diff --git a/DESCRIPTION b/DESCRIPTION index 0778ca2ab..40c47a7b9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.9.0.9025 -Date: 2020-02-16 +Version: 0.9.0.9026 +Date: 2020-02-17 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), @@ -28,9 +28,7 @@ Authors@R: c( person(role = "ctb", family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"), person(role = "ctb", - family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"), - person(role = "fnd", - given = "Stichting Certe Medische Diagnostiek en Advies", email = "medischedataanalyse@certe.nl")) + family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl")) Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) diff --git a/NEWS.md b/NEWS.md index 86f4ac813..85905b4e9 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,9 @@ -# AMR 0.9.0.9025 -## Last updated: 16-Feb-2020 +# AMR 0.9.0.9026 +## Last updated: 17-Feb-2020 ### New -* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 2020-01-01 (use `as.rsi()` to transform MICs and disk zones) -* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. +* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`. +* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: . This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R). * Support for LOINC and SNOMED codes * Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function: ```r diff --git a/R/amr.R b/R/amr.R index 54ee10812..f5a93aa47 100644 --- a/R/amr.R +++ b/R/amr.R @@ -38,15 +38,17 @@ #' - Getting properties for any microorganism (like Gram stain, species, genus or family) #' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name) #' - Plotting antimicrobial resistance -#' - Applying EUCAST expert rules +#' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code +#' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code +#' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI #' @section Read more on our website!: -#' On our website you can find [a tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html). +#' On our website you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html). #' @section Contact us: #' For suggestions, comments or questions, please contact us at: #' #' Matthijs S. Berends \cr -#' m.s.berends at umcg dot nl \cr +#' m.s.berends \[at\] umcg \[dot\] nl \cr #' Department of Medical Microbiology, University of Groningen \cr #' University Medical Center Groningen \cr #' Post Office Box 30001 \cr diff --git a/R/data.R b/R/data.R index fae093179..183032091 100755 --- a/R/data.R +++ b/R/data.R @@ -205,8 +205,8 @@ catalogue_of_life <- list( #' - `ab`\cr Antibiotic ID, see [as.ab()] #' - `ref_tbl`\cr Info about where the guideline rule can be found #' - `disk_dose`\cr Dose of the used disk diffusion method -#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimeters that leads to "S" -#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimeters that leads to "R" +#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S" +#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R" #' @details The repository of this `AMR` package contains a file comprising this exact data set: . This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. #' @inheritSection AMR Read more on our website! "rsi_translation" diff --git a/R/disk.R b/R/disk.R index d27cda648..909550645 100644 --- a/R/disk.R +++ b/R/disk.R @@ -21,7 +21,7 @@ #' Class 'disk' #' -#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50. +#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50. #' @inheritSection lifecycle Stable lifecycle #' @rdname as.disk #' @param x vector @@ -33,15 +33,22 @@ #' @seealso [as.rsi()] #' @inheritSection AMR Read more on our website! #' @examples -#' # interpret disk values -#' as.rsi(x = 12, -#' mo = as.mo("S. pneumoniae"), -#' ab = "AMX", +#' # transform existing disk zones to the `disk` class +#' df <- data.frame(microorganism = "E. coli", +#' AMP = 20, +#' CIP = 14, +#' GEN = 18, +#' TOB = 16) +#' df <- df %>% mutate_at(vars(AMP:TOB, as.disk)) +#' df +#' +#' # interpret disk values, see ?as.rsi +#' as.rsi(x = as.disk(18), +#' mo = "Strep pneu", # `mo` will be coerced with as.mo() +#' ab = "ampicillin", # and `ab` with as.ab() #' guideline = "EUCAST") -#' as.rsi(x = 12, -#' mo = as.mo("S. pneumoniae"), -#' ab = "AMX", -#' guideline = "CLSI") +#' +#' as.rsi(df) as.disk <- function(x, na.rm = FALSE) { if (is.disk(x)) { x diff --git a/R/eucast_rules.R b/R/eucast_rules.R index ba5d6667a..0fb430719 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -20,7 +20,7 @@ # ==================================================================== # # global variables -EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019" +EUCAST_VERSION_BREAKPOINTS <- "10.0, 2020" EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' Apply EUCAST rules @@ -655,9 +655,11 @@ eucast_rules <- function(x, cat(bold( case_when( rule_group_current %like% "breakpoint" ~ - paste0("\nEUCAST Clinical Breakpoints (v", EUCAST_VERSION_BREAKPOINTS, ")\n"), + paste0("\nEUCAST Clinical Breakpoints (", + red(paste0("v", EUCAST_VERSION_BREAKPOINTS)), ")\n"), rule_group_current %like% "expert" ~ - paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"), + paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (", + red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"), TRUE ~ "\nOther rules by this AMR package\n" ) diff --git a/R/proportion.R b/R/proportion.R index 1472a4d71..b8887e9c4 100755 --- a/R/proportion.R +++ b/R/proportion.R @@ -21,7 +21,7 @@ #' Calculate microbial resistance #' -#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in [dplyr::summarise()] and support grouped variables, please see *Examples*. +#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in `summarise()`][dplyr::summarise()] and also support grouped variables, please see *Examples*. #' #' [resistance()] should be used to calculate resistance, [susceptibility()] should be used to calculate susceptibility.\cr #' @inheritSection lifecycle Stable lifecycle @@ -40,11 +40,11 @@ #' #' **Remember that you should filter your table to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set. #' -#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can infuence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).* +#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the `count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).* #' #' The function [proportion_df()] takes any variable from `data` that has an [`rsi`] class (created with [as.rsi()]) and calculates the proportions R, I and S. The function [rsi_df()] works exactly like [proportion_df()], but adds the number of isolates. #' @section Combination therapy: -#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how [susceptibility()] works to calculate the %SI: +#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI: #' #' ``` #' -------------------------------------------------------------------- diff --git a/R/rsi.R b/R/rsi.R index 175410923..2ba399ac7 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -24,9 +24,9 @@ #' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning. #' @inheritSection lifecycle Stable lifecycle #' @rdname as.rsi -#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimeters) -#' @param mo a microorganism code, generated with [as.mo()] -#' @param ab an antimicrobial code, generated with [as.ab()] +#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres) +#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()] +#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()] #' @inheritParams first_isolate #' @param guideline defaults to the latest included EUCAST guideline, run `unique(rsi_translation$guideline)` for all options #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples* @@ -71,8 +71,10 @@ #' #' # a whole data set, even with combined MIC values and disk zones #' df <- data.frame(microorganism = "E. coli", -#' AMP = as.mic(12), -#' GEN = as.disk(18)) +#' AMP = as.mic(8), +#' CIP = as.mic(0.256), +#' GEN = as.disk(18), +#' TOB = as.disk(16)) #' as.rsi(df) #' #' @@ -239,12 +241,12 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) { if (guideline_coerced != guideline) { message(blue(paste0("Note: Using guideline ", bold(guideline_coerced), " as input for `guideline`."))) } - + new_rsi <- rep(NA_character_, length(x)) trans <- rsi_translation %>% filter(guideline == guideline_coerced & method == method_param) %>% mutate(lookup = paste(mo, ab)) - + lookup_mo <- paste(mo, ab) lookup_genus <- paste(mo_genus, ab) lookup_family <- paste(mo_family, ab) diff --git a/R/sysdata.rda b/R/sysdata.rda index 31aa159aa..a29011288 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/_pkgdown.yml b/_pkgdown.yml index ba74e29ac..e6248314a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -186,7 +186,3 @@ template: params: noindex: false bootswatch: "flatly" - docsearch: - # using algolia.com - api_key: "f737050abfd4d726c63938e18f8c496e" - index_name: "amr" diff --git a/data-raw/eucast_rules.tsv b/data-raw/eucast_rules.tsv index 3e9a31401..37bee0b9e 100644 --- a/data-raw/eucast_rules.tsv +++ b/data-raw/eucast_rules.tsv @@ -5,7 +5,7 @@ # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. # The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain". # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression) -# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J (2005, PMID 