mirror of https://github.com/msberends/AMR.git
1232 lines
52 KiB
R
Executable File
1232 lines
52 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
# ====================================================== #
|
|
# || Change the EUCAST version numbers in R/globals.R || #
|
|
# ====================================================== #
|
|
|
|
format_eucast_version_nr <- function(version, markdown = TRUE) {
|
|
# for documentation - adds title, version number, year and url in markdown language
|
|
lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
|
|
version <- format(unique(version), nsmall = 1)
|
|
txt <- character(0)
|
|
for (i in seq_len(length(version))) {
|
|
v <- version[i]
|
|
if (markdown == TRUE) {
|
|
txt <- c(txt, paste0(
|
|
"[", lst[[v]]$title, " ", lst[[v]]$version_txt, "](", lst[[v]]$url, ")",
|
|
" (", lst[[v]]$year, ")"
|
|
))
|
|
} else {
|
|
txt <- c(txt, paste0(
|
|
lst[[version]]$title, " ", lst[[v]]$version_txt,
|
|
" (", lst[[v]]$year, ")"
|
|
))
|
|
}
|
|
}
|
|
vector_and(txt, quotes = FALSE)
|
|
}
|
|
|
|
#' Apply EUCAST Rules
|
|
#'
|
|
#' @description
|
|
#' 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.
|
|
#'
|
|
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
|
|
#' @param x a data set with antibiotic columns, such as `amox`, `AMX` and `AMC`
|
|
#' @param info a [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions
|
|
#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using the [package option][AMR-options] [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
|
|
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
|
|
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
|
|
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
|
|
# @param version_resistant_phenotypes the version number to use for the EUCAST Expected Resistant Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_RESISTANTPHENOTYPES), reverse = TRUE)`.
|
|
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
|
|
#' @param ... column name of an antibiotic, see section *Antibiotics* below
|
|
#' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
|
|
#' @param administration route of administration, either `r vector_or(dosage$administration)`
|
|
#' @param only_sir_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
|
|
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
|
|
#' @inheritParams first_isolate
|
|
#' @details
|
|
#' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
|
|
#' **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
|
|
#'
|
|
#' 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].
|
|
#'
|
|
#' ### Custom Rules
|
|
#'
|
|
#' Custom rules can be created using [custom_eucast_rules()], e.g.:
|
|
#'
|
|
#' ```r
|
|
#' 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)
|
|
#' ```
|
|
#'
|
|
#' ### 'Other' Rules
|
|
#'
|
|
#' 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:
|
|
#'
|
|
#' 1. A drug **with** enzyme inhibitor will be set to S if the same drug **without** enzyme inhibitor is S
|
|
#' 2. A drug **without** enzyme inhibitor will be set to R if the same drug **with** enzyme inhibitor is R
|
|
#'
|
|
#' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
|
|
#'
|
|
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the [package option][AMR-options] [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
|
|
#' @section Antibiotics:
|
|
#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
|
|
#'
|
|
#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://atcddd.fhi.no/atc/structure_and_principles/))', sorted alphabetically:
|
|
#'
|
|
#' `r create_eucast_ab_documentation()`
|
|
#' @aliases EUCAST
|
|
#' @rdname eucast_rules
|
|
#' @export
|
|
#' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations.
