield rice (which are resistant # to the herbicide imazethapyr) with red rice (which are susceptible to # imazethapyr). They then crossed the hybrid offspring and examined the # F2 generation, where they found 772 resistant plants, 1611 moderately # resistant plants, and 737 susceptible plants. If resistance is controlled # by a single gene with two co-dominant alleles, you would expect a 1:2:1 # ratio.  x <- c(772, 1611, 737) g.test(x, p = c(1, 2, 1) / 4) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 4.1471, p-value = 0.1257 #>   # There is no significant difference from a 1:2:1 ratio. # Meaning: resistance controlled by a single gene with two co-dominant # alleles, is plausible.   # = EXAMPLE 2 = # Red crossbills (Loxia curvirostra) have the tip of the upper bill either # right or left of the lower bill, which helps them extract seeds from pine # cones. Some have hypothesized that frequency-dependent selection would # keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992) # observed 1752 right-billed and 1895 left-billed crossbills.  x <- c(1752, 1895) g.test(x) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 5.6085, p-value = 0.01787 #>   # There is a significant difference from a 1:1 ratio. # Meaning: there are significantly more left-billed birds."},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine (Clinical) Episodes — get_episode","title":"Determine (Clinical) Episodes — get_episode","text":"functions determine items vector can considered (start ) new episode, based argument episode_days. can used determine clinical episodes epidemiological analysis. get_episode() function returns index number episode per group, is_new_episode() function returns TRUE every new get_episode() index, thus equal !duplicated(get_episode(...)).","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine (Clinical) Episodes — get_episode","text":"","code":"get_episode(x, episode_days, ...)  is_new_episode(x, episode_days, ...)"},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine (Clinical) Episodes — get_episode","text":"x vector dates (class Date POSIXt), sorted internally determine episodes episode_days required episode length days, can also less day Inf, see Details ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine (Clinical) Episodes — get_episode","text":"get_episode(): integer vector is_new_episode(): logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine (Clinical) Episodes — get_episode","text":"functions get_episode() is_new_episode() differ way setting episode_days 365: Dates first sorted old new. oldest date mark start first episode. date, next date marked least episode_days days later start first episode. second marked date , next date marked least episode_days days later start second episode start third episode, . vector returned, original order restored. first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names allows different isolate selection methods. dplyr package required functions work, episode functions support variable grouping work conveniently inside dplyr verbs filter(), mutate() summarise().","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine (Clinical) Episodes — get_episode","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates df <- example_isolates[sample(seq_len(2000), size = 100), ]  get_episode(df$date, episode_days = 60) # indices #>   [1]  9 36  4 23 47 35 39 40  6 37 20  5  1 49  9 24 11 32 17  4 26 23 37 46 39 #>  [26] 14  7  6 13 29 13 31 40 34 46 48  9 34 33 45 31 29 26  4 15 31 21  9 12  8 #>  [51] 28 42 28 47 45  4 47 43 45 44 36  3 18 47  5 23 21 20 32 33 13 38 22 19 21 #>  [76] 30 41 33 35 47 16  2 44  1 16 29 35 32 10  9 13 25 46 45 24 28 20 27 46 49 is_new_episode(df$date, episode_days = 60) # TRUE/FALSE #>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE #>  [13]  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE #>  [25] FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE #>  [37] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE #>  [49]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE #>  [61] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE #>  [73]  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE #>  [85] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE #>  [97] FALSE  TRUE FALSE FALSE  # filter on results from the third 60-day episode only, using base R df[which(get_episode(df$date, 60) == 3), ] #> # A tibble: 1 × 46 #>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX   #>   <date>     <chr>   <dbl> <chr>  <chr> <mo>         <sir> <sir> <sir> <sir> #> 1 2002-11-21 450741     77 F      ICU   B_STPHY_EPDR R     NA    S     NA    #> # … with 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, #> #   FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, #> #   GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, #> #   NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, #> #   TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, #> #   AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, #> #   MUP <sir>, RIF <sir>  # the functions also work for less than a day, e.g. to include one per hour: get_episode(   c(     Sys.time(),     Sys.time() + 60 * 60   ),   episode_days = 1 / 24 ) #> [1] 1 2  # \\donttest{ if (require(\"dplyr\")) {   # is_new_episode() can also be used in dplyr verbs to determine patient   # episodes based on any (combination of) grouping variables:   df %>%     mutate(condition = sample(       x = c(\"A\", \"B\", \"C\"),       size = 100,       replace = TRUE     )) %>%     group_by(patient, condition) %>%     mutate(new_episode = is_new_episode(date, 365)) %>%     select(patient, date, condition, new_episode) %>%     arrange(patient, condition, date) } #> # A tibble: 100 × 4 #> # Groups:   patient, condition [99] #>    patient date       condition new_episode #>    <chr>   <date>     <chr>     <lgl>       #>  1 004531  2013-12-02 B         TRUE        #>  2 006827  2009-07-24 C         TRUE        #>  3 008218  2009-05-05 B         TRUE        #>  4 021368  2016-03-25 B         TRUE        #>  5 032343  2003-06-09 C         TRUE        #>  6 069276  2015-06-18 A         TRUE        #>  7 077922  2009-08-24 C         TRUE        #>  8 0DBB93  2009-05-08 C         TRUE        #>  9 125492  2017-09-15 C         TRUE        #> 10 126334  2009-11-26 A         TRUE        #> # … with 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward, patient) %>%     transmute(date,       patient,       new_index = get_episode(date, 60),       new_logical = is_new_episode(date, 60)     ) %>%     arrange(patient, ward, date) } #> # A tibble: 100 × 5 #> # Groups:   ward, patient [98] #>    ward       date       patient new_index new_logical #>    <chr>      <date>     <chr>       <int> <lgl>       #>  1 Clinical   2013-12-02 004531          1 TRUE        #>  2 Clinical   2009-07-24 006827          1 TRUE        #>  3 Clinical   2009-05-05 008218          1 TRUE        #>  4 Outpatient 2016-03-25 021368          1 TRUE        #>  5 Clinical   2003-06-09 032343          1 TRUE        #>  6 Clinical   2015-06-18 069276          1 TRUE        #>  7 Clinical   2009-08-24 077922          1 TRUE        #>  8 Clinical   2009-05-08 0DBB93          1 TRUE        #>  9 Clinical   2017-09-15 125492          1 TRUE        #> 10 Outpatient 2009-11-26 126334          1 TRUE        #> # … with 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward) %>%     summarise(       n_patients = n_distinct(patient),       n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),       n_episodes_60 = sum(is_new_episode(date, episode_days = 60)),       n_episodes_30 = sum(is_new_episode(date, episode_days = 30))     ) } #> # A tibble: 3 × 5 #>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30 #>   <chr>           <int>          <int>         <int>         <int> #> 1 Clinical           74             14            41            54 #> 2 ICU                20              7            16            17 #> 3 Outpatient          4              2             3             3  # grouping on patients and microorganisms leads to the same # results as first_isolate() when using 'episode-based': if (require(\"dplyr\")) {   x <- df %>%     filter_first_isolate(       include_unknown = TRUE,       method = \"episode-based\"     )    y <- df %>%     group_by(patient, mo) %>%     filter(is_new_episode(date, 365)) %>%     ungroup()    identical(x, y) } #> [1] TRUE  # but is_new_episode() has a lot more flexibility than first_isolate(), # since you can now group on anything that seems relevant: if (require(\"dplyr\")) {   df %>%     group_by(patient, mo, ward) %>%     mutate(flag_episode = is_new_episode(date, 365)) %>%     select(group_vars(.), flag_episode) } #> # A tibble: 100 × 4 #> # Groups:   patient, mo, ward [99] #>    patient mo           ward       flag_episode #>    <chr>   <mo>         <chr>      <lgl>        #>  1 838694  B_ACNTB      Clinical   TRUE         #>  2 919B60  B_STPHY_AURS Clinical   TRUE         #>  3 032343  B_STPHY_CONS Clinical   TRUE         #>  4 126334  B_STPHY_CONS Outpatient TRUE         #>  5 BF4515  B_ESCHR_COLI Clinical   TRUE         #>  6 B13995  B_STPHY_AURS Clinical   TRUE         #>  7 E99D61  B_STPHY_EPDR ICU        TRUE         #>  8 C54153  B_STPHY_EPDR Clinical   TRUE         #>  9 822116  B_STPHY_AURS ICU        TRUE         #> 10 B12887  B_ESCHR_COLI Clinical   TRUE         #> # … with 90 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"PCA Biplot with ggplot2 — ggplot_pca","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"Produces ggplot2 variant -called biplot PCA (principal component analysis), flexible appealing base R biplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"ggplot_pca(   x,   choices = 1:2,   scale = 1,   pc.biplot = TRUE,   labels = NULL,   labels_textsize = 3,   labels_text_placement = 1.5,   groups = NULL,   ellipse = TRUE,   ellipse_prob = 0.68,   ellipse_size = 0.5,   ellipse_alpha = 0.5,   points_size = 2,   points_alpha = 0.25,   arrows = TRUE,   arrows_colour = \"darkblue\",   arrows_size = 0.5,   arrows_textsize = 3,   arrows_textangled = TRUE,   arrows_alpha = 0.75,   base_textsize = 10,   ... )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"ggplot_pca() function based ggbiplot() function ggbiplot package Vince Vu, found GitHub: https://github.com/vqv/ggbiplot (retrieved: 2 March 2020, latest commit: 7325e88; 12 February 2015). per GPL-2 licence demands documentation code changes, changes made based source code : Rewritten code remove dependency packages plyr, scales grid Parametrised options, like arrow ellipse settings Hardened input possibilities defining exact type user input every argument Added total amount explained variance caption plot Cleaned syntax based lintr package, fixed grammatical errors added integrity checks Updated documentation","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"x object returned pca(), prcomp() princomp() choices length 2 vector specifying components plot. default     biplot strict sense. scale variables scaled lambda ^ scale     observations scaled lambda ^ (1-scale)     lambda singular values computed     princomp. Normally 0 <= scale <= 1, warning     issued specified scale outside range. pc.biplot true, use Gabriel (1971) refers \"principal component     biplot\", lambda = 1 observations scaled sqrt(n)     variables scaled sqrt(n).  inner products     variables approximate covariances distances observations     approximate Mahalanobis distance. labels optional vector labels observations. set, labels placed respective points. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). labels_textsize size text used labels labels_text_placement adjustment factor placement variable names (>=1 means away arrow head) groups optional vector groups labels, length labels. set, points labels coloured according groups. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). ellipse logical indicate whether normal data ellipse drawn group (set groups) ellipse_prob statistical size ellipse normal probability ellipse_size size ellipse line ellipse_alpha alpha (transparency) ellipse line points_size size points points_alpha alpha (transparency) points arrows logical indicate whether arrows drawn arrows_colour colour arrow text arrows_size size (thickness) arrow lines arrows_textsize size text end arrows arrows_textangled logical whether text end arrows angled arrows_alpha alpha (transparency) arrows text base_textsize text size plot elements except labels arrows ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"colours labels points can changed adding another scale layer colour, scale_colour_viridis_d() scale_colour_brewer().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    summary(pca_result)    # old base R plotting method:   biplot(pca_result)    # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      # still extendible with any ggplot2 function     ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", \"TMP\" #>   and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":null,"dir":"Reference","previous_headings":"","what":"AMR Plots with ggplot2 — ggplot_sir","title":"AMR Plots with ggplot2 — ggplot_sir","text":"Use functions create bar plots AMR data analysis. functions rely ggplot2 functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"ggplot_sir(   data,   position = NULL,   x = \"antibiotic\",   fill = \"interpretation\",   facet = NULL,   breaks = seq(0, 1, 0.1),   limits = NULL,   translate_ab = \"name\",   combine_SI = TRUE,   minimum = 30,   language = get_AMR_locale(),   nrow = NULL,   colours = c(S = \"#3CAEA3\", SI = \"#3CAEA3\", I = \"#F6D55C\", IR = \"#ED553B\", R =     \"#ED553B\"),   datalabels = TRUE,   datalabels.size = 2.5,   datalabels.colour = \"grey15\",   title = NULL,   subtitle = NULL,   caption = NULL,   x.title = \"Antimicrobial\",   y.title = \"Proportion\",   ... )  geom_sir(   position = NULL,   x = c(\"antibiotic\", \"interpretation\"),   fill = \"interpretation\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   ... )  facet_sir(facet = c(\"interpretation\", \"antibiotic\"), nrow = NULL)  scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)  scale_sir_colours(..., aesthetics = \"fill\")  theme_sir()  labels_sir_count(   position = NULL,   x = \"antibiotic\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   datalabels.size = 3,   datalabels.colour = \"grey15\" )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"AMR Plots with ggplot2 — ggplot_sir","text":"data data.frame column(s) class sir (see .sir()) position position adjustment bars, either \"fill\", \"stack\" \"dodge\" x variable show x axis, either \"antibiotic\" (default) \"interpretation\" grouping variable fill variable categorise using plots legend, either \"antibiotic\" (default) \"interpretation\" grouping variable facet variable split plots , either \"interpretation\" (default) \"antibiotic\" grouping variable breaks numeric vector positions limits numeric vector length two providing limits scale, use NA refer existing minimum maximum translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant), defaults TRUE minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. nrow (using facet) number rows colours named vactor colour used filling. default colours colour-blind friendly. datalabels show datalabels using labels_sir_count() datalabels.size size datalabels datalabels.colour colour datalabels title text show title plot subtitle text show subtitle plot caption text show caption plot x.title text show x axis description y.title text show y axis description ... arguments passed geom_sir() , case scale_sir_colours(), named values set colours. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. See Examples. aesthetics aesthetics apply colours , defaults \"fill\" can also (combination ) \"alpha\", \"colour\", \"fill\", \"linetype\", \"shape\" \"size\"","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"AMR Plots with ggplot2 — ggplot_sir","text":"default, names antibiotics shown plots using ab_name(). can set translate_ab argument. See count_df().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"the-functions","dir":"Reference","previous_headings":"","what":"The Functions","title":"AMR Plots with ggplot2 — ggplot_sir","text":"geom_sir() take variable data sir class (created .sir()) using sir_df() plot bars percentage S, , R. default behaviour bars stacked different antibiotics x axis. facet_sir() creates 2d plots (default based S//R) using ggplot2::facet_wrap(). scale_y_percent() transforms y axis 0 100% range using ggplot2::scale_y_continuous(). scale_sir_colours() sets colours bars (green S, yellow , red R). multilingual support. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. theme_sir() [ggplot2 theme][ggplot2::theme() minimal distraction. labels_sir_count() print datalabels bars percentage amount isolates using ggplot2::geom_text(). ggplot_sir() wrapper around functions uses data first input. makes possible use function pipe (%>%). See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"# \\donttest{ if (require(\"ggplot2\") && require(\"dplyr\")) {   # get antimicrobial results for drugs against a UTI:   ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +     geom_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # prettify the plot using some additional functions:   df <- example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)   ggplot(df) +     geom_sir() +     scale_y_percent() +     scale_sir_colours() +     labels_sir_count() +     theme_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # or better yet, simplify this using the wrapper function - a single command:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # get only proportions and no counts:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(datalabels = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # add other ggplot2 arguments as you like:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(       width = 0.5,       colour = \"black\",       size = 1,       linetype = 2,       alpha = 0.25     ) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # you can alter the colours with colour names:   example_isolates %>%     select(AMX) %>%     ggplot_sir(colours = c(SI = \"yellow\")) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # but you can also use the built-in colour-blind friendly colours for   # your plots, where \"S\" is green, \"I\" is yellow and \"R\" is red:   data.frame(     x = c(\"Value1\", \"Value2\", \"Value3\"),     y = c(1, 2, 3),     z = c(\"Value4\", \"Value5\", \"Value6\")   ) %>%     ggplot() +     geom_col(aes(x = x, y = y, fill = z)) +     scale_sir_colours(Value4 = \"S\", Value5 = \"I\", Value6 = \"R\") }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # resistance of ciprofloxacine per age group   example_isolates %>%     mutate(first_isolate = first_isolate()) %>%     filter(       first_isolate == TRUE,       mo == as.mo(\"Escherichia coli\")     ) %>%     # age_groups() is also a function in this AMR package:     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(x = \"age_group\") } #> Warning: Removed 6 rows containing missing values (`position_stack()`). #> Warning: Removed 6 rows containing missing values (`position_stack()`).  if (require(\"ggplot2\") && require(\"dplyr\")) {   # a shorter version which also adjusts data label colours:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(colours = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # it also supports groups (don't forget to use the group var on `x` or `facet`):   example_isolates %>%     filter(mo_is_gram_negative(), ward != \"Outpatient\") %>%     # select only UTI-specific drugs     select(ward, AMX, NIT, FOS, TMP, CIP) %>%     group_by(ward) %>%     ggplot_sir(       x = \"ward\",       facet = \"antibiotic\",       nrow = 1,       title = \"AMR of Anti-UTI Drugs Per Ward\",       x.title = \"Ward\",       datalabels = FALSE     ) } #> ℹ Using column 'mo' as input for mo_is_gram_negative()  # }"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess Antibiotic Column — guess_ab_col","title":"Guess Antibiotic Column — guess_ab_col","text":"tries find column name data set based information antibiotics data set. Also supports WHONET abbreviations.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"guess_ab_col(   x = NULL,   search_string = NULL,   verbose = FALSE,   only_sir_columns = FALSE )"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess Antibiotic Column — guess_ab_col","text":"x data.frame search_string text search x , checked .ab() value column x verbose logical indicate whether additional info printed only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (defaults FALSE)","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess Antibiotic Column — guess_ab_col","text":"column name x, NULL result found.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Guess Antibiotic Column — guess_ab_col","text":"can look antibiotic (trade) name abbreviation search x antibiotics data set column containing name code antibiotic.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"df <- data.frame(   amox = \"S\",   tetr = \"R\" )  guess_ab_col(df, \"amoxicillin\") #> [1] \"amox\" guess_ab_col(df, \"J01AA07\") # ATC code of tetracycline #> [1] \"tetr\"  guess_ab_col(df, \"J01AA07\", verbose = TRUE) #> Auto-guessing columns suitable for analysis #> ... #>  OK. #> ℹ Using column 'amox' as input for AMX (amoxicillin). #> ℹ Using column 'tetr' as input for TCY (tetracycline). #> ℹ Using column 'tetr' as input for J01AA07 (tetracycline). #> [1] \"tetr\" # NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).  # WHONET codes df <- data.frame(   AMP_ND10 = \"R\",   AMC_ED20 = \"S\" ) guess_ab_col(df, \"ampicillin\") #> [1] \"AMP_ND10\" guess_ab_col(df, \"J01CR02\") #> [1] \"AMC_ED20\" guess_ab_col(df, as.ab(\"augmentin\")) #> [1] \"AMC_ED20\""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Data set containing defined intrinsic resistance EUCAST bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant"},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"tibble 134 634 observations 2 variables: mo Microorganism ID ab Antibiotic ID","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"data set based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant #> # A tibble: 134,634 × 2 #>    mo      ab    #>    <mo>    <chr> #>  1 B_GRAMP ATM   #>  2 B_GRAMP COL   #>  3 B_GRAMP NAL   #>  4 B_GRAMP PLB   #>  5 B_GRAMP TEM   #>  6 B_ABTRP ATM   #>  7 B_ABTRP COL   #>  8 B_ABTRP NAL   #>  9 B_ABTRP PLB   #> 10 B_ABTRP TEM   #> # … with 134,624 more rows"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"According binomial nomenclature, lowest four taxonomic levels (family, genus, species, subspecies) printed italics. function finds taxonomic names within strings makes italic.","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(string, type = c(\"markdown\", \"ansi\"))  italicize_taxonomy(string, type = c(\"markdown\", \"ansi\"))"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"string character (vector) type type conversion taxonomic names, either \"markdown\" \"ansi\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"function finds taxonomic names makes italic based microorganisms data set. taxonomic names can italicised using markdown (default) adding * taxonomic names, using ANSI colours adding \\033[3m \\033[23m taxonomic names. multiple ANSI colours available, conversion occur. function also supports abbreviation genus followed species, \"E. coli\" \"K. pneumoniae ozaenae\".","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(\"An overview of Staphylococcus aureus isolates\") #> [1] \"An overview of *Staphylococcus aureus* isolates\" italicise_taxonomy(\"An overview of S. aureus isolates\") #> [1] \"An overview of *S. aureus* isolates\"  cat(italicise_taxonomy(\"An overview of S. aureus isolates\", type = \"ansi\")) #> An overview of S. aureus isolates"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":null,"dir":"Reference","previous_headings":"","what":"Join microorganisms to a Data Set — join","title":"Join microorganisms to a Data Set — join","text":"Join data set microorganisms easily existing data set character vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Join microorganisms to a Data Set — join","text":"","code":"inner_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  left_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  right_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  full_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  semi_join_microorganisms(x, by = NULL, ...)  anti_join_microorganisms(x, by = NULL, ...)"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Join microorganisms to a Data Set — join","text":"x existing data set join, character vector. case character vector, resulting data.frame contain column 'x' values. variable join - left empty search column class mo (created .mo()) \"mo\" column name exists x, otherwise column name x values exist microorganisms$mo (= \"bacteria_id\"), another column microorganisms (named, like = c(\"bacteria_id\" = \"fullname\")) suffix non-joined duplicate variables x y, suffixes added output disambiguate . character vector length 2. ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Join microorganisms to a Data Set — join","text":"data.frame","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Join microorganisms to a Data Set — join","text":"Note: opposed join() functions dplyr, character vectors supported default existing columns get suffix \"2\" newly joined columns get suffix. dplyr package installed, join functions used. Otherwise, much slower merge() interaction() functions base R used.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Join microorganisms to a Data Set — join","text":"","code":"left_join_microorganisms(as.mo(\"K. pneumoniae\")) #> # A tibble: 1 × 22 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # … with 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, #> #   source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, #> #   gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, #> #   snomed <list> left_join_microorganisms(\"B_KLBSL_PNMN\") #> # A tibble: 1 × 22 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # … with 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, #> #   source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, #> #   gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, #> #   snomed <list>  df <- data.frame(   date = seq(     from = as.Date(\"2018-01-01\"),     to = as.Date(\"2018-01-07\"),     by = 1   ),   bacteria = as.mo(c(     \"S. aureus\", \"MRSA\", \"MSSA\", \"STAAUR\",     \"E. coli\", \"E. coli\", \"E. coli\"   )),   stringsAsFactors = FALSE ) colnames(df) #> [1] \"date\"     \"bacteria\"  df_joined <- left_join_microorganisms(df, \"bacteria\") colnames(df_joined) #>  [1] \"date\"            \"bacteria\"        \"fullname\"        \"status\"          #>  [5] \"kingdom\"         \"phylum\"          \"class\"           \"order\"           #>  [9] \"family\"          \"genus\"           \"species\"         \"subspecies\"      #> [13] \"rank\"            \"ref\"             \"source\"          \"lpsn\"            #> [17] \"lpsn_parent\"     \"lpsn_renamed_to\" \"gbif\"            \"gbif_parent\"     #> [21] \"gbif_renamed_to\" \"prevalence\"      \"snomed\"           # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     left_join_microorganisms() %>%     colnames() } #> Joining, by = \"mo\" #>  [1] \"date\"            \"patient\"         \"age\"             \"gender\"          #>  [5] \"ward\"            \"mo\"              \"PEN\"             \"OXA\"             #>  [9] \"FLC\"             \"AMX\"             \"AMC\"             \"AMP\"             #> [13] \"TZP\"             \"CZO\"             \"FEP\"             \"CXM\"             #> [17] \"FOX\"             \"CTX\"             \"CAZ\"             \"CRO\"             #> [21] \"GEN\"             \"TOB\"             \"AMK\"             \"KAN\"             #> [25] \"TMP\"             \"SXT\"             \"NIT\"             \"FOS\"             #> [29] \"LNZ\"             \"CIP\"             \"MFX\"             \"VAN\"             #> [33] \"TEC\"             \"TCY\"             \"TGC\"             \"DOX\"             #> [37] \"ERY\"             \"CLI\"             \"AZM\"             \"IPM\"             #> [41] \"MEM\"             \"MTR\"             \"CHL\"             \"COL\"             #> [45] \"MUP\"             \"RIF\"             \"fullname\"        \"status\"          #> [49] \"kingdom\"         \"phylum\"          \"class\"           \"order\"           #> [53] \"family\"          \"genus\"           \"species\"         \"subspecies\"      #> [57] \"rank\"            \"ref\"             \"source\"          \"lpsn\"            #> [61] \"lpsn_parent\"     \"lpsn_renamed_to\" \"gbif\"            \"gbif_parent\"     #> [65] \"gbif_renamed_to\" \"prevalence\"      \"snomed\"          # }"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"functions can used determine first weighted isolates considering phenotype isolate selection (see first_isolate()). Using phenotype-based method determine first isolates reliable methods disregard phenotypes.","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"key_antimicrobials(   x = NULL,   col_mo = NULL,   universal = c(\"ampicillin\", \"amoxicillin/clavulanic acid\", \"cefuroxime\",     \"piperacillin/tazobactam\", \"ciprofloxacin\", \"trimethoprim/sulfamethoxazole\"),   gram_negative = c(\"gentamicin\", \"tobramycin\", \"colistin\", \"cefotaxime\", \"ceftazidime\",     \"meropenem\"),   gram_positive = c(\"vancomycin\", \"teicoplanin\", \"tetracycline\", \"erythromycin\",     \"oxacillin\", \"rifampin\"),   antifungal = c(\"anidulafungin\", \"caspofungin\", \"fluconazole\", \"miconazole\", \"nystatin\",     \"voriconazole\"),   only_sir_columns = FALSE,   ... )  all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)  antimicrobials_equal(   y,   z,   type = c(\"points\", \"keyantimicrobials\"),   ignore_I = TRUE,   points_threshold = 2,   ... )"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"x data.frame antibiotics columns, like AMX amox. Can left blank determine automatically col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). universal names broad-spectrum antimicrobial drugs, case-insensitive. Set NULL ignore. See Details default antimicrobial drugs gram_negative names antibiotic drugs Gram-positives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs gram_positive names antibiotic drugs Gram-negatives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs antifungal names antifungal drugs fungi, case-insensitive. Set NULL ignore. See Details default antifungal drugs only_sir_columns logical indicate whether columns must included transformed class sir (see .sir()) beforehand (defaults FALSE) ... ignored, place allow future extensions y, z character vectors compare type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"key_antimicrobials() all_antimicrobials() functions context-aware. means x argument can left blank used inside data.frame call, see Examples. function key_antimicrobials() returns character vector 12 antimicrobial results every isolate. function all_antimicrobials() returns character vector antimicrobial drug results every isolate. vectors can compared using antimicrobials_equal(), check two isolates generally antibiogram. Missing invalid values replaced dot (\".