16217180). +# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx). # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<< # ------------------------------------------------------------------------------------------------------------------------------- if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group @@ -37,7 +37,6 @@ genus is Staphylococcus ERY S AZM, CLR, RXT S Staphylococcus Breakpoints genus is Staphylococcus ERY I AZM, CLR, RXT I Staphylococcus Breakpoints genus is Staphylococcus ERY R AZM, CLR, RXT R Staphylococcus Breakpoints genus is Staphylococcus TCY S DOX, MNO S Staphylococcus Breakpoints -genus_species is Enterococcus faecium AMP R all_betalactams R Enterococcus Breakpoints genus is Enterococcus AMP S AMX, AMC, PIP, TZP S Enterococcus Breakpoints genus is Enterococcus AMP I AMX, AMC, PIP, TZP I Enterococcus Breakpoints genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints @@ -47,7 +46,8 @@ genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints -genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX, MFX S Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S MFX S Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ NOR S LVX I Streptococcus groups A, B, C, G Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints @@ -56,7 +56,8 @@ genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Strept genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae AMP R AMX, AMC, PIP, TZP R Streptococcus pneumoniae Breakpoints -genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae NOR S MFX S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae NOR S LVX I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY S AZM, CLR, RXT S Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pneumoniae Breakpoints genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints @@ -122,6 +123,11 @@ genus_species is Kingella kingae ERY S AZM, CLR S Kingella kingae Breakpoints genus_species is Kingella kingae ERY I AZM, CLR I Kingella kingae Breakpoints genus_species is Kingella kingae ERY R AZM, CLR R Kingella kingae Breakpoints genus_species is Kingella kingae TCY S DOX S Kingella kingae Breakpoints +genus_species is Kingella kingae TCY I DOX I Kingella kingae Breakpoints +genus_species is Kingella kingae TCY R DOX R Kingella kingae Breakpoints +genus_species is Burkholderia pseudomallei TCY S DOX S Burkholderia pseudomallei Breakpoints +genus_species is Burkholderia pseudomallei TCY I DOX I Burkholderia pseudomallei Breakpoints +genus_species is Burkholderia pseudomallei TCY R DOX R Burkholderia pseudomallei Breakpoints order is Enterobacterales PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, TIC R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, AMC, CZO, FOX R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules @@ -146,7 +152,7 @@ genus_species is Acinetobacter pittii aminopenicillins, AMC, CZO, CTX, CRO, AT genus_species is Acinetobacter nosocomialis aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Acinetobacter calcoaceticus aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Achromobacter xylosoxidans aminopenicillins, CZO, CTX, CRO, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules -fullname like ^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Ochrobactrum anthropi aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules genus_species is Pseudomonas aeruginosa aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules diff --git a/data-raw/internals.R b/data-raw/internals.R index 5eb0e43eb..a247a0253 100644 --- a/data-raw/internals.R +++ b/data-raw/internals.R @@ -31,7 +31,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv", header = TRUE, strip.white = TRUE, na = c(NA, "", NULL)) -# take the order of the reference.rule_group column in the orginal data file +# take the order of the reference.rule_group column in the original data file eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group, levels = unique(eucast_rules_file$reference.rule_group), ordered = TRUE) diff --git a/data-raw/read_EUCAST.R b/data-raw/read_EUCAST.R index 34dcdcb97..7c8af6d5e 100644 --- a/data-raw/read_EUCAST.R +++ b/data-raw/read_EUCAST.R @@ -24,6 +24,8 @@ library(dplyr) library(cleaner) library(AMR) +# USE THIS FUNCTION TO READ THE EUCAST EXCEL FILE THAT CONTAINS THE BREAKPOINT TABLES + read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") { message("Getting sheet ", sheet) diff --git a/docs/404.html b/docs/404.html index 7c553f0ab..a805869c4 100644 --- a/docs/404.html +++ b/docs/404.html @@ -40,12 +40,6 @@ - - - - - - @@ -84,7 +78,7 @@ AMR (for R) - 0.9.0.9025 + 0.9.0.9026 @@ -210,12 +204,6 @@ - - @@ -240,7 +228,7 @@ Content not found. Please use links in the navbar.