|
|
#' @source
|
|
#' - EUCAST Expert Rules. Version 2.0, 2012.\cr
|
|
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
|
|
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
|
|
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
|
|
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
|
|
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
|
|
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
|
|
#' - 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)
|
|
#' - 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)
|
|
#' @inheritSection AMR Reference Data Publicly Available
|
|
#' @examples
|
|
#' \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)
|
|
#'
|
|
#'
|
|
#' # apply EUCAST rules: some results wil be changed
|
|
#' b <- eucast_rules(a)
|
|
#'
|
|
#' head(b)
|
|
#'
|
|
#'
|
|
#' # do not apply EUCAST rules, but rather get a data.frame
|
|
#' # containing all details about the transformations:
|
|
#' c <- eucast_rules(a, verbose = TRUE)
|
|
#' head(c)
|
|
#' }
|
|
#'
|
|
#' # Dosage guidelines:
|
|
#'
|
|
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
|
|
#'
|
|
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
|
|
eucast_rules <- function(x,
|
|
col_mo = NULL,
|
|
info = interactive(),
|
|
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
|
|
verbose = FALSE,
|
|
version_breakpoints = 12.0,
|
|
version_expertrules = 3.3,
|
|
# TODO version_resistant_phenotypes = 1.2,
|
|
ampc_cephalosporin_resistance = NA,
|
|
only_sir_columns = FALSE,
|
|
custom_rules = NULL,
|
|
...) {
|
|
meet_criteria(x, allow_class = "data.frame")
|
|
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
|
|
meet_criteria(info, allow_class = "logical", has_length = 1)
|
|
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom"))
|
|
meet_criteria(verbose, allow_class = "logical", has_length = 1)
|
|
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
|
|
meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
|
|
# meet_criteria(version_resistant_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)))
|
|
meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
|
|
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
|
|
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
|
|
|
|
add_MO_lookup_to_AMR_env()
|
|
|
|
if ("custom" %in% rules && is.null(custom_rules)) {
|
|
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
|
|
immediate = TRUE
|
|
)
|
|
rules <- rules[rules != "custom"]
|
|
if (length(rules) == 0) {
|
|
if (isTRUE(info)) {
|
|
message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
|
|
}
|
|
return(x)
|
|
}
|
|
}
|
|
|
|
x_deparsed <- deparse(substitute(x))
|
|
if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
|
|
x_deparsed <- "your_data"
|
|
}
|
|
|
|
breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
|
|
expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
|
|
# resistantphenotypes_info <- EUCAST_VERSION_RESISTANTPHENOTYPES[[which(as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)) == version_resistant_phenotypes)]]
|
|
|
|
# support old setting (until AMR v1.3.0)
|
|
if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
|
|
rules <- getOption("AMR.eucast_rules")
|
|
}
|
|
|
|
if (interactive() && isTRUE(verbose) && isTRUE(info)) {
|
|
txt <- paste0(
|
|
"WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
|
|
"\n\nThis may overwrite your existing data if you use e.g.:",
|
|
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?"
|
|
)
|
|
showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE)
|
|
if (!is.null(showQuestion)) {
|
|
q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
|
|
} else {
|
|
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
|
|
}
|
|
if (q_continue %in% c(FALSE, 2)) {
|
|
message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
|
|
return(x)
|
|
}
|
|
}
|
|
|
|
# try to find columns based on type
|
|
# -- mo
|
|
if (is.null(col_mo)) {
|
|
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
|
|
stop_if(is.null(col_mo), "`col_mo` must be set")
|
|
}
|
|
|
|
decimal.mark <- getOption("OutDec")
|
|
big.mark <- ifelse(decimal.mark != ",", ",", " ")
|
|
formatnr <- function(x, big = big.mark, dec = decimal.mark) {
|
|
trimws(format(x, big.mark = big, decimal.mark = dec))
|
|
}
|
|
|
|
warned <- FALSE
|
|
warn_lacking_sir_class <- character(0)
|
|
txt_ok <- function(n_added, n_changed, warned = FALSE) {
|
|
if (warned == FALSE) {
|
|
if (n_added + n_changed == 0) {