\") key_antimicrobials() ignored antimicrobials_equal(). Please see first_isolate() function important functions enable 'phenotype-based' method determination first isolates. default antimicrobial drugs used rows (set universal) : Ampicillin Amoxicillin/clavulanic acid Cefuroxime Ciprofloxacin Piperacillin/tazobactam Trimethoprim/sulfamethoxazole default antimicrobial drugs used Gram-negative bacteria (set gram_negative) : Cefotaxime Ceftazidime Colistin Gentamicin Meropenem Tobramycin default antimicrobial drugs used Gram-positive bacteria (set gram_positive) : Erythromycin Oxacillin Rifampin Teicoplanin Tetracycline Vancomycin default antimicrobial drugs used fungi (set antifungal) : Anidulafungin Caspofungin Fluconazole Miconazole Nystatin Voriconazole","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # output of the `key_antimicrobials()` function could be like this: strainA <- \"SSSRR.S.R..S\" strainB <- \"SSSIRSSSRSSS\"  # those strings can be compared with: antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\") #> [1] TRUE # TRUE, because I is ignored (as well as missing values)  antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\", ignore_I = FALSE) #> [1] FALSE # FALSE, because I is not ignored and so the 4th [character] differs  # \\donttest{ if (require(\"dplyr\")) {   # set key antibiotics to a new variable   my_patients <- example_isolates %>%     mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`     mutate(       # now calculate first isolates       first_regular = first_isolate(col_keyantimicrobials = FALSE),       # and first WEIGHTED isolates       first_weighted = first_isolate(col_keyantimicrobials = \"keyab\")     )    # Check the difference in this data set, 'weighted' results in more isolates:   sum(my_patients$first_regular, na.rm = TRUE)   sum(my_patients$first_weighted, na.rm = TRUE) } #> [1] 1395 # }"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":null,"dir":"Reference","previous_headings":"","what":"Kurtosis of the Sample — kurtosis","title":"Kurtosis of the Sample — kurtosis","text":"Kurtosis measure \"tailedness\" probability distribution real-valued random variable. normal distribution kurtosis 3 excess kurtosis 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for default kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for matrix kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for data.frame kurtosis(x, na.rm = FALSE, excess = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kurtosis of the Sample — kurtosis","text":"x vector values, matrix data.frame na.rm logical indicate whether NA values stripped computation proceeds excess logical indicate whether excess kurtosis returned, defined kurtosis minus 3.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(rnorm(10000)) #> [1] 3.147968 kurtosis(rnorm(10000), excess = TRUE) #> [1] -0.003239662"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":null,"dir":"Reference","previous_headings":"","what":"Vectorised Pattern Matching with Keyboard Shortcut — like","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Convenient wrapper around grepl() match pattern: x %like% pattern. always returns logical vector always case-insensitive (use x %like_case% pattern case-sensitive matching). Also, pattern can long x compare items index vectors, can length iterate cases.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"like(x, pattern, ignore.case = TRUE)  x %like% pattern  x %unlike% pattern  x %like_case% pattern  x %unlike_case% pattern"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Idea like function data.table package, although altered explained Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"x character vector matches sought, object can coerced .character() character vector. pattern character vector containing regular expressions (character string fixed = TRUE) matched given character vector. Coerced .character() character string possible. ignore.case FALSE, pattern matching case sensitive TRUE, case ignored matching.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"like() %like%/%unlike% functions: case-insensitive (use %like_case%/%unlike_case% case-sensitive matching) Support multiple patterns Check pattern valid regular expression sets fixed = TRUE , greatly improve speed (vectorised pattern) Always use compatibility Perl unless fixed = TRUE, greatly improve speed Using RStudio? %like%/%unlike% functions can also directly inserted code Addins menu can keyboard shortcut like Shift+Ctrl+L Shift+Cmd+L (see menu Tools > Modify Keyboard Shortcuts...). keep pressing shortcut, inserted text iterated %like% -> %unlike% -> %like_case% -> %unlike_case%.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"a <- \"This is a test\" b <- \"TEST\" a %like% b #> [1] TRUE b %like% a #> [1] FALSE  # also supports multiple patterns a <- c(\"Test case\", \"Something different\", \"Yet another thing\") b <- c(\"case\", \"diff\", \"yet\") a %like% b #> [1] TRUE TRUE TRUE a %unlike% b #> [1] FALSE FALSE FALSE  a[1] %like% b #> [1]  TRUE FALSE FALSE a %like% b[1] #> [1]  TRUE FALSE FALSE  # \\donttest{ # get isolates whose name start with 'Entero' (case-insensitive) example_isolates[which(mo_name() %like% \"^entero\"), ] #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # … with 96 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir>  if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_name() %like% \"^ent\") } #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # … with 96 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, #> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, #> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, #> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, #> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, #> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, #> #   COL <sir>, MUP <sir>, RIF <sir> # }"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Determine isolates multidrug-resistant organisms (MDRO) according international, national custom guidelines.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"mdro(   x = NULL,   guideline = \"CMI2012\",   col_mo = NULL,   info = interactive(),   pct_required_classes = 0.5,   combine_SI = TRUE,   verbose = FALSE,   only_sir_columns = FALSE,   ... )  custom_mdro_guideline(..., as_factor = TRUE)  brmo(x = NULL, only_sir_columns = FALSE, ...)  mrgn(x = NULL, only_sir_columns = FALSE, ...)  mdr_tb(x = NULL, only_sir_columns = FALSE, ...)  mdr_cmi2012(x = NULL, only_sir_columns = FALSE, ...)  eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"See supported guidelines list publications used function.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"x data.frame antibiotics columns, like AMX amox. Can left blank automatic determination. guideline specific guideline follow, see sections Supported international / national guidelines Using Custom Guidelines . left empty, publication Magiorakos et al. (see ) followed. col_mo column name names codes microorganisms (see .mo()), defaults first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console, defaults print interactive sessions pct_required_classes minimal required percentage antimicrobial classes must available per isolate, rounded . example, default guideline, 17 antimicrobial classes must available S. aureus. Setting pct_required_classes argument 0.5 (default) means every S. aureus isolate least 8 different classes must available. lower number available classes return NA isolate. combine_SI logical indicate whether values S must merged one, resistance considered isolates R, . default behaviour mdro() function, follows redefinition EUCAST interpretation (increased exposure) 2019, see section 'Interpretation S, R' . using combine_SI = FALSE, resistance considered isolates R . verbose logical turn Verbose mode (default ). Verbose mode, function return MDRO results, instead returns data set logbook form extensive info isolates MDRO-positive, . only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (defaults FALSE) ... case custom_mdro_guideline(): set rules, see section Using Custom Guidelines . Otherwise: column name antibiotic, see section Antibiotics . as_factor logical indicate whether returned value ordered factor (TRUE, default), otherwise character vector","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"CMI 2012 paper - function mdr_cmi2012() mdro(): Ordered factor levels Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR) TB guideline - function mdr_tb() mdro(..., guideline = \"TB\"): Ordered factor levels Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant German guideline - function mrgn() mdro(..., guideline = \"MRGN\"): Ordered factor levels Negative < 3MRGN < 4MRGN Everything else, except custom guidelines: Ordered factor levels Negative < Positive, unconfirmed < Positive. value \"Positive, unconfirmed\" means , according guideline, entirely sure isolate multi-drug resistant confirmed additional (e.g. molecular) tests","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"functions context-aware. means x argument can left blank used inside data.frame call, see Examples. pct_required_classes argument, values 1 divided 100. support fractions (0.75 3/4) percentages (75). Note: Every test involves Enterobacteriaceae family, internally performed using newly named order Enterobacterales, since Enterobacteriaceae family taxonomically reclassified Adeolu et al. 2016. , Enterobacteriaceae family Enterobacteriales () order. species old Enterobacteriaceae family still new Enterobacterales (without ) order, divided multiple families. way tests performed now mdro() function makes sure results 2016 2016 identical.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"supported-international-national-guidelines","dir":"Reference","previous_headings":"","what":"Supported International / National Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. \"Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.\" Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.3\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.3 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.2\" European international guideline - EUCAST Expert Rules Version 3.2 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 \"Intrinsic Resistance Exceptional Phenotypes Tables\" (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization \"Companion handbook guidelines programmatic management drug-resistant tuberculosis\" (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7; doi:10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu \"WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)\" (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"using-custom-guidelines","dir":"Reference","previous_headings":"","what":"Using Custom Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   row/isolate matches first rule, value first ~ (case 'Elderly Type ') set MDRO value. Otherwise, second rule tried . number rules unlimited. can print rules set console overview. Colours help reading console supports colours.   outcome function can used guideline argument mdro() function:   Rules can also combined custom rules using c():   rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(CIP == \"R\" & age > 60 ~ \"Elderly Type A\",                                 ERY == \"R\" & age > 60 ~ \"Elderly Type B\") custom #> A set of custom MDRO rules: #>   1. CIP is \"R\" and age is higher than 60 -> Elderly Type A #>   2. ERY is \"R\" and age is higher than 60 -> Elderly Type B #>   3. Otherwise -> Negative #> #> Unmatched rows will return NA. x <- mdro(example_isolates,           guideline = custom) table(x) #>       Negative Elderly Type A Elderly Type B #>           1070            198            732 x <- mdro(example_isolates,           guideline = c(custom,                         custom_mdro_guideline(ERY == \"R\" & age > 50 ~ \"Elderly Type C\"))) table(x) #>       Negative Elderly Type A Elderly Type B Elderly Type C #>            961            198            732            109"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, S01AE08), amoxicillin (AMX, J01MA02), amoxicillin/clavulanic acid (AMC, J01MA23), ampicillin (AMP, J01MA04), ampicillin/sulbactam (SAM, J01MA08), arbekacin (ARB, J01MA19), aspoxicillin (APX, J01MA16), azidocillin (AZD, J01MA15), azithromycin (AZM, J01MA11), azlocillin (AZL, J01MA25), aztreonam (ATM, J01MA12), bacampicillin (BAM, J01MA24), bekanamycin (BEK, J01MA07), benzathine benzylpenicillin (BNB, J01MA14), benzathine phenoxymethylpenicillin (BNP, D10AF05), benzylpenicillin (PEN, J01MA06), besifloxacin (BES, J01MA01), biapenem (BIA, J01MA18), carbenicillin (CRB, J01MA03), carindacillin (CRN, J01MA17), cefacetrile (CAC, J01MA10), cefaclor (CEC, J01MA21), cefadroxil (CFR, J01MA09), cefalexin (LEX, J01MA05), cefaloridine (RID, P01AA05), cefalotin (CEP, J01MA22), cefamandole (MAN, J01MA13), cefapirin (HAP, J01CA01), cefatrizine (CTZ, J01CA04), cefazedone (CZD, J01CA12), cefazolin (CZO, J01CR05), cefcapene (CCP, J01CA13), cefdinir (CDR, J01AA02), cefditoren (DIT, J01FA10), cefepime (FEP, J01FA09), cefetamet (CAT, J01CR02), cefixime (CFM, J01AA08), cefmenoxime (CMX, J01FA06), cefmetazole (CMZ, J01CF04), cefodizime (DIZ, J01CF05), cefonicid (CID, J01CR01), cefoperazone (CFP, J01CA19), cefoperazone/sulbactam (CSL, J01CE04), ceforanide (CND, J01CA09), cefotaxime (CTX, J01DF01), cefotaxime/clavulanic acid (CTC, J01CA06), cefotetan (CTT, J01CE08), cefotiam (CTF, J01CE10), cefoxitin (FOX, J01CE01), cefozopran (ZOP, J01CA03), cefpiramide (CPM, J01CA05), cefpirome (CPO, J01CE07), cefpodoxime (CPD, J01CF02), cefprozil (CPR, J01CF01), cefroxadine (CRD, J01CA07), cefsulodin (CFS, J01CA18), ceftaroline (CPT, J01CA11), ceftazidime (CAZ, J01CA14), ceftazidime/clavulanic acid (CCV, J01CF03), cefteram (CEM, J01CA10), ceftezole (CTL, J01CF06), ceftibuten (CTB, J01CE06), ceftizoxime (CZX, J01CE05), ceftobiprole medocaril (CFM1, J01CE02), ceftolozane/tazobactam (CZT, J01CA02), ceftriaxone (CRO, J01CA08), ceftriaxone/beta-lactamase inhibitor (CEB, J01CE09), cefuroxime (CXM, J01CE03), cephradine (CED, J01CG01), chloramphenicol (CHL, J01CA16), ciprofloxacin (CIP, J01CR04), clarithromycin (CLR, J01CA15), clindamycin (CLI, J01CG02), clometocillin (CLM, J01CA17), cloxacillin (CLO, J01CR03), colistin (COL, J01DB10), cycloserine (CYC, J01DC04), dalbavancin (DAL, J01DB05), daptomycin (DAP, J01DB01), delafloxacin (DFX, J01DB02), dibekacin (DKB, J01DB03), dicloxacillin (DIC, J01DC03), dirithromycin (DIR, J01DB08), doripenem (DOR, J01DB07), doxycycline (DOX, J01DB06), enoxacin (ENX, J01DB04), epicillin (EPC, J01DD17), ertapenem (ETP, J01DD15), erythromycin (ERY, J01DD16), fleroxacin (FLE, J01DE01), flucloxacillin (FLC, J01DD10), flurithromycin (FLR1, J01DD08), fosfomycin (FOS, J01DD05), framycetin (FRM, J01DC09), fusidic acid (FUS, J01DD09), garenoxacin (GRN, J01DC06), gatifloxacin (GAT, J01DD12), gemifloxacin (GEM, J01DD62), gentamicin (GEN, J01DC11), grepafloxacin (GRX, J01DD01), hetacillin (HET, J01DD51), imipenem (IPM, J01DC05), imipenem/relebactam (IMR, J01DC07), isepamicin (ISE, J01DC01), josamycin (JOS, J01DE03), kanamycin (KAN, J01DD11), lascufloxacin (LSC, J01DE02), latamoxef (LTM, J01DD13), levofloxacin (LVX, J01DC10), levonadifloxacin (LND, J01DB11), lincomycin (LIN, J01DD03), linezolid (LNZ, J01DI02), lomefloxacin (LOM, J01DD02), loracarbef (LOR, J01DD52), mecillinam (MEC, J01DD18), meropenem (MEM, J01DB12), meropenem/vaborbactam (MEV, J01DD14), metampicillin (MTM, J01DD07), meticillin (MET, J01DI01), mezlocillin (MEZ, J01DI54), micronomicin (MCR, J01DD04), midecamycin (MID, J01DD63), minocycline (MNO, J01DC02), miocamycin (MCM, J01DB09), moxifloxacin (MFX, J01DD06), nadifloxacin (NAD, J01DC08), nafcillin (NAF, J01DH05), nalidixic acid (NAL, J01DH04), neomycin (NEO, J01DH03), netilmicin (NET, J01DH51), nitrofurantoin (NIT, J01DH56), norfloxacin (, J01DH02), ofloxacin (OFX, J01DH52), oleandomycin (OLE, J01DH55), oritavancin (ORI, J01DH06), oxacillin (OXA, J01XA02), panipenem (PAN, J01XA01), pazufloxacin (PAZ, J01XC01), pefloxacin (PEF, J01FA13), penamecillin (PNM, J01FA01), pheneticillin (PHE, J01FA14), phenoxymethylpenicillin (PHN, J01FA07), piperacillin (PIP, J01FA03), piperacillin/tazobactam (TZP, J01FA11), pivampicillin (PVM, J01FA05), pivmecillinam (PME, J01FA12), plazomicin (PLZ, J01FA16), polymyxin B (PLB, J01FA02), pristinamycin (PRI, J01FA15), procaine benzylpenicillin (PRB, J01FA08), propicillin (PRP, J01FF02), prulifloxacin (PRU, J01FG01), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J04AB02), rifampicin (RIF, J01XX09), rokitamycin (ROK, J01XX08), roxithromycin (RXT, J01AA07), rufloxacin (RFL, J01XB01), sisomicin (SIS, J01XB02), sitafloxacin (SIT, J01XE01), solithromycin (SOL, J01AA12), sparfloxacin (SPX, J01EA01), spiramycin (SPI, J01XX01), streptoduocin (STR, J01BA01), streptomycin (STR1, J01GB06), sulbactam (SUL, J01GB12), sulbenicillin (SBC, J01GB13), sulfadiazine (SDI, J01GB09), sulfadiazine/trimethoprim (SLT1, D09AA01), sulfadimethoxine (SUD, J01GB03), sulfadimidine (SDM, J01GB11), sulfadimidine/trimethoprim (SLT2, J01GB04), sulfafurazole (SLF, S01AA22), sulfaisodimidine (SLF1, J01GB05), sulfalene (SLF2, J01GB07), sulfamazone (SZO, J01GB14), sulfamerazine (SLF3, J01GB10), sulfamerazine/trimethoprim (SLT3, J01GB08), sulfamethizole (SLF4, J01GA02), sulfamethoxazole (SMX, J01GA01), sulfamethoxypyridazine (SLF5, J01GB01), sulfametomidine (SLF6, J01EE01), sulfametoxydiazine (SLF7, J01MB02), sulfametrole/trimethoprim (SLT4, J01FF01), sulfamoxole (SLF8, J01XA04), sulfamoxole/trimethoprim (SLT5, J01XA05), sulfanilamide (SLF9, J01XA03), sulfaperin (SLF10, J04AB01), sulfaphenazole (SLF11, J01XX11), sulfapyridine (SLF12, J01EC02), sulfathiazole (SUT, J01ED01), sulfathiourea (SLF13, J01EB03), sultamicillin (SLT6, J01EB05), talampicillin (TAL, J01EB01), tazobactam (TAZ, J01ED02), tebipenem (TBP, J01ED09), tedizolid (TZD, J01ED07), teicoplanin (TEC, J01EB02), telavancin (TLV, J01EC01), telithromycin (TLT, J01ED05), temafloxacin (TMX, J01ED03), temocillin (TEM, J01ED04), tetracycline (TCY, J01EC03), ticarcillin (TIC, J01EB06), ticarcillin/clavulanic acid (TCC, J01ED06), tigecycline (TGC, J01ED08), tilbroquinol (TBQ, J01EB04), tobramycin (TOB, J01EB07), tosufloxacin (TFX, J01EB08), trimethoprim (TMP, J01EE02), trimethoprim/sulfamethoxazole (SXT, J01EE05), troleandomycin (TRL, J01EE07), trovafloxacin (TVA, J01EE03), vancomycin (VAN, J01EE04)","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"out <- mdro(example_isolates, guideline = \"EUCAST\") #>  (16 isolates had no test results) str(out) #>  Ord.factor w/ 3 levels \"Negative\"<\"Positive, unconfirmed\"<..: 1 1 1 1 1 1 1 1 1 1 ... table(out) #> out #>              Negative Positive, unconfirmed              Positive  #>                  1978                     0                     6   out <- mdro(example_isolates,   guideline = custom_mdro_guideline(     AMX == \"R\" ~ \"Custom MDRO 1\",     VAN == \"R\" ~ \"Custom MDRO 2\"   ) ) table(out) #> out #>      Negative Custom MDRO 1 Custom MDRO 2  #>           870           804           326   # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     mdro() %>%     table()    # no need to define `x` when used inside dplyr verbs:   example_isolates %>%     mutate(MDRO = mdro()) %>%     pull(MDRO) %>%     table() } #>  (16 isolates had no test results) #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #>  (16 isolates had no test results) #> Warning: There was 1 warning in `mutate()`. #> ℹ In argument: `MDRO = mdro()`. #> Caused by warning: #> ! in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #> . #>                         Negative       Multi-drug-resistant (MDR)  #>                             1601                              128  #> Extensively drug-resistant (XDR)          Pandrug-resistant (PDR)  #>                                0                                0  # }"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Mean AMR Distance — mean_amr_distance","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Calculates normalised mean antimicrobial resistance multiple observations, help identify similar isolates without comparing antibiograms hand.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"mean_amr_distance(x, ...)  # S3 method for sir mean_amr_distance(x, ..., combine_SI = TRUE)  # S3 method for data.frame mean_amr_distance(x, ..., combine_SI = TRUE)  amr_distance_from_row(amr_distance, row)"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"x vector class sir, mic disk, data.frame containing columns classes ... variables select (supports tidyselect language column1:column4 (.mic), can thus also antibiotic selectors combine_SI logical indicate whether values S must merged one, input consists S+vs. R (susceptible vs. resistant), defaults TRUE amr_distance outcome mean_amr_distance() row index, row number","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"mean AMR distance effectively Z-score; normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. MIC values (see .mic()) transformed log2() first; distance thus calculated (log2(x) - mean(log2(x))) / sd(log2(x)). SIR values (see .sir()) transformed using \"S\" = 1, \"\" = 2, \"R\" = 3. combine_SI TRUE (default), \"\" considered 1. data sets, mean AMR distance calculated per column, mean per row returned, see Examples. Use amr_distance_from_row() subtract distances distance one row, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"interpretation","dir":"Reference","previous_headings":"","what":"Interpretation","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Isolates distances less 0.01 difference considered similar. Differences lower 0.025 considered suspicious.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"sir <- random_sir(10) sir #> Class 'sir' #>  [1] R I S S S S S S R S mean_amr_distance(sir) #>  [1]  1.8973666 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 #>  [7] -0.4743416 -0.4743416  1.8973666 -0.4743416  mic <- random_mic(10) mic #> Class 'mic' #>  [1] 0.25   0.001  0.01   1      4      0.125  0.125  8      2      0.0625 mean_amr_distance(mic) #>  [1]  0.06516456 -1.92394777 -1.09443897  0.56457861  1.06399267 -0.18454247 #>  [7] -0.18454247  1.31369970  0.81428564 -0.43424950 # equal to the Z-score of their log2: (log2(mic) - mean(log2(mic))) / sd(log2(mic)) #>  [1]  0.06516456 -1.92394777 -1.09443897  0.56457861  1.06399267 -0.18454247 #>  [7] -0.18454247  1.31369970  0.81428564 -0.43424950  disk <- random_disk(10) disk #> Class 'disk' #>  [1] 12 30 18 33 24 27 16 46 50 32 mean_amr_distance(disk) #>  [1] -1.36485665  0.09748976 -0.87740785  0.34121416 -0.38995904 -0.14623464 #>  [7] -1.03989078  1.39735324  1.72231911  0.25997270  y <- data.frame(   id = LETTERS[1:10],   amox = random_sir(10, ab = \"amox\", mo = \"Escherichia coli\"),   cipr = random_disk(10, ab = \"cipr\", mo = \"Escherichia coli\"),   gent = random_mic(10, ab = \"gent\", mo = \"Escherichia coli\"),   tobr = random_mic(10, ab = \"tobr\", mo = \"Escherichia coli\") ) y #>    id amox cipr  gent   tobr #> 1   A    R   24     4      1 #> 2   B    S   20 <=0.5    0.5 #> 3   C    S   26     1      8 #> 4   D    S   21 <=0.5   >=16 #> 5   E    R   26     2 <=0.25 #> 6   F    S   18     4      2 #> 7   G    R   21     2      1 #> 8   H    S   29     2      8 #> 9   I    R   23     1 <=0.25 #> 10  J    R   19     2      1 mean_amr_distance(y) #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\" and #>   \"tobr\" #>  [1]  0.584051604 -0.989329211  0.140243831 -0.328508012  0.257166131 #>  [6] -0.197313482  0.138976310  0.585319125 -0.187909163 -0.002697134 y$amr_distance <- mean_amr_distance(y, where(is.mic)) #> Error in .subset(x, j): invalid subscript type 'list' y[order(y$amr_distance), ] #> Error in order(y$amr_distance): argument 1 is not a vector  if (require(\"dplyr\")) {   y %>%     mutate(       amr_distance = mean_amr_distance(y),       check_id_C = amr_distance_from_row(amr_distance, id == \"C\")     ) %>%     arrange(check_id_C) } #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\" and #>   \"tobr\" #>    id amox cipr  gent   tobr amr_distance  check_id_C #> 1   C    S   26     1      8  0.140243831 0.000000000 #> 2   G    R   21     2      1  0.138976310 0.001267521 #> 3   E    R   26     2 <=0.25  0.257166131 0.116922299 #> 4   J    R   19     2      1 -0.002697134 0.142940965 #> 5   I    R   23     1 <=0.25 -0.187909163 0.328152995 #> 6   F    S   18     4      2 -0.197313482 0.337557314 #> 7   A    R   24     4      1  0.584051604 0.443807773 #> 8   H    S   29     2      8  0.585319125 0.445075294 #> 9   D    S   21 <=0.5   >=16 -0.328508012 0.468751843 #> 10  B    S   20 <=0.5    0.5 -0.989329211 1.129573042 if (require(\"dplyr\")) {   # support for groups   example_isolates %>%     filter(mo_genus() == \"Enterococcus\" & mo_species() != \"\") %>%     select(mo, TCY, carbapenems()) %>%     group_by(mo) %>%     mutate(dist = mean_amr_distance(.)) %>%     arrange(mo, dist) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ Using column 'mo' as input for mo_species() #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Calculating mean AMR distance based on columns \"TCY\", \"IPM\" and \"MEM\" #> # A tibble: 63 × 5 #> # Groups:   mo [4] #>    mo           TCY   IPM   MEM     dist #>    <mo>         <sir> <sir> <sir>  <dbl> #>  1 B_ENTRC_AVIM S     S     NA     0     #>  2 B_ENTRC_AVIM S     S     NA     0     #>  3 B_ENTRC_CSSL NA    S     NA    NA     #>  4 B_ENTRC_FACM S     S     NA    -2.66  #>  5 B_ENTRC_FACM S     R     R     -0.423 #>  6 B_ENTRC_FACM S     R     R     -0.423 #>  7 B_ENTRC_FACM NA    R     R      0.224 #>  8 B_ENTRC_FACM NA    R     R      0.224 #>  9 B_ENTRC_FACM NA    R     R      0.224 #> 10 B_ENTRC_FACM NA    R     R      0.224 #> # … with 53 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","title":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","text":"data set containing commonly used codes microorganisms, laboratory systems WHONET. Define set_mo_source(). searched using .mo() consequently mo_* functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","text":"tibble 5 910 observations 2 variables: code Commonly used code microorganism mo ID microorganism microorganisms data set","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 5 910 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes #> # A tibble: 5,910 × 2 #>    code    mo        #>    <chr>   <mo>      #>  1 _FAM_A- B_GRAMN   #>  2 _FAM_A+ B_GRAMP   #>  3 _FAM_AC B_GRAMP   #>  4 _FAM_AE B_GRAMN   #>  5 _FAM_AN B_GRAMN   #>  6 _FAM_AO B_GRAMP   #>  7 _FAM_AP   UNKNOWN #>  8 _FAM_AS F_FUNGUS  #>  9 _FAM_AT   UNKNOWN #> 10 _FAM_AV   UNKNOWN #> # … with 5,900 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 52 142 Microorganisms — microorganisms","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"data set containing full microbial taxonomy (last updated: 11 December, 2022) five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF). data set backbone AMR package. MO codes can looked using .mo().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"","code":"microorganisms"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"tibble 52 142 observations 22 variables: mo ID microorganism used package fullname Full name, like \"Escherichia coli\". taxonomic ranks genus, species subspecies, 'pasted' text genus, species, subspecies. taxonomic ranks higher genus, name taxon. status  Status taxon, either \"accepted\" \"synonym\" kingdom, phylum, class, order, family, genus, species, subspecies Taxonomic rank microorganism rank Text taxonomic rank microorganism, \"species\" \"genus\" ref Author(s) year related scientific publication. contains first surname year latest authors, e.g. \"Wallis et al. 2006 emend. Smith Jones 2018\" becomes \"Smith et al., 2018\". field directly retrieved source specified column source. Moreover, accents removed comply CRAN allows ASCII characters, e.g. \"Váňová\" becomes \"Vanova\". lpsn Identifier ('Record number') List Prokaryotic names Standing Nomenclature (LPSN). first/highest LPSN identifier keep one identifier per row. example, Acetobacter ascendens LPSN Record number 7864 11011. first available microorganisms data set. lpsn_parent LPSN identifier parent taxon lpsn_renamed_to LPSN identifier currently valid taxon gbif Identifier ('taxonID') Global Biodiversity Information Facility (GBIF) gbif_parent GBIF identifier parent taxon gbif_renamed_to GBIF identifier currently valid taxon source Either \"GBIF\", \"LPSN\" \"manually added\" (see Source) prevalence Prevalence microorganism according Bartlett et al. (2022, doi:10.1099/mic.0.001269 ), see mo_matching_score() full explanation snomed Systematized Nomenclature Medicine (SNOMED) code microorganism, version 1 July, 2021 (see Source). Use mo_snomed() retrieve quickly, see mo_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Grimont et al. (2007). Antigenic Formulae Salmonella Serovars, 9th Edition. Collaborating Centre Reference Research Salmonella (WHOCC-SALM). Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"Please note entries based List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (see ). Since sources incorporate entries based (recent) publications International Journal Systematic Evolutionary Microbiology (IJSEM), can happen year publication sometimes later one might expect. example, Staphylococcus pettenkoferi described first time Diagnostic Microbiology Infectious Disease 2002 (doi:10.1016/s0732-8893(02)00399-1 ), 2007 publication IJSEM followed (doi:10.1099/ijs.0.64381-0 ). Consequently, AMR package returns 2007 mo_year(\"S. pettenkoferi\").","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"included-taxa","dir":"Reference","previous_headings":"","what":"Included Taxa","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"Included taxonomic data : ~36 000 (sub)species kingdoms Archaea Bacteria ~7 900 (sub)species kingdom Fungi. kingdom Fungi large taxon almost 300,000 different (sub)species, microbial (rather macroscopic, like mushrooms). , fungi fit scope package. relevant fungi covered (species Aspergillus, Candida, Cryptococcus, Histoplasma, Pneumocystis, Saccharomyces Trichophyton). ~5 100 (sub)species kingdom Protozoa ~1 400 (sub)species ~40 relevant genera kingdom Animalia (Strongyloides Taenia) ~9 800 previously accepted names included (sub)species (taxonomically renamed) complete taxonomic tree included (sub)species: kingdom subspecies identifier parent taxons year first author related scientific publication","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"manual-additions","dir":"Reference","previous_headings":"","what":"Manual additions","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"convenience, entries added manually: ~1 500 entries city-like serovars Salmonellae 11 entries Streptococcus (beta-haemolytic: groups , B, C, D, F, G, H, K unspecified; : viridans, milleri) 2 entries Staphylococcus (coagulase-negative (CoNS) coagulase-positive (CoPS)) 1 entry Blastocystis (B.  hominis), although officially exist (Noel et al. 2005, PMID 15634993) 1 entry Moraxella (M. catarrhalis), formally named Branhamella catarrhalis (Catlin, 1970) though change never accepted within field clinical microbiology 6 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast, unknown fungus, unknown anaerobic bacteria) syntax used transform original data cleansed R format, can found : https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"about-the-records-from-lpsn-see-source-","dir":"Reference","previous_headings":"","what":"About the Records from LPSN (see Source)","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"LPSN main source bacteriological taxonomy AMR package. List Prokaryotic names Standing Nomenclature (LPSN) provides comprehensive information nomenclature prokaryotes. LPSN free use service founded Jean P. Euzeby 1997 later maintained Aidan C. Parte.