We plot resistance trends over time for amoxicillin.
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AMR (for R)
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2.1.1.9232
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diff --git a/reference/resistance_predict.html b/reference/resistance_predict.html
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diff --git a/reference/top_n_microorganisms.html b/reference/top_n_microorganisms.html
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AMR (for R)
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diff --git a/search.json b/search.json
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-[{"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 !) reliable data 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. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> #> 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 #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLPN\") #> Class 'mo' #> [1] B_KLBSL_PNMN mo_family(\"K. pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"K. pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"K. pneumoniae\") #> [1] \"pneumoniae\" mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\" mo_ref(\"K. pneumoniae\") #> [1] \"Trevisan, 1887\" mo_snomed(\"K. pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\" \"1098201000112108\" \"409801009\" #> [5] \"56415008\" \"714315002\" \"713926009\" our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE) #> ℹ Retrieved values from the microorganisms.codes data set for \"ESCCOL\", #> \"KLEPNE\", \"STAAUR\", and \"STRPNE\". #> ℹ Microorganism translation was uncertain for four microorganisms. Run #> mo_uncertainties() to review these uncertainties, or use #> add_custom_microorganisms() to add custom entries. 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. #> Colour keys: 0.000-0.549 0.550-0.649 0.650-0.749 0.750-1.000 #> #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> Also matched: Enterococcus crotali (0.650), Escherichia coli coli #> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii #> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591), #> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae #> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae #> dissolvens (0.565) #> -------------------------------------------------------------------------------- #> \"K. pneumoniae\" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786) #> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella #> pneumoniae ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), #> Klebsiella pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii #> (0.500), Klebsiella planticola (0.500), Kingella potus (0.400), #> Kluyveromyces pseudotropicale (0.386), Kluyveromyces pseudotropicalis #> (0.363), and Kosakonia pseudosacchari (0.361) #> -------------------------------------------------------------------------------- #> \"S. aureus\" -> Staphylococcus aureus (B_STPHY_AURS, 0.690) #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus #> argenteus (0.625), Staphylococcus aureus anaerobius (0.625), #> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595), #> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587), #> Staphylococcus argensis (0.587), Streptococcus australis (0.587), and #> Salmonella choleraesuis arizonae (0.562) #> -------------------------------------------------------------------------------- #> \"S. pneumoniae\" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750) #> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus #> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545), #> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans #> (0.533), Staphylococcus pseudintermedius (0.532), Serratia #> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus #> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus #> periodonticum (0.519) #> #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"antibiotic-results","dir":"Articles","previous_headings":"Preparation","what":"Antibiotic results","title":"How to conduct AMR data analysis","text":"column antibiotic test results must also cleaned. AMR package comes three new data types work test results: mic minimal inhibitory concentrations (MIC), disk disk diffusion diameters, sir SIR data interpreted already. package can also determine SIR values based MIC disk diffusion values, read .sir() page. now, just clean SIR columns data using dplyr: basically cleaning, time start data inclusion.","code":"# method 1, be explicit about the columns: our_data <- our_data %>% mutate_at(vars(AMX:GEN), as.sir) # method 2, let the AMR package determine the eligible columns our_data <- our_data %>% mutate_if(is_sir_eligible, as.sir) # result: our_data #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> #> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S #> 2 R7 A 2018-04-03 B_KLBSL_PNMN R I S S #> 3 P3 A 2014-09-19 B_ESCHR_COLI R S S S #> 4 P10 A 2015-12-10 B_ESCHR_COLI S I S S #> 5 B7 A 2015-03-02 B_ESCHR_COLI S S S S #> 6 W3 A 2018-03-31 B_STPHY_AURS R S R S #> 7 J8 A 2016-06-14 B_ESCHR_COLI R S S S #> 8 M3 A 2015-10-25 B_ESCHR_COLI R S S S #> 9 J3 A 2019-06-19 B_ESCHR_COLI S S S S #> 10 G6 A 2015-04-27 B_STPHY_AURS S S S S #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"first-isolates","dir":"Articles","previous_headings":"Preparation","what":"First isolates","title":"How to conduct AMR data analysis","text":"need know isolates can actually use analysis without repetition bias. 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. Read methods first_isolate() page. outcome function can easily added data: 91% suitable resistance analysis! can now filter filter() function, also dplyr package: future use, two syntaxes can shortened: end 2 724 isolates analysis. Now data looks like: Time analysis.","code":"our_data <- our_data %>% mutate(first = first_isolate(info = TRUE)) #> ℹ 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. #> ℹ Basing inclusion on all antimicrobial results, using a points threshold #> of 2 #> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a #> microbial ID was available) our_data_1st <- our_data %>% filter(first == TRUE) our_data_1st <- our_data %>% filter_first_isolate() our_data_1st #> # A tibble: 2,724 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE #> 2 R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE #> 3 P3 A 2014-09-19 B_ESCHR_COLI R S S S TRUE #> 4 P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE #> 5 B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE #> 6 W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE #> 7 M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE #> 8 J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE #> 9 G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE #> 10 P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE #> # ℹ 2,714 more rows"},{"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":"base R summary() function gives good first impression, comes support new mo sir classes now data set:","code":"summary(our_data_1st) #> patient_id hospital date #> Length:2724 Length:2724 Min. :2011-01-01 #> Class :character Class :character 1st Qu.:2013-04-07 #> Mode :character Mode :character Median :2015-06-03 #> Mean :2015-06-09 #> 3rd Qu.:2017-08-11 #> Max. :2019-12-27 #> bacteria AMX AMC #> Class :mo Class:sir Class:sir #> :0 %S :41.6% (n=1133) %S :52.6% (n=1432) #> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> #1 :B_ESCHR_COLI %I :16.4% (n=446) %I :12.2% (n=333) #> #2 :B_STPHY_AURS %R :42.0% (n=1145) %R :35.2% (n=959) #> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) #> CIP GEN first #> Class:sir Class:sir Mode:logical #> %S :52.5% (n=1431) %S :61.0% (n=1661) TRUE:2724 #> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) #> %I : 6.5% (n=176) %I : 3.0% (n=82) #> %R :41.0% (n=1117) %R :36.0% (n=981) #> %NI : 0.0% (n=0) %NI : 0.0% (n=0) glimpse(our_data_1st) #> Rows: 2,724 #> Columns: 9 #> $ patient_id \"J3\", \"R7\", \"P3\", \"P10\", \"B7\", \"W3\", \"M3\", \"J3\", \"G6\", \"P4\"… #> $ hospital \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\",… #> $ date 2012-11-21, 2018-04-03, 2014-09-19, 2015-12-10, 2015-03-02… #> $ bacteria \"B_ESCHR_COLI\", \"B_KLBSL_PNMN\", \"B_ESCHR_COLI\", \"B_ESCHR_COL… #> $ AMX R, R, R, S, S, R, R, S, S, S, S, R, S, S, R, R, R, R, S, R,… #> $ AMC I, I, S, I, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, S,… #> $ CIP S, S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S,… #> $ GEN S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,… #> $ first TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,… # number of unique values per column: sapply(our_data_1st, n_distinct) #> patient_id hospital date bacteria AMX AMC CIP #> 260 3 1854 4 3 3 3 #> GEN first #> 3 1"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"availability-of-species","dir":"Articles","previous_headings":"Analysing the data","what":"Availability of species","title":"How to conduct AMR data analysis","text":"just get idea species distributed, create frequency table count() based name microorganisms:","code":"our_data %>% count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #> `mo_name(bacteria)` n #> #> 1 Escherichia coli 1518 #> 2 Staphylococcus aureus 730 #> 3 Streptococcus pneumoniae 426 #> 4 Klebsiella pneumoniae 326 our_data_1st %>% count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #> `mo_name(bacteria)` n #> #> 1 Escherichia coli 1321 #> 2 Staphylococcus aureus 682 #> 3 Streptococcus