|
|
cat(font_subtle(" (no changes)\n"))
|
|
} else {
|
|
# opening
|
|
if (n_added > 0 && n_changed == 0) {
|
|
cat(font_green(" ("))
|
|
} else if (n_added == 0 && n_changed > 0) {
|
|
cat(font_blue(" ("))
|
|
} else {
|
|
cat(font_grey(" ("))
|
|
}
|
|
# additions
|
|
if (n_added > 0) {
|
|
if (n_added == 1) {
|
|
cat(font_green("1 value added"))
|
|
} else {
|
|
cat(font_green(formatnr(n_added), "values added"))
|
|
}
|
|
}
|
|
# separator
|
|
if (n_added > 0 && n_changed > 0) {
|
|
cat(font_grey(", "))
|
|
}
|
|
# changes
|
|
if (n_changed > 0) {
|
|
if (n_changed == 1) {
|
|
cat(font_blue("1 value changed"))
|
|
} else {
|
|
cat(font_blue(formatnr(n_changed), "values changed"))
|
|
}
|
|
}
|
|
# closing
|
|
if (n_added > 0 && n_changed == 0) {
|
|
cat(font_green(")\n"))
|
|
} else if (n_added == 0 && n_changed > 0) {
|
|
cat(font_blue(")\n"))
|
|
} else {
|
|
cat(font_grey(")\n"))
|
|
}
|
|
}
|
|
warned <<- FALSE
|
|
}
|
|
}
|
|
|
|
cols_ab <- get_column_abx(
|
|
x = x,
|
|
soft_dependencies = c(
|
|
"AMC",
|
|
"AMP",
|
|
"AMX",
|
|
"CIP",
|
|
"ERY",
|
|
"FOX1",
|
|
"GEN",
|
|
"MFX",
|
|
"NAL",
|
|
"NOR",
|
|
"PEN",
|
|
"PIP",
|
|
"TCY",
|
|
"TIC",
|
|
"TOB"
|
|
),
|
|
hard_dependencies = NULL,
|
|
verbose = verbose,
|
|
info = info,
|
|
only_sir_columns = only_sir_columns,
|
|
fn = "eucast_rules",
|
|
...
|
|
)
|
|
|
|
if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
|
|
# ampicillin column is missing, but amoxicillin is available
|
|
if (isTRUE(info)) {
|
|
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
|
|
}
|
|
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
|
|
}
|
|
|
|
# data preparation ----
|
|
if (isTRUE(info) && NROW(x) > 10000) {
|
|
message_("Preparing data...", appendLF = FALSE, as_note = FALSE)
|
|
}
|
|
|
|
# Some helper functions ---------------------------------------------------
|
|
get_antibiotic_names <- function(x) {
|
|
x <- x %pm>%
|
|
strsplit(",") %pm>%
|
|
unlist() %pm>%
|
|
trimws2() %pm>%
|
|
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>%
|
|
sort() %pm>%
|
|
paste(collapse = ", ")
|
|
x <- gsub("_", " ", x, fixed = TRUE)
|
|
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
|
x <- gsub("except TGC", paste("except", ab_name("TGC", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
|
x <- gsub("cephalosporins (1st|2nd|3rd|4th|5th)", "cephalosporins (\\1 gen.)", x)
|
|
x
|
|
}
|
|
format_antibiotic_names <- function(ab_names, ab_results) {
|
|
ab_names <- trimws2(unlist(strsplit(ab_names, ",")))
|
|
ab_results <- trimws2(unlist(strsplit(ab_results, ",")))
|
|
if (length(ab_results) == 1) {
|
|
if (length(ab_names) == 1) {
|
|
# like FOX S
|
|
x <- paste(ab_names, "is")
|
|
} else if (length(ab_names) == 2) {
|
|
# like PEN,FOX S
|
|
x <- paste(paste0(ab_names, collapse = " and "), "are both")
|
|
} else {
|
|
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
|
|
# nolint start
|
|
# x <- paste(paste0(ab_names, collapse = " and "), "are all")
|
|
# nolint end
|
|
}
|
|
return(paste0(x, " '", ab_results, "'"))
|
|
} else {
|
|
if (length(ab_names) == 2) {
|
|
# like PEN,FOX S,R
|
|
paste0(
|
|
ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "'"
|
|
)
|
|
} else {
|
|
# like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment)
|
|
paste0(
|
|
ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "' and ",
|
|
ab_names[3], " is '", ab_results[3], "'"
|
|
)
|
|
}
|
|
}
|
|
}
|
|
as.sir_no_warning <- function(x) {
|
|
if (is.sir(x)) {
|
|
return(x)
|
|
}
|
|
suppressWarnings(as.sir(x))
|
|
}
|
|
|
|
# Preparing the data ------------------------------------------------------
|
|
|
|
verbose_info <- data.frame(
|
|
rowid = character(0),
|
|
col = character(0),
|
|
mo_fullname = character(0),
|
|
old = as.sir(character(0)),
|
|
new = as.sir(character(0)),
|
|
rule = character(0),
|
|
rule_group = character(0),
|
|
rule_name = character(0),
|
|
rule_source = character(0),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
|
|
old_cols <- colnames(x)
|
|
old_attributes <- attributes(x)
|
|
x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
|
|
rownames(x) <- NULL # will later be restored with old_attributes
|
|
# create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination)
|
|
x$`.rowid` <- vapply(
|
|
FUN.VALUE = character(1),
|
|
as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]),
|
|
stringsAsFactors = FALSE
|
|
)),
|
|
function(x) {
|
|
x[is.na(x)] <- "."