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 52 142 Microorganisms — microorganisms","text":"","code":"microorganisms #> # A tibble: 52,142 × 22 #>    mo               fullname      status kingdom phylum class order family genus #>    <mo>             <chr>         <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> #>  1 B_GRAMN          (unknown Gra… accep… Bacter… (unkn… \"(un… \"(un… \"(unk… \"(un… #>  2 B_GRAMP          (unknown Gra… accep… Bacter… (unkn… \"(un… \"(un… \"(unk… \"(un… #>  3 B_ANAER          (unknown ana… accep… Bacter… (unkn… \"(un… \"(un… \"(unk… \"(un… #>  4 F_FUNGUS         (unknown fun… accep… Fungi   (unkn… \"(un… \"(un… \"(unk… \"(un… #>  5   UNKNOWN        (unknown nam… accep… (unkno… (unkn… \"(un… \"(un… \"(unk… \"(un… #>  6 F_YEAST          (unknown yea… accep… Fungi   (unkn… \"(un… \"(un… \"(unk… \"(un… #>  7 B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… \"Abd… \"Abd… \"Abdi… \"\"    #>  8 B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… \"Abd… \"Abd… \"\"     \"\"    #>  9 B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… \"Abd… \"\"    \"\"     \"\"    #> 10 B_[PHL]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… \"\"    \"\"    \"\"     \"\"    #> # … with 52,132 more rows, and 13 more variables: species <chr>, #> #   subspecies <chr>, rank <chr>, ref <chr>, source <chr>, lpsn <chr>, #> #   lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>, #> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Matching Score for Microorganisms — mo_matching_score","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm used .mo() mo_* functions determine probable match taxonomic records based user input.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_matching_score(x, n)"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"x user input value(s) n full taxonomic name, exists microorganisms$fullname","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm originally described : Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 . Later, work Bartlett et al. bacterial pathogens infecting humans (2022, doi:10.1099/mic.0.001269 ) incorporated.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"Dr. Matthijs Berends, 2018","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_reset_session() #> ℹ Reset 17 previously matched input values.  as.mo(\"E. coli\") #> Class 'mo' #> [1] B_ESCHR_COLI mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #>  #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #>              Based on input \"E coli\" #> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii #>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi #>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides #>               (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae #>               cloacae (0.571), Ehrlichia canis (0.567), Enterobacter cloacae #>               dissolvens (0.565), Eikenella corrodens (0.553), Erwinia cancerogena #>               (0.553), Enterobacter cloacae (0.550), Enterococcus cecorum (0.550), #>               Ehrlichia chaffeensis (0.548), Enterobacter cancerogena (0.542), #>               Enterobacter cancerogenus (0.540), Ezakiella coagulans (0.484), #>               Effusibacillus consociatus (0.462), Enterococcus crotali (0.433), #>               Erwinia coffeiphila (0.404), Eubacterium coprostanoligenes (0.402), #>               Enterococcus columbae (0.397), Enterococcus camelliae (0.394) and #>               Eubacterium cellulosolvens (0.385) [showing first 25]  mo_matching_score(   x = \"E. coli\",   n = c(\"Escherichia coli\", \"Entamoeba coli\") ) #> [1] 0.6875000 0.1587302"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of a Microorganism — mo_property","title":"Get Properties of a Microorganism — mo_property","text":"Use functions return specific property microorganism based latest accepted taxonomy. input values evaluated internally .mo(), makes possible use microbial abbreviations, codes names input. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of a Microorganism — mo_property","text":"","code":"mo_name(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_fullname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_shortname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_subspecies(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_species(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_genus(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_family(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_order(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_class(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_phylum(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_kingdom(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_domain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_type(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_status(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_pathogenicity(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gramstain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_negative(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_positive(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_yeast(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_intrinsic_resistant(   x,   ab,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_snomed(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_ref(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_authors(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_year(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_lpsn(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gbif(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_rank(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_taxonomy(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_synonyms(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_current(x, language = get_AMR_locale(), ...)  mo_info(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_url(   x,   open = FALSE,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_property(   x,   property = \"fullname\",   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of a Microorganism — mo_property","text":"x character (vector) can coerced valid microorganism code .mo(). Can left blank auto-guessing column containing microorganism codes used data set, see Examples. language language translate text like \"growth\", defaults system language (see get_AMR_locale()) keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). ... arguments passed .mo(), 'minimum_matching_score', 'ignore_pattern', 'remove_from_input' ab (vector ) text can coerced valid antibiotic drug code .ab() open browse URL using browseURL() property one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\" \"snomed\", must \"shortname\"","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of a Microorganism — mo_property","text":"integer case mo_year() ordered factor case mo_pathogenicity() list case mo_taxonomy(), mo_synonyms(), mo_snomed() mo_info() named character case mo_url() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of a Microorganism — mo_property","text":"functions , default, keep old taxonomic properties, synonyms automatically replaced current taxonomy. Take example Enterobacter aerogenes, initially named 1960 renamed Klebsiella aerogenes 2017: mo_genus(\"Enterobacter aerogenes\") return \"Klebsiella\" (note renaming) mo_genus(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Enterobacter\" (-per-session warning name outdated) mo_ref(\"Enterobacter aerogenes\") return \"Tindall et al., 2017\" (note) mo_ref(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Hormaeche et al., 1960\" (warning) short name (mo_shortname()) returns first character genus full species, \"E. coli\", species subspecies. Exceptions abbreviations staphylococci (\"CoNS\", Coagulase-Negative Staphylococci) beta-haemolytic streptococci (\"GBS\", Group B Streptococci). Please bear mind e.g. E. coli mean Escherichia coli (kingdom Bacteria) well Entamoeba coli (kingdom Protozoa). Returning full name done using .mo() internally, giving priority bacteria human pathogens, .e. \"E. coli\" considered Escherichia coli. result, mo_fullname(mo_shortname(\"Entamoeba coli\")) returns \"Escherichia coli\". Since top-level taxonomy sometimes referred 'kingdom' sometimes 'domain', functions mo_kingdom() mo_domain() return exact results. Determination human pathogenicity (mo_pathogenicity()) strongly based Bartlett et al. (2022, doi:10.1099/mic.0.001269 ). function returns factor levels Pathogenic, Potentially pathogenic, Non-pathogenic, Unknown. Determination Gram stain (mo_gramstain()) based taxonomic kingdom phylum. Originally, Cavalier-Smith defined -called subkingdoms Negibacteria Posibacteria (2002, PMID 11837318), considered phyla Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, Tenericutes. phyla later renamed Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota (2021, PMID 34694987). Bacteria phyla considered Gram-positive AMR package, except members class Negativicutes (within phylum Bacillota) Gram-negative. bacteria considered Gram-negative. Species outside kingdom Bacteria return value NA. Functions mo_is_gram_negative() mo_is_gram_positive() always return TRUE FALSE (NA input NA MO code UNKNOWN), thus always return FALSE species outside taxonomic kingdom Bacteria. Determination yeasts (mo_is_yeast()) based taxonomic kingdom class. Budding yeasts fungi phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). True yeasts aggregated underlying order Saccharomycetales. Thus, microorganisms member taxonomic class Saccharomycetes, function return TRUE. returns FALSE otherwise (NA input NA MO code UNKNOWN). Determination intrinsic resistance (mo_is_intrinsic_resistant()) based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). mo_is_intrinsic_resistant() function can vectorised argument x (input microorganisms) ab (input antibiotics). function mo_url() return direct URL online database entry, also shows scientific reference concerned species. SNOMED codes (mo_snomed()) version 1 July, 2021. See Source microorganisms data set info. Old taxonomic names (-called 'synonyms') can retrieved mo_synonyms(), current taxonomic name can retrieved mo_current(). functions return full names. output translated possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Get Properties of a Microorganism — mo_property","text":"function uses .mo() internally, uses advanced algorithm translate arbitrary user input valid taxonomy using -called matching score. can read public algorithm MO matching score page.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of a Microorganism — mo_property","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019 Microorganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of a Microorganism — mo_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of a Microorganism — mo_property","text":"","code":"# taxonomic tree -----------------------------------------------------------  mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_phylum(\"Klebsiella pneumoniae\") #> [1] \"Pseudomonadota\" mo_class(\"Klebsiella pneumoniae\") #> [1] \"Gammaproteobacteria\" mo_order(\"Klebsiella pneumoniae\") #> [1] \"Enterobacterales\" mo_family(\"Klebsiella pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"Klebsiella pneumoniae\") #> [1] \"pneumoniae\" mo_subspecies(\"Klebsiella pneumoniae\") #> [1] \"\"   # full names and short names -----------------------------------------------  mo_name(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_fullname(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_shortname(\"Klebsiella pneumoniae\") #> [1] \"K. pneumoniae\"   # other properties ---------------------------------------------------------  mo_pathogenicity(\"Klebsiella pneumoniae\") #> [1] Pathogenic #> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\" mo_snomed(\"Klebsiella pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_rank(\"Klebsiella pneumoniae\") #> [1] \"species\" mo_url(\"Klebsiella pneumoniae\") #>                                Klebsiella pneumoniae  #> \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\"  mo_is_yeast(c(\"Candida\", \"Trichophyton\", \"Klebsiella\")) #> [1]  TRUE FALSE FALSE   # scientific reference -----------------------------------------------------  mo_ref(\"Klebsiella pneumoniae\") #> [1] \"Trevisan, 1887\" mo_authors(\"Klebsiella pneumoniae\") #> [1] \"Trevisan\" mo_year(\"Klebsiella pneumoniae\") #> [1] 1887 mo_lpsn(\"Klebsiella pneumoniae\") #> [1] \"777151\" mo_gbif(\"Klebsiella pneumoniae\") #> [1] \"3221874\" mo_synonyms(\"Klebsiella pneumoniae\") #> NULL   # abbreviations known in the field -----------------------------------------  mo_genus(\"MRSA\") #> [1] \"Staphylococcus\" mo_species(\"MRSA\") #> [1] \"aureus\" mo_shortname(\"VISA\") #> [1] \"S. aureus\" mo_gramstain(\"VISA\") #> [1] \"Gram-positive\"  mo_genus(\"EHEC\") #> [1] \"Escherichia\" mo_species(\"EHEC\") #> [1] \"coli\"   # known subspecies ---------------------------------------------------------  mo_fullname(\"K. pneu rh\") #> [1] \"Klebsiella pneumoniae rhinoscleromatis\" mo_shortname(\"K. pneu rh\") #> [1] \"K. pneumoniae\"  # \\donttest{ # Becker classification, see ?as.mo ----------------------------------------  mo_fullname(\"Staph epidermidis\") #> [1] \"Staphylococcus epidermidis\" mo_fullname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"Coagulase-negative Staphylococcus (CoNS)\" mo_shortname(\"Staph epidermidis\") #> [1] \"S. epidermidis\" mo_shortname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"CoNS\"   # Lancefield classification, see ?as.mo ------------------------------------  mo_fullname(\"Strep agalactiae\") #> [1] \"Streptococcus agalactiae\" mo_fullname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"Streptococcus Group B\" mo_shortname(\"Strep agalactiae\") #> [1] \"S. agalactiae\" mo_shortname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"GBS\"   # language support  --------------------------------------------------------  mo_gramstain(\"Klebsiella pneumoniae\", language = \"de\") # German #> [1] \"Gramnegativ\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"nl\") # Dutch #> [1] \"Gram-negatief\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"es\") # Spanish #> [1] \"Gram negativo\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"el\") # Greek #> [1] \"Αρνητικό κατά Gram\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"uk\") # Ukrainian #> [1] \"Грамнегативні\"  # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_kingdom(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, no effect #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, translated #> [1] \"细菌\"  mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"de\") #> [1] \"Streptococcus Gruppe A\" mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"uk\") #> [1] \"Streptococcus Група A\"   # other --------------------------------------------------------------------  # gram stains and intrinsic resistance can be used as a filter in dplyr verbs if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_gram_positive()) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 18 × 2 #>    `mo_genus()`        n #>    <chr>           <int> #>  1 Staphylococcus    840 #>  2 Streptococcus     275 #>  3 Enterococcus       83 #>  4 Corynebacterium    17 #>  5 Micrococcus         6 #>  6 Gemella             3 #>  7 Aerococcus          2 #>  8 Cutibacterium       1 #>  9 Dermabacter         1 #> 10 Fusibacter          1 #> 11 Globicatella        1 #> 12 Granulicatella      1 #> 13 