pneumoniae 402 #> 4 Klebsiella pneumoniae 319"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"select-and-filter-with-antibiotic-selectors","dir":"Articles","previous_headings":"Analysing the data","what":"Select and filter with antibiotic selectors","title":"How to conduct AMR data analysis","text":"Using -called antibiotic class selectors, can select filter columns based antibiotic class antibiotic results :","code":"our_data_1st %>% select(date, aminoglycosides()) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 2,724 × 2 #> date GEN #> #> 1 2012-11-21 S #> 2 2018-04-03 S #> 3 2014-09-19 S #> 4 2015-12-10 S #> 5 2015-03-02 S #> 6 2018-03-31 S #> 7 2015-10-25 S #> 8 2019-06-19 S #> 9 2015-04-27 S #> 10 2011-06-21 S #> # ℹ 2,714 more rows our_data_1st %>% select(bacteria, betalactams()) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 2,724 × 3 #> bacteria AMX AMC #> #> 1 B_ESCHR_COLI R I #> 2 B_KLBSL_PNMN R I #> 3 B_ESCHR_COLI R S #> 4 B_ESCHR_COLI S I #> 5 B_ESCHR_COLI S S #> 6 B_STPHY_AURS R S #> 7 B_ESCHR_COLI R S #> 8 B_ESCHR_COLI S S #> 9 B_STPHY_AURS S S #> 10 B_ESCHR_COLI S S #> # ℹ 2,714 more rows our_data_1st %>% select(bacteria, where(is.sir)) #> # A tibble: 2,724 × 5 #> bacteria AMX AMC CIP GEN #> #> 1 B_ESCHR_COLI R I S S #> 2 B_KLBSL_PNMN R I S S #> 3 B_ESCHR_COLI R S S S #> 4 B_ESCHR_COLI S I S S #> 5 B_ESCHR_COLI S S S S #> 6 B_STPHY_AURS R S R S #> 7 B_ESCHR_COLI R S S S #> 8 B_ESCHR_COLI S S S S #> 9 B_STPHY_AURS S S S S #> 10 B_ESCHR_COLI S S S S #> # ℹ 2,714 more rows # filtering using AB selectors is also possible: our_data_1st %>% filter(any(aminoglycosides() == \"R\")) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 981 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE #> 2 X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE #> 3 B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE #> 4 V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE #> 5 C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE #> 6 R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE #> 7 S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE #> 8 P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE #> 9 Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE #> 10 K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE #> # ℹ 971 more rows our_data_1st %>% filter(all(betalactams() == \"R\")) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 462 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 2 R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE #> 3 R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE #> 4 R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE #> 5 B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE #> 6 I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE #> 7 N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> # ℹ 452 more rows # even works in base R (since R 3.0): our_data_1st[all(betalactams() == \"R\"), ] #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #> (amoxicillin/clavulanic acid) #> # A tibble: 462 × 9 #> patient_id hospital date bacteria AMX AMC CIP GEN first #> #> 1 M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE #> 2 R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE #> 3 R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE #> 4 R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE #> 5 B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE #> 6 I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE #> 7 N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE #> 8 Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE #> 9 X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE #> 10 V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE #> # ℹ 452 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"generate-antibiograms","dir":"Articles","previous_headings":"Analysing the data","what":"Generate antibiograms","title":"How to conduct AMR data analysis","text":"Since AMR v2.0 (March 2023), easy create different types antibiograms, support 20 different languages. four antibiogram types, proposed Klinker et al. (2021, DOI 10.1177/20499361211011373), supported new antibiogram() function: Traditional Antibiogram (TA) e.g, susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Combination Antibiogram (CA) e.g, sdditional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Syndromic Antibiogram (SA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Weighted-Incidence Syndromic Combination Antibiogram (WISCA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure section, show use antibiogram() function create antibiogram types. starters, included example_isolates data set looks like:","code":"example_isolates #> # A tibble: 2,000 × 46 #> date patient age gender ward mo