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New mo algorithm, prepare for 2.0
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Dr. Matthijs Berends
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -46,14 +50,13 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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))
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}
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}
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vector_and(txt, quotes = FALSE)
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}
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#' Apply EUCAST Rules
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#'
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#' @description
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#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
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#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
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#'
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
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#' @param x a data set with antibiotic columns, such as `amox`, `AMX` and `AMC`
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@ -73,21 +76,20 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
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#' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
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#'
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#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
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#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms].
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#'
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#' ## Custom Rules
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#' ### Custom Rules
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#'
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#' Custom rules can be created using [custom_eucast_rules()], e.g.:
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#'
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#' ```{r}
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#' ```r
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#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
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#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
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#'
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#' eucast_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE)
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#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
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#' ```
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#'
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#'
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#' ## 'Other' Rules
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#' ### 'Other' Rules
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#'
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#' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
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#'
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@ -118,7 +120,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
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#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
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#' @inheritSection AMR Reference Data Publicly Available
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#' @examples
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#' \donttest{
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#' a <- data.frame(
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@ -199,8 +200,6 @@ eucast_rules <- function(x,
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x_deparsed <- "your_data"
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}
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check_dataset_integrity()
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breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
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expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
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@ -333,8 +332,8 @@ eucast_rules <- function(x,
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x <- x %pm>%
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strsplit(",") %pm>%
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unlist() %pm>%
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trimws() %pm>%
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vapply(FUN.VALUE = character(1), function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE, fast_mode = TRUE) else x) %pm>%
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trimws2() %pm>%
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vapply(FUN.VALUE = character(1), function(x) if (x %in% AMR::antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE, fast_mode = TRUE) else x) %pm>%
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sort() %pm>%
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paste(collapse = ", ")
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x <- gsub("_", " ", x, fixed = TRUE)
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@ -344,8 +343,8 @@ eucast_rules <- function(x,
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x
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}
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format_antibiotic_names <- function(ab_names, ab_results) {
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ab_names <- trimws(unlist(strsplit(ab_names, ",")))
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ab_results <- trimws(unlist(strsplit(ab_results, ",")))
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ab_names <- trimws2(unlist(strsplit(ab_names, ",")))
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ab_results <- trimws2(unlist(strsplit(ab_results, ",")))
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if (length(ab_results) == 1) {
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if (length(ab_names) == 1) {
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# like FOX S
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@ -423,13 +422,13 @@ eucast_rules <- function(x,
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# big speed gain! only analyse unique rows:
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pm_distinct(`.rowid`, .keep_all = TRUE) %pm>%
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as.data.frame(stringsAsFactors = FALSE)
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x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]))
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x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = info)
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# rename col_mo to prevent interference with joined columns
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colnames(x)[colnames(x) == col_mo] <- ".col_mo"
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col_mo <- ".col_mo"
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# join to microorganisms data set
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x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
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x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
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x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
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x$genus_species <- trimws(paste(x$genus, x$species))
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if (info == TRUE & NROW(x) > 10000) {
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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@ -437,11 +436,11 @@ eucast_rules <- function(x,
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if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
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all_staph <- MO_lookup[which(MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
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all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL))
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all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
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}
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if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
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all_strep <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), , drop = FALSE]
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all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL))
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all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
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}
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n_added <- 0
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@ -461,10 +460,10 @@ eucast_rules <- function(x,
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))
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))
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}
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ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
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ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
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colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
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ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$enzyme_name)
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ab_enzyme$base_ab <- antibiotics[match(ab_enzyme$base_name, antibiotics$name), "ab", drop = TRUE]
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ab_enzyme$base_ab <- AMR::antibiotics[match(ab_enzyme$base_name, AMR::antibiotics$name), "ab", drop = TRUE]
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ab_enzyme <- subset(ab_enzyme, !is.na(base_ab))
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# make ampicillin and amoxicillin interchangable
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ampi <- subset(ab_enzyme, base_ab == "AMX")
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@ -1073,11 +1072,11 @@ edit_rsi <- function(x,
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)
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txt_error <- function() {
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if (info == TRUE) cat("", font_red_bg(font_white(" ERROR ")), "\n\n")
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if (info == TRUE) cat("", font_red_bg(" ERROR "), "\n\n")
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}
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txt_warning <- function() {
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if (warned == FALSE) {
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if (info == TRUE) cat(" ", font_rsi_I_bg(" WARNING "), sep = "")
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if (info == TRUE) cat(" ", font_orange_bg(" WARNING "), sep = "")
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}
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warned <<- TRUE
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}
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@ -1179,7 +1178,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
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meet_criteria(administration, allow_class = "character", is_in = dosage$administration[!is.na(dosage$administration)], has_length = 1)
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meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
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# show used version_breakpoints number once per session (pkg_env will reload every session)
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# show used version_breakpoints number once per session (AMR_env will reload every session)
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if (message_not_thrown_before("eucast_dosage", "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
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message_(
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"Dosages for antimicrobial drugs, as meant for ",
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