Lactobacillus       1 #> 14 Leuconostoc         1 #> 15 Listeria            1 #> 16 Paenibacillus       1 #> 17 Rothia              1 #> 18 Schaalia            1 if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_intrinsic_resistant(ab = \"vanco\")) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 20 × 2 #>    `mo_genus()`         n #>    <chr>            <int> #>  1 Escherichia        467 #>  2 Klebsiella          77 #>  3 Proteus             39 #>  4 Pseudomonas         30 #>  5 Serratia            25 #>  6 Enterobacter        23 #>  7 Citrobacter         11 #>  8 Haemophilus          8 #>  9 Acinetobacter        6 #> 10 Morganella           6 #> 11 Pantoea              4 #> 12 Salmonella           3 #> 13 Neisseria            2 #> 14 Stenotrophomonas     2 #> 15 Campylobacter        1 #> 16 Enterococcus         1 #> 17 Hafnia               1 #> 18 Lactobacillus        1 #> 19 Leuconostoc          1 #> 20 Pseudescherichia     1  # get a list with the complete taxonomy (from kingdom to subspecies) mo_taxonomy(\"Klebsiella pneumoniae\") #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>   # get a list with the taxonomy, the authors, Gram-stain, # SNOMED codes, and URL to the online database mo_info(\"Klebsiella pneumoniae\") #> $mo #> [1] \"B_KLBSL_PNMN\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $url #> [1] \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\" #>  #> $ref #> [1] \"Trevisan, 1887\" #>  #> $snomed #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  # }"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":null,"dir":"Reference","previous_headings":"","what":"User-Defined Reference Data Set for Microorganisms — mo_source","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"functions can used predefine reference used .mo() consequently mo_* functions (mo_genus() mo_gramstain()). fastest way organisation (analysis) specific codes picked translated package, since bother setting .","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"","code":"set_mo_source(   path,   destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\") )  get_mo_source(destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\"))"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"path location reference file, can text file (comma-, tab- pipe-separated) Excel file (see Details). Can also \"\", NULL FALSE delete reference file. destination destination compressed data file, default user's home directory.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"reference file can text file separated commas (CSV) tabs pipes, Excel file (either 'xls' 'xlsx' format) R object file (extension '.rds'). use Excel file, need readxl package installed. set_mo_source() check file validity: must data.frame, must column named \"mo\" contains values microorganisms$mo microorganisms$fullname must reference column defined values. tests pass, set_mo_source() read file R ask export \"~/mo_source.rds\". CRAN policy disallows packages write file system, although 'exceptions may allowed interactive sessions package obtains confirmation user'. reason, function works interactive sessions user can specifically confirm allow file created. destination file can set destination argument defaults user's home directory. can also set option AMR_mo_source, e.g. options(AMR_mo_source = \"/location/file.rds\"). created compressed data file \"mo_source.rds\" used default MO determination (function .mo() consequently mo_* functions like mo_genus() mo_gramstain()). location timestamp original file saved attribute compressed data file. function get_mo_source() return data set reading \"mo_source.rds\" readRDS(). original file changed (checking location timestamp original file), call set_mo_source() update data file automatically used interactive session. Reading Excel file (.xlsx) one row size 8-9 kB. compressed file created set_mo_source() size 0.1 kB can read get_mo_source() couple microseconds (millionths second).","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"how-to-setup","dir":"Reference","previous_headings":"","what":"How to Setup","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"Imagine data sheet Excel file. first column contains organisation specific codes, second column contains valid taxonomic names:   save \"home//ourcodes.xlsx\". Now set source:   now created file \"~/mo_source.rds\" contents Excel file. first column foreign values 'mo' column kept creating RDS file. now can use functions:   edit Excel file , say, adding row 4 like :   ...new usage MO function package update data file:   delete reference data file, just use \"\", NULL FALSE input set_mo_source():   original file (previous case Excel file) moved deleted, mo_source.rds file removed upon next use .mo() mo_* function.","code":"|         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 |                    |                       | set_mo_source(\"home/me/ourcodes.xlsx\") #> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>       \"Organisation XYZ\" and \"mo\" as.mo(\"lab_mo_ecoli\") #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_mo_kpneumoniae\") #> [1] \"Klebsiella\"  # other input values still work too as.mo(c(\"Escherichia coli\", \"E. coli\", \"lab_mo_ecoli\")) #> NOTE: Translation to one microorganism was guessed with uncertainty. #>       Use mo_uncertainties() to review it. #> Class 'mo' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI |         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 | lab_Staph_aureus   | Staphylococcus aureus | 5 |                    |                       | as.mo(\"lab_mo_ecoli\") #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>        \"Organisation XYZ\" and \"mo\" #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_Staph_aureus\") #> [1] \"Staphylococcus\" set_mo_source(NULL) #> Removed mo_source file '/Users/me/mo_source.rds'"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Principal Component Analysis (for AMR) — pca","title":"Principal Component Analysis (for AMR) — pca","text":"Performs principal component analysis (PCA) based data set automatic determination afterwards plotting groups labels, automatic filtering suitable (.e. non-empty numeric) variables.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"pca(   x,   ...,   retx = TRUE,   center = TRUE,   scale. = TRUE,   tol = NULL,   rank. = NULL )"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Principal Component Analysis (for AMR) — pca","text":"x data.frame containing numeric columns ... columns x selected PCA, can unquoted since supports quasiquotation. retx logical value indicating whether rotated variables     returned. center logical value indicating whether variables     shifted zero centered. Alternately, vector     length equal number columns x can supplied.     value passed scale. scale. logical value indicating whether variables     scaled unit variance analysis takes     place.  default FALSE consistency S,     general scaling advisable.  Alternatively, vector length     equal number columns x can supplied.      value passed scale. tol value indicating magnitude components     omitted. (Components omitted     standard deviations less equal tol times     standard deviation first component.)  default null     setting, components omitted (unless rank. specified     less min(dim(x)).).  settings tol     tol = 0 tol = sqrt(.Machine$double.eps),     omit essentially constant components. rank. optionally, number specifying maximal rank, .e.,     maximal number principal components used.  Can set     alternative addition tol, useful notably     desired rank considerably smaller dimensions matrix.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Principal Component Analysis (for AMR) — pca","text":"object classes pca prcomp","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Principal Component Analysis (for AMR) — pca","text":"pca() function takes data.frame input performs actual PCA R function prcomp(). result pca() function prcomp object, additional attribute non_numeric_cols vector column names columns contain numeric values. probably groups labels, used ggplot_pca().","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    pca_result   summary(pca_result)    # old base R plotting method:   biplot(pca_result)   # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", \"TMP\" #>   and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plotting for Classes sir, mic and disk — plot","title":"Plotting for Classes sir, mic and disk — plot","text":"Functions plot classes sir, mic disk, support base R ggplot2.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"# S3 method for mic plot(   x,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   main = deparse(substitute(x)),   ylab = \"Frequency\",   xlab = \"Minimum Inhibitory Concentration (mg/L)\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic autoplot(   object,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   title = deparse(substitute(object)),   ylab = \"Frequency\",   xlab = \"Minimum Inhibitory Concentration (mg/L)\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic fortify(object, ...)  # S3 method for disk plot(   x,   main = deparse(substitute(x)),   ylab = \"Frequency\",   xlab = \"Disk diffusion diameter (mm)\",   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk autoplot(   object,   mo = NULL,   ab = NULL,   title = deparse(substitute(object)),   ylab = \"Frequency\",   xlab = \"Disk diffusion diameter (mm)\",   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk fortify(object, ...)  # S3 method for sir plot(   x,   ylab = \"Percentage\",   xlab = \"Antimicrobial Interpretation\",   main = deparse(substitute(x)),   language = get_AMR_locale(),   ... )  # S3 method for sir autoplot(   object,   title = deparse(substitute(object)),   xlab = \"Antimicrobial Interpretation\",   ylab = \"Frequency\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   ... )  # S3 method for sir fortify(object, ...)"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plotting for Classes sir, mic and disk — plot","text":"x, object values created .mic(), .disk() .sir() (random_* variants, random_mic()) mo (vector ) text can coerced valid microorganism code .mo() ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline interpretation guideline use, defaults latest included EUCAST guideline, see Details main, title title plot xlab, ylab axis title colours_SIR colours use filling bars, must vector three values (order S, R). default colours colour-blind friendly. language language used translate 'Susceptible', 'Increased exposure'/'Intermediate' 'Resistant', defaults system language (see get_AMR_locale()) can overwritten setting option AMR_locale, e.g. options(AMR_locale = \"de\"), see translate. Use language = NULL language = \"\" prevent translation. expand logical indicate whether range x axis expanded lowest highest value. MIC values, intermediate values factors 2 starting highest MIC value. disk diameters, whole diameter range filled. ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plotting for Classes sir, mic and disk — plot","text":"autoplot() functions return ggplot model extendible ggplot2 function. fortify() functions return data.frame extension usage ggplot2::ggplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plotting for Classes sir, mic and disk — plot","text":"interpretation \"\" named \"Increased exposure\" EUCAST guidelines since 2019, named \"Intermediate\" cases. interpreting MIC values well disk diffusion diameters, supported guidelines used input guideline argument : \"EUCAST 2022\", \"EUCAST 2021\", \"EUCAST 2020\", \"EUCAST 2019\", \"EUCAST 2018\", \"EUCAST 2017\", \"EUCAST 2016\", \"EUCAST 2015\", \"EUCAST 2014\", \"EUCAST 2013\", \"CLSI 2022\", \"CLSI 2021\", \"CLSI 2020\", \"CLSI 2019\", \"CLSI 2018\", \"CLSI 2017\", \"CLSI 2016\", \"CLSI 2015\", \"CLSI 2014\" \"CLSI 2013\". Simply using \"CLSI\" \"EUCAST\" input automatically select latest version guideline.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"some_mic_values <- random_mic(size = 100) some_disk_values <- random_disk(size = 100, mo = \"Escherichia coli\", ab = \"cipro\") some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))  plot(some_mic_values)  plot(some_disk_values)  plot(some_sir_values)   # when providing the microorganism and antibiotic, colours will show interpretations: plot(some_mic_values, mo = \"S. aureus\", ab = \"ampicillin\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\", language = \"uk\")   # \\donttest{ if (require(\"ggplot2\")) {   autoplot(some_mic_values) }  if (require(\"ggplot2\")) {   autoplot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(some_sir_values) }  # }"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Antimicrobial Resistance — proportion","title":"Calculate Antimicrobial Resistance — proportion","text":"functions can used calculate (co-)resistance susceptibility microbial isolates (.e. percentage S, SI, , IR R). functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. resistance() used calculate resistance, susceptibility() used calculate susceptibility.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"resistance(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  susceptibility(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  sir_confidence_interval(   ...,   ab_result = \"R\",   minimum = 30,   as_percent = FALSE,   only_all_tested = FALSE,   confidence_level = 0.95,   side = \"both\" )  proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )  sir_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Antimicrobial Resistance — proportion","text":"M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Antimicrobial Resistance — proportion","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. Use multiple columns calculate (lack ) co-resistance: probability one two drugs resistant susceptible result. See Examples. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. as_percent logical indicate whether output must returned hundred fold % sign (character). value 0.123456 returned \"12.3%\". only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy ab_result antibiotic results test , must one values \"S\", \"\", \"R\" confidence_level confidence level returned confidence interval. calculation, number S SI isolates, R isolates compared total number available isolates R, S, using binom.test(), .e., Clopper-Pearson method. side side confidence interval return. Defaults \"\" length 2 vector, can also (abbreviated ) \"min\"/\"left\"/\"lower\"/\"less\" \"max\"/\"right\"/\"higher\"/\"greater\". data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text, defaults system language (see get_AMR_locale()) can also set option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant), defaults TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Antimicrobial Resistance — proportion","text":"double , as_percent = TRUE, character.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Antimicrobial Resistance — proportion","text":"function resistance() equal function proportion_R(). function susceptibility() equal function proportion_SI(). Use sir_confidence_interval() calculate confidence interval, relies binom.test(), .e., Clopper-Pearson method. function returns vector length 2 default antimicrobial resistance. Change side argument \"left\"/\"min\" \"right\"/\"max\" return single value, change ab_result argument e.g. c(\"S\", \"\") test antimicrobial susceptibility, see Examples. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. functions meant count isolates, calculate proportion resistance/susceptibility. Use count() functions count isolates. function susceptibility() essentially equal count_susceptible() / count_all(). Low counts can influence outcome - proportion functions may camouflage , since return proportion (albeit dependent minimum argument). function proportion_df() takes variable data sir class (created .sir()) calculates proportions S, , R. also supports grouped variables. function sir_df() works exactly like proportion_df(), adds number isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Calculate Antimicrobial Resistance — proportion","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Calculate Antimicrobial Resistance — proportion","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>, #> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, #> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, #> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, #> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, #> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, #> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>   # base R ------------------------------------------------------------ # determines %R resistance(example_isolates$AMX) #> [1] 0.5955556 sir_confidence_interval(example_isolates$AMX) #> [1] 0.5688204 0.6218738 sir_confidence_interval(example_isolates$AMX,   confidence_level = 0.975 ) #> [1] 0.5650148 0.6255670  # determines %S+I: susceptibility(example_isolates$AMX) #> [1] 0.4044444 sir_confidence_interval(example_isolates$AMX,   ab_result = c(\"S\", \"I\") ) #> [1] 0.3781262 0.4311796  # be more specific proportion_S(example_isolates$AMX) #> [1] 0.4022222 proportion_SI(example_isolates$AMX) #> [1] 0.4044444 proportion_I(example_isolates$AMX) #> [1] 0.002222222 proportion_IR(example_isolates$AMX) #> [1] 0.5977778 proportion_R(example_isolates$AMX) #> [1] 0.5955556  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       r = resistance(CIP),       n = n_sir(CIP)     ) # n_sir works like n_distinct in dplyr, see ?n_sir } #> # A tibble: 3 × 3 #>   ward           r     n #>   <chr>      <dbl> <int> #> 1 Clinical   0.147   869 #> 2 ICU        0.190   447 #> 3 Outpatient 0.161    93 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       cipro_R = resistance(CIP),       ci_min = sir_confidence_interval(CIP, side = \"min\"),       ci_max = sir_confidence_interval(CIP, side = \"max\"),     ) } #> # A tibble: 3 × 4 #>   ward       cipro_R ci_min ci_max #>   <chr>        <dbl>  <dbl>  <dbl> #> 1 Clinical     0.147 0.124   0.173 #> 2 ICU          0.190 0.155   0.230 #> 3 Outpatient   0.161 0.0932  0.252 if (require(\"dplyr\")) {   # scoped dplyr verbs with antibiotic selectors   # (you could also use across() of course)   example_isolates %>%     group_by(ward) %>%     summarise_at(       c(aminoglycosides(), carbapenems()),       resistance     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 7 #>   ward         GEN   TOB   AMK   KAN    IPM    MEM #>   <chr>      <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl> #> 1 Clinical   0.229 0.315 0.626     1 0.0498 0.0458 #> 2 ICU        0.290 0.400 0.662     1 0.0862 0.0894 #> 3 Outpatient 0.2   0.368 0.605    NA 0.0541 0.0541 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = resistance(CIP, as_percent = TRUE),       SI = susceptibility(CIP, as_percent = TRUE),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Calculate co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy:   example_isolates %>% susceptibility(AMC) # %SI = 76.3%   example_isolates %>% count_all(AMC) #   n = 1879    example_isolates %>% susceptibility(GEN) # %SI = 75.4%   example_isolates %>% count_all(GEN) #   n = 1855    example_isolates %>% susceptibility(AMC, GEN) # %SI = 94.1%   example_isolates %>% count_all(AMC, GEN) #   n = 1939     # See Details on how `only_all_tested` works. Example:   example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN),       denominator = count_all(AMC, GEN),       proportion = susceptibility(AMC, GEN)     )    example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE),       denominator = count_all(AMC, GEN, only_all_tested = TRUE),       proportion = susceptibility(AMC, GEN, only_all_tested = TRUE)     )     example_isolates %>%     group_by(ward) %>%     summarise(       cipro_p = susceptibility(CIP, as_percent = TRUE),       cipro_n = count_all(CIP),       genta_p = susceptibility(GEN, as_percent = TRUE),       genta_n = count_all(GEN),       combination_p = susceptibility(CIP, GEN, as_percent = TRUE),       combination_n = count_all(CIP, GEN)     )    # Get proportions S/I/R immediately of all sir columns   example_isolates %>%     select(AMX, CIP) %>%     proportion_df(translate = FALSE)    # It also supports grouping variables   # (use sir_df to also include the count)   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     sir_df(translate = FALSE) } #> # A tibble: 12 × 7 #>    ward       antibiotic interpretation value ci_min ci_max isolates #>  * <chr>      <chr>      <ord>          <dbl>  <dbl>  <dbl>    <int> #>  1 Clinical   AMX        SI             0.423 0.389   0.457      357 #>  2 Clinical   AMX        R              0.577 0.543   0.611      487 #>  3 Clinical   CIP        SI             0.853 0.827   0.876      741 #>  4 Clinical   CIP        R              0.147 0.124   0.173      128 #>  5 ICU        AMX        SI             0.369 0.323   0.417      158 #>  6 ICU        AMX        R              0.631 0.583   0.677      270 #>  7 ICU        CIP        SI             0.810 0.770   0.845      362 #>  8 ICU        CIP        R              0.190 0.155   0.230       85 #>  9 Outpatient AMX        SI             0.397 0.288   0.515       31 #> 10 Outpatient AMX        R              0.603 0.485   0.712       47 #> 11 Outpatient CIP        SI             0.839 0.748   0.907       78 #> 12 Outpatient CIP        R              0.161 0.0932  0.252       15 # }"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":null,"dir":"Reference","previous_headings":"","what":"Random MIC Values/Disk Zones/SIR Generation — random","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"functions can used generating random MIC values disk diffusion diameters, AMR data analysis practice. providing microorganism antimicrobial drug, generated results reflect reality much possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(size = NULL, mo = NULL, ab = NULL, ...)  random_disk(size = NULL, mo = NULL, ab = NULL, ...)  random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"size desired size returned vector. used data.frame call dplyr verb, get current (group) size left blank. mo character can coerced valid microorganism code .mo() ab character can coerced valid antimicrobial drug code .ab() ... ignored, place allow future extensions prob_SIR vector length 3: probabilities \"S\" (1st value), \"\" (2nd value) \"R\" (3rd value)","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"class mic random_mic() (see .mic()) class disk random_disk() (see .disk())","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"base R function sample() used generating values. Generated values based EUCAST 2022 guideline implemented clinical_breakpoints data set. create specific generated values per bug drug, set mo /ab argument.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(25) #> Class 'mic' #>  [1] <=0.001 0.01    0.5     0.005   16      0.01    0.125   2       0.005   #> [10] 1       8       0.5     0.01    64      128     256     128     0.5     #> [19] 2       256     0.005   0.125   1       <=0.001 2       random_disk(25) #> Class 'disk' #>  [1] 49 14  6 19 16 27 29 24 37 47 22 42 45 48 38 50 50 44 29 42  9 34 48 42 47 random_sir(25) #> Class 'sir' #>  [1] R S S R I S I R R R S I R S R I S S R R S I I S R  # \\donttest{ # make the random generation more realistic by setting a bug and/or drug: random_mic(25, \"Klebsiella pneumoniae\") # range 0.0625-64 #> Class 'mic' #>  [1] 0.001  8      0.001  0.025  0.5    16     0.5    0.005  1      16     #> [11] 0.0625 16     0.025  0.5    0.5    64     0.125  0.25   0.001  0.002  #> [21] 0.025  32     2      2      0.25   random_mic(25, \"Klebsiella pneumoniae\", \"meropenem\") # range 0.0625-16 #> Class 'mic' #>  [1] 2     >=32  >=32  8     16    4     1     <=0.5 >=32  1     1     8     #> [13] 8     2     <=0.5 8     8     16    4     16    2     >=32  16    <=0.5 #> [25] <=0.5 random_mic(25, \"Streptococcus pneumoniae\", \"meropenem\") # range 0.0625-4 #> Class 'mic' #>  [1] 0.5    4      0.125  2      1      0.0625 0.0625 8      0.5    0.5    #> [11] 0.0625 0.125  0.025  4      8      1      4      0.0625 0.0625 4      #> [21] 0.025  0.025  2      8      4       random_disk(25, \"Klebsiella pneumoniae\") # range 8-50 #> Class 'disk' #>  [1] 48 32 50 49 47 30 38 18 49 32 25 47 11 48 17 38 12 42 50 43 45 46 43 48 49 random_disk(25, \"Klebsiella pneumoniae\", \"ampicillin\") # range 11-17 #> Class 'disk' #>  [1] 17 15 13 16 12 17 17 14 15 12 12 14 17 13 17 11 12 15 14 11 17 17 15 15 13 random_disk(25, \"Streptococcus pneumoniae\", \"ampicillin\") # range 12-27 #> Class 'disk' #>  [1] 26 20 22 24 25 19 19 20 21 21 16 19 24 22 23 17 18 25 26 22 17 15 19 19 15 # }"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":null,"dir":"Reference","previous_headings":"","what":"Predict Antimicrobial Resistance — resistance_predict","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Create prediction model predict antimicrobial resistance next years statistical solid ground. Standard errors (SE) returned columns se_min se_max. See Examples real live example.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"resistance_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  sir_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  # S3 method for resistance_predict plot(x, main = paste(\"Resistance Prediction of\", x_name), ...)  ggplot_sir_predict(   x,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )  # S3 method for resistance_predict autoplot(   object,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predict Antimicrobial Resistance — resistance_predict","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_ab column name x containing antimicrobial interpretations (\"R\", \"\" \"S\") col_date column name date, used calculate years column consist years already, defaults first column date class year_min lowest year use prediction model, dafaults lowest year col_date year_max highest year use prediction model, defaults 10 years today year_every unit sequence lowest year found data year_max minimum minimal amount available isolates per year include. Years containing less observations estimated model. model statistical model choice. generalised linear regression model binomial distribution (.e. using glm(..., family = binomial), assuming period zero resistance followed period increasing resistance leading slowly resistance. See Details valid options. I_as_S logical indicate whether values \"\" treated \"S\" (otherwise treated \"R\"). default, TRUE, follows redefinition EUCAST interpretation (increased exposure) 2019, see section Interpretation S, R . preserve_measurements logical indicate whether predictions years actually available data overwritten original data. standard errors years NA. info logical indicate whether textual analysis printed name summary() statistical model. ... arguments passed functions main title plot ribbon logical indicate whether ribbon shown (default) error bars object model data plotted","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predict Antimicrobial Resistance — resistance_predict","text":"data.frame extra class resistance_predict columns: year value, estimated preserve_measurements = FALSE, combination observed estimated otherwise se_min, lower bound standard error minimum 0 (standard error never go 0%) se_max upper bound standard error maximum 1 (standard error never go 100%) observations, total number available observations year, .e. \\(S + + R\\) observed, original observed resistant percentages estimated, estimated resistant percentages, calculated model Furthermore, model available attribute: attributes(x)$model, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Valid options statistical model (argument model) : \"binomial\" \"binom\" \"logit\": generalised linear regression model binomial distribution \"loglin\" \"poisson\": generalised log-linear regression model poisson distribution \"lin\" \"linear\": linear regression model","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Predict Antimicrobial Resistance — resistance_predict","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"x <- resistance_predict(example_isolates,   col_ab = \"AMX\",   year_min = 2010,   model = \"binomial\" ) plot(x)  # \\donttest{ if (require(\"ggplot2\")) {   ggplot_sir_predict(x) }   # using dplyr: if (require(\"dplyr\")) {   x <- example_isolates %>%     filter_first_isolate() %>%     filter(mo_genus(mo) == \"Staphylococcus\") %>%     resistance_predict(\"PEN\", model = \"binomial\")   print(plot(x))    # get the model from the object   mymodel <- attributes(x)$model   summary(mymodel) }  #> NULL #>  #> Call: #> glm(formula = df_matrix ~ year, family = binomial) #>  #> Deviance Residuals:  #>     Min       1Q   Median       3Q      Max   #> -1.4150  -0.1855   0.0000   0.4096   0.9277   #>  #> Coefficients: #>             Estimate Std. Error z value Pr(>|z|) #> (Intercept) 47.02915   72.98739   0.644    0.519 #> year        -0.02280    0.03637  -0.627    0.531 #>  #> (Dispersion parameter for binomial family taken to be 1) #>  #>     Null deviance: 5.9620  on 11  degrees of freedom #> Residual deviance: 5.5701  on 10  degrees of freedom #> AIC: 50.533 #>  #> Number of Fisher Scoring iterations: 4 #>   # create nice plots with ggplot2 yourself if (require(\"dplyr\") && require(\"ggplot2\")) {   data <- example_isolates %>%     filter(mo == as.mo(\"E. coli\")) %>%     resistance_predict(       col_ab = \"AMX\",       col_date = \"date\",       model = \"binomial\",       info = FALSE,       minimum = 15     )   head(data)   autoplot(data) }  # }"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":null,"dir":"Reference","previous_headings":"","what":"Skewness of the Sample — skewness","title":"Skewness of the Sample — skewness","text":"Skewness measure asymmetry probability distribution real-valued random variable mean. negative ('left-skewed'): left tail longer; mass distribution concentrated right histogram. positive ('right-skewed'): right tail longer; mass distribution concentrated left histogram. normal distribution skewness 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Skewness of the Sample — skewness","text":"","code":"skewness(x, na.rm = FALSE)  # S3 method for default skewness(x, na.rm = FALSE)  # S3 method for matrix skewness(x, na.rm = FALSE)  # S3 method for data.frame skewness(x, na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Skewness of the Sample — skewness","text":"x vector values, matrix data.frame na.rm logical value indicating whether NA values stripped computation proceeds","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Skewness of the Sample — skewness","text":"","code":"skewness(runif(1000)) #> [1] 0.001867225"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate Strings from the AMR Package — translate","title":"Translate Strings from the AMR Package — translate","text":"language-dependent output AMR functions, mo_name(), mo_gramstain(), mo_type() ab_name().","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate Strings from the AMR Package — translate","text":"","code":"get_AMR_locale()  set_AMR_locale(language)  reset_AMR_locale()  translate_AMR(x, language = get_AMR_locale())"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate Strings from the AMR Package — translate","text":"language language choose. Use one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) Ukrainian (uk). x text translate","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate Strings from the AMR Package — translate","text":"currently 20 supported languages English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) Ukrainian (uk). languages translations available antimicrobial drugs colloquial microorganism names. permanently silence -per-session language note non-English operating system, can set option AMR_locale .Rprofile file like :   save file. Please read adding updating language Wiki.","code":"# Open .Rprofile file utils::file.edit(\"~/.Rprofile\")  # Then add e.g. Italian support to that file using: options(AMR_locale = \"Italian\")"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"changing-the-default-language","dir":"Reference","previous_headings":"","what":"Changing the Default Language","title":"Translate Strings from the AMR Package — translate","text":"system language used default (returned Sys.getenv(\"LANG\") , LANG set, Sys.getlocale(\"LC_COLLATE\")), language supported. language used can overwritten two ways checked order: Setting option AMR_locale, either using e.g. set_AMR_locale(\"German\") running e.g. options(AMR_locale = \"German\"). Note setting R option works session. Save command options(AMR_locale = \"(language)\") .Rprofile file apply every session. Run utils::file.edit(\"~/.Rprofile\") edit .Rprofile file. Setting system variable LANGUAGE LANG, e.g. adding LANGUAGE=\"de_DE.utf8\" .Renviron file home directory. Thus, option AMR_locale set, system variables LANGUAGE LANG ignored.","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate Strings from the AMR Package — translate","text":"","code":"# Current settings (based on system language) ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacin\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Coagulase-negative Staphylococcus (CoNS)\"  # setting another language set_AMR_locale(\"Spanish\") #> ℹ Using Spanish (Español) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacina\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Staphylococcus coagulasa negativo (SCN)\"  # setting yet another language set_AMR_locale(\"Greek\") #> ℹ Using Greek (Ελληνικά) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Σιπροφλοξασίνη\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)\"  # setting yet another language set_AMR_locale(\"Ukrainian\") #> ℹ Using Ukrainian (Українська) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ципрофлоксацин\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Коагулазонегативний стафілокок (КНС)\"  # set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1: set_AMR_locale(\"Deutsch\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"German\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"de\") #> ℹ Using German (Deutsch) for the AMR package for this session. ab_name(\"amox/clav\") #> Warning: More than one result was found for item 1: amoxicillin and clavulansäure #> [1] \"Amoxicillin/Clavulansäure\"  # reset to system default reset_AMR_locale() #> ℹ Using the English language (English) for the AMR package for this #>   session. ab_name(\"amox/clav\") #> [1] \"Amoxicillin/clavulanic acid\""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"amr-1829137","dir":"Changelog","previous_headings":"","what":"AMR 1.8.2.9137","title":"AMR 1.8.2.9137","text":"(beta version eventually become v2.0! ’re happy reach new major milestone soon!) new major release AMR package, great new additions also breaking changes current users. listed . TL;DR functions arguments ‘rsi’ replaced ‘sir’, interpretation MIC values (now .sir() instead .rsi()) - old functions still work now Many new interesting functions, antibiogram() (generating traditional/combined/syndromic/WISCA antibiograms), sir_confidence_interval() mean_amr_distance(), add_custom_microorganisms() add custom microorganisms package Clinical breakpoints added EUCAST 2022 CLSI 2022 Microbiological taxonomy (microorganisms data set) updated 2022 now based LPSN GBIF Much increased algorithms translate user input valid taxonomy, e.g. using recent scientific work per-species human pathogenicity 20 new antibiotics added updated DDDs ATC codes Extended support antiviral agents (antivirals data set), many new functions Now available 20 languages Many small bug fixes","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/news/index.html","id":"sir-vs-rsi-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"SIR vs. RSI","title":"AMR 1.8.2.9137","text":"milestone version, replaced mentions RSI SIR, comply actually commonly used field clinical microbiology comes tri-form regarding AMR. existing functions .rsi(), rsi_df() ggplot_rsi() still work, replacements .sir(), sir_df(), ggplot_sir() now current functions AMR data analysis. warning thrown session remind users . data set rsi_translation now called clinical_breakpoints better reflect content. ‘RSI functions’ removed future version, late 2023 / early 2024.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"new-antibiogram-function-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"New antibiogram function","title":"AMR 1.8.2.9137","text":"new antibiogram() function, users can now generate traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). , follow logic previously described work Klinker et al. (2021, DOI 10.1177/20499361211011373) Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2). help page antibiogram() extensively elaborates use cases, antibiogram() also supports printing R Markdown Quarto, support 20 languages. Furthermore, different plotting methods implemented allow graphical visualisations well.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"interpretation-of-mic-and-disk-diffusion-values-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Interpretation of MIC and disk diffusion values","title":"AMR 1.8.2.9137","text":"clinical breakpoints intrinsic resistance EUCAST 2022 CLSI 2022 added .sir(). EUCAST 2022 (v12.0) now new default guideline MIC disks diffusion interpretations, eucast_rules() apply EUCAST Expert Rules. default guideline (EUCAST) can now changed new AMR_guideline option, : options(AMR_guideline = \"CLSI 2020\"). new arguments include_PKPD (default: TRUE) include_screening (default: FALSE), users can now specify whether breakpoints screening PK/PD table included interpreting MICs disks diffusion values. options can set globally, can read new manual. Interpretation guidelines older 10 years removed, oldest now included guidelines EUCAST CLSI 2013.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"supported-languages-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Supported languages","title":"AMR 1.8.2.9137","text":"added support following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish Ukrainian. antibiotic names now available languages, AMR package automatically determine supported language based user’s system language. grateful valuable input colleagues countries. AMR package now available 20 languages total, according download stats used almost countries world!","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"microbiological-taxonomy-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Microbiological taxonomy","title":"AMR 1.8.2.9137","text":"microorganisms data set longer relies Catalogue Life, List Prokaryotic names Standing Nomenclature (LPSN) supplemented ‘backbone taxonomy’ Global Biodiversity Information Facility (GBIF). structure data set changed include separate LPSN GBIF identifiers. Almost previous MO codes retained. contains 1,400 taxonomic names 2022. previously relied experience categorise species pathogenic groups, happy encounter recent work Bartlett et al. (2022, DOI 10.1099/mic.0.001269) extensively studied medical-scientific literature categorise bacterial species groups. See mo_matching_score() work incorporated prevalence column microorganisms data set. Using results, .mo() mo_*() functions now much better capable converting user input valid taxonomic records. new function add_custom_microorganisms() allows users add custom microorganisms AMR package. also made following changes regarding included taxonomy microorganisms functions: Updated full microbiological taxonomy according latest daily LPSN data set (December 2022) latest yearly GBIF taxonomy backbone (November 2022) Support 1,516 city-like serovars Salmonella, Salmonella Goldcoast. Formally, serovars belonging S. enterica species, reported name genus city. reason, serovars subspecies column microorganisms data set “enterica” species column, full name contain species name (enterica). new argument keep_synonyms allows correct updated taxonomy, favour now deleted argument allow_uncertain increased tremendously speed returns generally consequent results Sequential coercion now extremely fast results stored package environment, although coercion unknown values must run per session. Previous results can reset/removed new mo_reset_session() function. Support microorganism codes ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) MO matching score algorithm (mo_matching_score()) now counts deletions substitutions 2 instead 1, impacts outcome .mo() mo_*() function CRAN allows packages around 5 MB maximum, packages exempted package one Chromista relevant comes antimicrobial resistance, thus lacking primary scope package Chromista almost never clinically relevant, thus lacking secondary scope package microorganisms.old data set removed, previously accepted names now included microorganisms data set. new column status contains \"accepted\" currently accepted names \"synonym\" taxonomic synonyms; currently invalid names. previously accepted names now microorganisms ID - available - LPSN, GBIF SNOMED CT identifier.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antibiotic-agents-and-selectors-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Antibiotic agents and selectors","title":"AMR 1.8.2.9137","text":"new function add_custom_antimicrobials() allows users add custom antimicrobial codes names AMR package. antibiotics data set greatly updated: following 20 antibiotics added (also includes new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), thioacetazone (TAT) Added missing ATC codes Updated DDDs PubChem Compound IDs Updated antibiotic name spelling, now used WHOCC (cephalexin -> cefalexin, phenethicillin -> pheneticillin) Antibiotic code “CEI” ceftolozane/tazobactam replaced “CZT” comply EARS-Net WHONET 2022. old code still work cases using .ab() ab_*() functions. Support antimicrobial interpretation anaerobic bacteria, adding ‘placeholder’ code B_ANAER microorganisms data set adding breakpoints anaerobics clinical_breakpoints data set, used .sir() interpretion MIC disk diffusion values Also, added support using antibiotic selectors scoped dplyr verbs (without using vars()), : ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() examples.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antiviral-agents-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Antiviral agents","title":"AMR 1.8.2.9137","text":"now added extensive support antiviral agents! first time, AMR package extensive support antiviral drugs work names, codes data way. antivirals data set extended 18 new drugs (also new J05AJ ATC group) now also contains antiviral identifiers LOINC codes new data type av (antivirals) added, functionally similar ab antibiotics Functions .av(), av_name(), av_atc(), av_synonyms(), av_from_text() added siblings ab_*() equivalents","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-new-functions-1-8-2-9137","dir":"Changelog","previous_headings":"New","what":"Other new functions","title":"AMR 1.8.2.9137","text":"Function sir_confidence_interval() add confidence intervals AMR calculation. now also included sir_df() proportion_df(). Function mean_amr_distance() calculate mean AMR distance. mean AMR distance normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. Function sir_interpretation_history() view history previous runs .sir() (previously .rsi()). returns ‘logbook’ selected guideline, reference table specific interpretation row data set .sir() run. Function mo_current() get currently valid taxonomic name microorganism Function add_custom_antimicrobials() add custom antimicrobial codes names AMR package","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"changes-1-8-2-9137","dir":"Changelog","previous_headings":"","what":"Changes","title":"AMR 1.8.2.9137","text":"Argument combine_IR removed package (affecting functions count_df(), proportion_df(), sir_df() plotting functions), since replaced combine_SI three years ago Using units ab_ddd(..., units = \"...\") deprecated time now supported anymore. Use ab_ddd_units() instead. Support data.frame-enhancing R packages, specifically: data.table::data.table, janitor::tabyl, tibble::tibble, tsibble::tsibble. AMR package functions data set output (sir_df() bug_drug_combinations()), now return data type input. data sets package now tibble, instead base R data.frames. Older R versions still supported, even support tibbles. data sets now also continually exported Apache Feather Apache Parquet formats. can find info article website. Fixed certain EUCAST breakpoints MIC values Allow NA values (e.g. .sir(.disk(NA), ...)) Fix bug-drug combinations multiple breakpoints different body sites Interpretation MIC disk zones now informative availability breakpoints robust Removed .integer() method MIC values, since MIC integer values running table() MIC values consequently failed able retrieve level position (’s normally .integer() factors work) Fixed determination Gram stains (mo_gramstain()), since taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, Tenericutes renamed respectively Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota 2021 droplevels() MIC now return common factor default lose mic class. Use droplevels(..., .mic = TRUE) keep mic class. Small fix using ab_from_text() Fixes reading text files using set_mo_source(), now also allows source file contain valid taxonomic names instead valid microorganism ID package Fixed bug mdro() using similar column names Magiorakos guideline Using random_*() function (random_mic()) now possible directly calling package without loading first: AMR::random_mic(10) Extended support vctrs package, used internally tidyverse. allows change values class mic, disk, sir, mo ab tibbles, use antibiotic selectors selecting/filtering, e.g. df[carbapenems() == \"R\", ] Fix using info = FALSE mdro() interpretation guidelines using .sir() amoxicillin, rules ampicillin used amoxicillin rules available Fix using ab_atc() non-existing ATC codes Black white message texts now reversed colour using RStudio dark theme mo_snomed() now returns class character, numeric anymore (make long SNOMED codes readable) Fix using .ab() NA values Updated support WHONET 2022 microorganism codes Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined CLSI) interpreted ‘’ comply EUCAST’s ‘’ .sir() Fix mo_shortname() case higher taxonomic ranks (order, class, phylum) Cleaning columns .sir(), .mic(), .disk() now show column name warning invalid results Fix using g.test() zeroes 2x2 table get_episode() now returns class integer instead numeric since always whole numbers","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-1-8-2-9137","dir":"Changelog","previous_headings":"","what":"Other","title":"AMR 1.8.2.9137","text":"Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, Anita Williams contributors, thank valuable input New website make use new Bootstrap 5 pkgdown 2.0. website now contains results examples automatically regenerated every change repository, using GitHub Actions R Rmd files project now styled using styler package Set scalar conditional expressions (&& ||) possible comply upcoming R 4.3 enormous lot code cleaning, fixing small bugs along way changelog contains changes AMR v2.0 later. prior versions, please see archive.","code":""}]