PEN OXA FLC AMX #> #> 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 #> # ℹ 1,990 more rows #> # ℹ 36 more variables: 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 , …"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"traditional-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Traditional Antibiogram","title":"How to conduct AMR data analysis","text":"create traditional antibiogram, simply state antibiotics used. antibiotics argument antibiogram() function supports (combination) previously mentioned antibiotic class selectors: Notice antibiogram() function automatically prints right format using Quarto R Markdown (page), even applies italics taxonomic names (using italicise_taxonomy() internally). also uses language OS either English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. next example, force language Spanish using language argument:","code":"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) antibiogram(example_isolates, mo_transform = \"gramstain\", antibiotics = aminoglycosides(), ab_transform = \"name\", language = \"es\") #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"combined-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Combined Antibiogram","title":"How to conduct AMR data analysis","text":"create combined antibiogram, use antibiotic codes names plus + character like :","code":"combined_ab <- antibiogram(example_isolates, antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"), ab_transform = NULL) combined_ab"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"syndromic-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Syndromic Antibiogram","title":"How to conduct AMR data analysis","text":"create syndromic antibiogram, syndromic_group argument must used. can column data, e.g. ifelse() calculations based certain columns:","code":"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)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"weighted-incidence-syndromic-combination-antibiogram-wisca","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Weighted-Incidence Syndromic Combination Antibiogram (WISCA)","title":"How to conduct AMR data analysis","text":"create Weighted-Incidence Syndromic Combination Antibiogram (WISCA), simply set wisca = TRUE antibiogram() function, use dedicated wisca() function. Unlike traditional antibiograms, WISCA provides syndrome-based susceptibility estimates, weighted pathogen incidence antimicrobial susceptibility patterns. WISCA uses Bayesian decision model integrate data multiple pathogens, improving empirical therapy guidance, especially low-incidence infections. pathogen-agnostic, meaning results syndrome-based rather stratified microorganism. reliable results, ensure data includes first isolates (use first_isolate()) consider filtering top n species (use top_n_microorganisms()), WISCA outcomes meaningful based robust incidence estimates. patient- syndrome-specific WISCA, run function grouped tibble, .e., using group_by() first:","code":"example_isolates %>% wisca(antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"), minimum = 10) # Recommended threshold: ≥30 example_isolates %>% top_n_microorganisms(n = 10) %>% group_by(age_group = age_groups(age, c(25, 50, 75)), gender) %>% wisca(antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-antibiograms","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Plotting antibiograms","title":"How to conduct AMR data analysis","text":"Antibiograms can plotted using autoplot() ggplot2 packages, since AMR package provides extension function: calculate antimicrobial resistance sensible way, also correcting results, use resistance() susceptibility() functions.","code":"autoplot(combined_ab)"},{"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:","code":"our_data_1st %>% resistance(AMX) #> [1] 0.4203377 our_data_1st %>% group_by(hospital) %>% summarise(amoxicillin = resistance(AMX)) #> # A tibble: 3 × 2 #> hospital amoxicillin #> #> 1 A 0.340 #> 2 B 0.551 #> 3 C 0.370"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"interpreting-mic-and-disk-diffusion-values","dir":"Articles","previous_headings":"Analysing the data","what":"Interpreting MIC and Disk Diffusion Values","title":"How to conduct AMR data analysis","text":"Minimal inhibitory concentration (MIC) values disk diffusion diameters can interpreted clinical breakpoints (SIR) using .sir(). ’s example randomly generated MIC values Klebsiella pneumoniae ciprofloxacin: allows direct interpretation according EUCAST CLSI breakpoints, facilitating automated AMR data processing.","code":"set.seed(123) mic_values <- random_mic(100) sir_values <- as.sir(mic_values, mo = \"K. pneumoniae\", ab = \"cipro\", guideline = \"EUCAST 2024\") #> #> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with #> all the details of the breakpoint interpretations. #> #> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin), EUCAST 2024... NOTE #> • Multiple breakpoints available for ciprofloxacin (CIP) in Klebsiella pneumoniae - assuming body site 'Non-meningitis'. my_data <- tibble(MIC = mic_values, SIR = sir_values) my_data #> # A tibble: 100 × 2 #> MIC SIR #> #> 1 16.000 R #> 2 0.005 S #> 3 1.000 R #> 4 >=256.000 R #> 5 2.000 R #> 6 0.025 S #> 7 16.000 R #> 8 0.025 S #> 9 0.500 I #> 10 0.005 S #> # ℹ 90 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-mic-and-sir-interpretations","dir":"Articles","previous_headings":"Analysing the data","what":"Plotting MIC and SIR Interpretations","title":"How to conduct AMR data analysis","text":"can visualise MIC distributions SIR interpretations using ggplot2, using new scale_y_mic() y-axis scale_colour_sir() colour-code SIR categories. plot provides intuitive way assess susceptibility patterns across different groups incorporating clinical breakpoints. straightforward less manual approach, ggplot2’s function autoplot() extended package directly plot MIC disk diffusion values: Author: Dr. Matthijs Berends, 23rd Feb 2025","code":"# add a group my_data$group <- rep(c(\"A\", \"B\", \"C\", \"D\"), each = 25) ggplot(my_data, aes(x = group, y = MIC, colour = SIR)) + geom_jitter(width = 0.2, size = 2) + geom_boxplot(fill = NA, colour = \"grey40\") + scale_y_mic() + scale_colour_sir() + labs(title = \"MIC Distribution and SIR Interpretation\", x = \"Sample Groups\", y = \"MIC (mg/L)\") autoplot(mic_values) # by providing `mo` and `ab`, colours will indicate the SIR interpretation: autoplot(mic_values, mo = \"K. pneumoniae\", ab = \"cipro\", guideline = \"EUCAST 2024\")"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"AMR for Python","text":"AMR package R powerful tool antimicrobial resistance (AMR) analysis. provides extensive features handling microbial antimicrobial data. However, work primarily Python, now intuitive option available: AMR Python package. Python package wrapper around AMR R package. uses rpy2 package internally. Despite need R installed, Python users can now easily work AMR data directly Python code.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"prerequisites","dir":"Articles","previous_headings":"","what":"Prerequisites","title":"AMR for Python","text":"package tested virtual environment (venv). can set environment running: can activate environment, venv ready work .","code":"# linux and macOS: python -m venv /path/to/new/virtual/environment # Windows: python -m venv C:\\path\\to\\new\\virtual\\environment"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"install-amr","dir":"Articles","previous_headings":"","what":"Install AMR","title":"AMR for Python","text":"Since Python package available official Python Package Index, can just run: Make sure R installed. need install AMR R package, installed automatically. Linux: macOS (using Homebrew): Windows, visit CRAN download page download install R.","code":"pip install AMR # Ubuntu / Debian sudo apt install r-base # Fedora: sudo dnf install R # CentOS/RHEL sudo yum install R brew install r"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"cleaning-taxonomy","dir":"Articles","previous_headings":"Examples of Usage","what":"Cleaning Taxonomy","title":"AMR for Python","text":"’s example demonstrates clean microorganism drug names using AMR Python package:","code":"import pandas as pd import AMR # Sample data data = { \"MOs\": ['E. coli', 'ESCCOL', 'esco', 'Esche coli'], \"Drug\": ['Cipro', 'CIP', 'J01MA02', 'Ciproxin'] } df = pd.DataFrame(data) # Use AMR functions to clean microorganism and drug names df['MO_clean'] = AMR.mo_name(df['MOs']) df['Drug_clean'] = AMR.ab_name(df['Drug']) # Display the results print(df)"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"explanation","dir":"Articles","previous_headings":"Examples of Usage > Cleaning Taxonomy","what":"Explanation","title":"AMR for Python","text":"mo_name: function standardises microorganism names. , different variations Escherichia coli (“E. coli”, “ESCCOL”, “esco”, “Esche coli”) converted correct, standardised form, “Escherichia coli”. ab_name: Similarly, function standardises antimicrobial names. different representations ciprofloxacin (e.g., “Cipro”, “CIP”, “J01MA02”, “Ciproxin”) converted standard name, “Ciprofloxacin”.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"calculating-amr","dir":"Articles","previous_headings":"Examples of Usage","what":"Calculating AMR","title":"AMR for Python","text":"","code":"import AMR import pandas as pd df = AMR.example_isolates result = AMR.resistance(df[\"AMX\"]) print(result) [0.59555556]"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"generating-antibiograms","dir":"Articles","previous_headings":"Examples of Usage","what":"Generating Antibiograms","title":"AMR for Python","text":"One core functions AMR package generating antibiogram, table summarises antimicrobial susceptibility bacterial isolates. ’s can generate antibiogram Python: example, generate antibiogram selecting various antibiotics.","code":"result2a = AMR.antibiogram(df[[\"mo\", \"AMX\", \"CIP\", \"TZP\"]]) print(result2a) result2b = AMR.antibiogram(df[[\"mo\", \"AMX\", \"CIP\", \"TZP\"]], mo_transform = \"gramstain\") print(result2b)"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"taxonomic-data-sets-now-in-python","dir":"Articles","previous_headings":"Examples of Usage","what":"Taxonomic Data Sets Now in Python!","title":"AMR for Python","text":"Python user, might like important data sets AMR R package, microorganisms, antimicrobials, clinical_breakpoints, example_isolates, now available regular Python data frames:","code":"AMR.microorganisms AMR.antimicrobials"},{"path":"https://msberends.github.io/AMR/articles/AMR_for_Python.html","id":"conclusion","dir":"Articles","previous_headings":"","what":"Conclusion","title":"AMR for Python","text":"AMR Python package, Python users can now effortlessly call R functions AMR R package. eliminates need complex rpy2 configurations provides clean, easy--use interface antimicrobial resistance analysis. examples provided demonstrate can applied typical workflows, standardising microorganism antimicrobial names calculating resistance. just running import AMR, users can seamlessly integrate robust features R AMR package Python workflows. Whether ’re cleaning data analysing resistance patterns, AMR Python package makes easy work AMR data Python.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"example-1-using-antimicrobial-selectors","dir":"Articles","previous_headings":"","what":"Example 1: Using Antimicrobial Selectors","title":"AMR with tidymodels","text":"leveraging power tidymodels AMR package, ’ll build reproducible machine learning workflow predict Gramstain microorganism two important antibiotic classes: aminoglycosides beta-lactams.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"objective","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors","what":"Objective","title":"AMR with tidymodels","text":"goal build predictive model using tidymodels framework determine Gramstain microorganism based microbial data. : Preprocess data using selector functions aminoglycosides() betalactams(). Define logistic regression model prediction. Use structured tidymodels workflow preprocess, train, evaluate model.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"data-preparation","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors","what":"Data Preparation","title":"AMR with tidymodels","text":"begin loading required libraries preparing example_isolates dataset AMR package. Explanation: aminoglycosides() betalactams() dynamically select columns antimicrobials classes. drop_na() ensures model receives complete cases training.","code":"# Load required libraries library(AMR) # For AMR data analysis library(tidymodels) # For machine learning workflows, and data manipulation (dplyr, tidyr, ...) #> ── Attaching packages ────────────────────────────────────── tidymodels 1.3.0 ── #> ✔ broom 1.0.8 ✔ recipes 1.2.1 #> ✔ dials 1.4.0 ✔ rsample 1.2.1 #> ✔ dplyr 1.1.4 ✔ tibble 3.2.1 #> ✔ ggplot2 3.5.1 ✔ tidyr 1.3.1 #> ✔ infer 1.0.7 ✔ tune 1.3.0 #> ✔ modeldata 1.4.0 ✔ workflows 1.2.0 #> ✔ parsnip 1.3.1 ✔ workflowsets 1.1.0 #> ✔ purrr 1.0.4 ✔ yardstick 1.3.2 #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ── #> ✖ purrr::discard() masks scales::discard() #> ✖ dplyr::filter() masks stats::filter() #> ✖ dplyr::lag() masks stats::lag() #> ✖ recipes::step() masks stats::step() # Your data could look like this: example_isolates #> # A tibble: 2,000 × 46 #> date patient age gender ward mo PEN OXA FLC AMX #> #> 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 #> # ℹ 1,990 more rows #> # ℹ 36 more variables: 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 , … # Select relevant columns for prediction data <- example_isolates %>% # select AB results dynamically select(mo, aminoglycosides(), betalactams()) %>% # replace NAs with NI (not-interpretable) mutate(across(where(is.sir), ~replace_na(.x, \"NI\")), # make factors of SIR columns across(where(is.sir), as.integer), # get Gramstain of microorganisms mo = as.factor(mo_gramstain(mo))) %>% # drop NAs - the ones without a Gramstain (fungi, etc.) drop_na() #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM' #> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime), #> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem)"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"defining-the-workflow","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors","what":"Defining the Workflow","title":"AMR with tidymodels","text":"now define tidymodels workflow, consists three steps: preprocessing, model specification, fitting.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"preprocessing-with-a-recipe","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors > Defining the Workflow","what":"1. Preprocessing with a Recipe","title":"AMR with tidymodels","text":"create recipe preprocess data modelling. recipe includes least one preprocessing operation, like step_corr(), necessary parameters can estimated training set using prep(): Explanation: recipe(mo ~ ., data = data) take mo column outcome columns predictors. step_corr() removes predictors (.e., antibiotic columns) higher correlation 90%. Notice recipe contains just antimicrobial selector functions - need define columns specifically. preparation (retrieved prep()) can see columns variables ‘AMX’ ‘CTX’ removed correlate much existing, variables.","code":"# Define the recipe for data preprocessing resistance_recipe <- recipe(mo ~ ., data = data) %>% step_corr(c(aminoglycosides(), betalactams()), threshold = 0.9) resistance_recipe #> #> ── Recipe ────────────────────────────────────────────────────────────────────── #> #> ── Inputs #> Number of variables by role #> outcome: 1 #> predictor: 20 #> #> ── Operations #> • Correlation filter on: c(aminoglycosides(), betalactams()) prep(resistance_recipe) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For betalactams() using columns 'PEN' (benzylpenicillin), 'OXA' #> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'TZP' #> (piperacillin/tazobactam), 'CZO' (cefazolin), 'FEP' (cefepime), 'CXM' #> (cefuroxime), 'FOX' (cefoxitin), 'CTX' (cefotaxime), 'CAZ' (ceftazidime), #> 'CRO' (ceftriaxone), 'IPM' (imipenem), and 'MEM' (meropenem) #> #> ── Recipe ────────────────────────────────────────────────────────────────────── #> #> ── Inputs #> Number of variables by role #> outcome: 1 #> predictor: 20 #> #> ── Training information #> Training data contained 1968 data points and no incomplete rows. #> #> ── Operations #> • Correlation filter on: AMX CTX | Trained"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"specifying-the-model","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors > Defining the Workflow","what":"2. Specifying the Model","title":"AMR with tidymodels","text":"define logistic regression model since resistance prediction binary classification task. Explanation: logistic_reg() sets logistic regression model. set_engine(\"glm\") specifies use R’s built-GLM engine.","code":"# Specify a logistic regression model logistic_model <- logistic_reg() %>% set_engine(\"glm\") # Use the Generalised Linear Model engine logistic_model #> Logistic Regression Model Specification (classification) #> #> Computational engine: glm"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"building-the-workflow","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors > Defining the Workflow","what":"3. Building the Workflow","title":"AMR with tidymodels","text":"bundle recipe model together workflow, organises entire modeling process.","code":"# Combine the recipe and model into a workflow resistance_workflow <- workflow() %>% add_recipe(resistance_recipe) %>% # Add the preprocessing recipe add_model(logistic_model) # Add the logistic regression model resistance_workflow #> ══ Workflow ════════════════════════════════════════════════════════════════════ #> Preprocessor: Recipe #> Model: logistic_reg() #> #> ── Preprocessor ──────────────────────────────────────────────────────────────── #> 1 Recipe Step #> #> • step_corr() #> #> ── Model ─────────────────────────────────────────────────────────────────────── #> Logistic Regression Model Specification (classification) #> #> Computational engine: glm"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"training-and-evaluating-the-model","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors","what":"Training and Evaluating the Model","title":"AMR with tidymodels","text":"train model, split data training testing sets. , fit workflow training set evaluate performance. Explanation: initial_split() splits data training testing sets. fit() trains workflow training set. Notice fit(), antimicrobial selector functions internally called . training, functions called since stored recipe. Next, evaluate model testing data. Explanation: predict() generates predictions testing set. metrics() computes evaluation metrics like accuracy kappa. appears can predict Gram stain 99.5% accuracy based AMR results aminoglycosides beta-lactam antibiotics. ROC curve looks like :","code":"# Split data into training and testing sets set.seed(123) # For reproducibility data_split <- initial_split(data, prop = 0.8) # 80% training, 20% testing training_data <- training(data_split) # Training set testing_data <- testing(data_split) # Testing set # Fit the workflow to the training data fitted_workflow <- resistance_workflow %>% fit(training_data) # Train the model # Make predictions on the testing set predictions <- fitted_workflow %>% predict(testing_data) # Generate predictions probabilities <- fitted_workflow %>% predict(testing_data, type = \"prob\") # Generate probabilities predictions <- predictions %>% bind_cols(probabilities) %>% bind_cols(testing_data) # Combine with true labels predictions #> # A tibble: 394 × 24 #> .pred_class `.pred_Gram-negative` `.pred_Gram-positive` mo GEN TOB #> #> 1 Gram-positive 1.07e- 1 8.93e- 1 Gram-p… 5 5 #> 2 Gram-positive 3.17e- 8 1.00e+ 0 Gram-p… 5 1 #> 3 Gram-negative 9.99e- 1 1.42e- 3 Gram-n… 5 5 #> 4 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 5 5 #> 5 Gram-negative 9.46e- 1 5.42e- 2 Gram-n… 5 5 #> 6 Gram-positive 1.07e- 1 8.93e- 1 Gram-p… 5 5 #> 7 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 1 5 #> 8 Gram-positive 2.22e-16 1 e+ 0 Gram-p… 4 4 #> 9 Gram-negative 1 e+ 0 2.22e-16 Gram-n… 1 1 #> 10 Gram-positive 6.05e-11 1.00e+ 0 Gram-p… 4 4 #> # ℹ 384 more rows #> # ℹ 18 more variables: AMK , KAN , PEN , OXA , FLC , #> # AMX , AMC , AMP , TZP , CZO , FEP , #> # CXM , FOX , CTX , CAZ , CRO , IPM , MEM # Evaluate model performance metrics <- predictions %>% metrics(truth = mo, estimate = .pred_class) # Calculate performance metrics metrics #> # A tibble: 2 × 3 #> .metric .estimator .estimate #> #> 1 accuracy binary 0.995 #> 2 kap binary 0.989 # To assess some other model properties, you can make our own `metrics()` function our_metrics <- metric_set(accuracy, kap, ppv, npv) # add Positive Predictive Value and Negative Predictive Value metrics2 <- predictions %>% our_metrics(truth = mo, estimate = .pred_class) # run again on our `our_metrics()` function metrics2 #> # A tibble: 4 × 3 #> .metric .estimator .estimate #> #> 1 accuracy binary 0.995 #> 2 kap binary 0.989 #> 3 ppv binary 0.987 #> 4 npv binary 1 predictions %>% roc_curve(mo, `.pred_Gram-negative`) %>% autoplot()"},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"conclusion","dir":"Articles","previous_headings":"Example 1: Using Antimicrobial Selectors","what":"Conclusion","title":"AMR with tidymodels","text":"post, demonstrated build machine learning pipeline tidymodels framework AMR package. combining selector functions like aminoglycosides() betalactams() tidymodels, efficiently prepared data, trained model, evaluated performance. workflow extensible antimicrobial classes resistance patterns, empowering users analyse AMR data systematically reproducibly.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"example-2-predicting-amr-over-time","dir":"Articles","previous_headings":"","what":"Example 2: Predicting AMR Over Time","title":"AMR with tidymodels","text":"second example, aim predict antimicrobial resistance (AMR) trends time using tidymodels. model resistance three antibiotics (amoxicillin AMX, amoxicillin-clavulanic acid AMC, ciprofloxacin CIP), based historical data grouped year hospital ward.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"objective-1","dir":"Articles","previous_headings":"Example 2: Predicting AMR Over Time","what":"Objective","title":"AMR with tidymodels","text":"goal : Prepare dataset aggregating resistance data time. Define regression model predict AMR trends. Use tidymodels preprocess, train, evaluate model.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html","id":"data-preparation-1","dir":"Articles","previous_headings":"Example 2: Predicting AMR Over Time","what":"Data Preparation","title":"AMR with tidymodels","text":"start transforming example_isolates dataset structured time-series format. Explanation: - mo_name(mo): Converts microbial codes proper species names. - resistance(): Converts AMR results numeric values (proportion resistant isolates). - group_by(year, ward, species): Aggregates resistance rates year ward.","code":"# Load required libraries library(AMR) library(tidymodels) # Transform dataset data_time <- example_isolates %>% top_n_microorganisms(n = 10) %>% # Filter on the top #10 species mutate(year = as.integer(format(date, \"%Y\")), # Extract year from date gramstain = mo_gramstain(mo)) %>% # Get taxonomic names group_by(year, gramstain) %>% summarise(across(c(AMX, AMC, CIP), function(x) resistance(x, minimum = 0), .names = \"res_{.col}\"), .groups = \"drop\") %>% filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values #> ℹ Using column 'mo' as input for col_mo. data_time #> # A tibble: 32 × 5 #> year gramstain res_AMX res_AMC res_CIP #>