|
|
paste0(x, collapse = "")
|
|
}
|
|
)
|
|
|
|
# save original table, with the new .rowid column
|
|
x.bak <- x
|
|
# keep only unique rows for MO and ABx
|
|
x <- x %pm>%
|
|
pm_arrange(`.rowid`) %pm>%
|
|
# big speed gain! only analyse unique rows:
|
|
pm_distinct(`.rowid`, .keep_all = TRUE) %pm>%
|
|
as.data.frame(stringsAsFactors = FALSE)
|
|
x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = info)
|
|
# rename col_mo to prevent interference with joined columns
|
|
colnames(x)[colnames(x) == col_mo] <- ".col_mo"
|
|
col_mo <- ".col_mo"
|
|
# join to microorganisms data set
|
|
x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
|
|
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
|
|
x$genus_species <- trimws(paste(x$genus, x$species))
|
|
if (isTRUE(info) && NROW(x) > 10000) {
|
|
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
|
|
}
|
|
|
|
if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
|
|
all_staph <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
|
|
all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
|
|
}
|
|
if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
|
|
all_strep <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Streptococcus"), , drop = FALSE]
|
|
all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
|
|
}
|
|
|
|
n_added <- 0
|
|
n_changed <- 0
|
|
|
|
# Other rules: enzyme inhibitors ------------------------------------------
|
|
if (any(c("all", "other") %in% rules)) {
|
|
if (isTRUE(info)) {
|
|
cat("\n")
|
|
cat(word_wrap(
|
|
font_bold(paste0(
|
|
"Rules by this AMR package (",
|
|
font_red(paste0(
|
|
"v", utils::packageDescription("AMR")$Version, ", ",
|
|
format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y")
|
|
)), "), see ?eucast_rules\n"
|
|
))
|
|
))
|
|
}
|
|
ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
|
|
colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
|
|
ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$enzyme_name)
|
|
ab_enzyme$base_ab <- AMR::antibiotics[match(ab_enzyme$base_name, AMR::antibiotics$name), "ab", drop = TRUE]
|
|
ab_enzyme <- subset(ab_enzyme, !is.na(base_ab))
|
|
# make ampicillin and amoxicillin interchangable
|
|
ampi <- subset(ab_enzyme, base_ab == "AMX")
|
|
ampi$base_ab <- "AMP"
|
|
ampi$base_name <- ab_name("AMP", language = NULL)
|
|
amox <- subset(ab_enzyme, base_ab == "AMP")
|
|
amox$base_ab <- "AMX"
|
|
amox$base_name <- ab_name("AMX", language = NULL)
|
|
# merge and sort
|
|
ab_enzyme <- rbind_AMR(ab_enzyme, ampi, amox)
|
|
ab_enzyme <- ab_enzyme[order(ab_enzyme$enzyme_name), , drop = FALSE]
|
|
|
|
for (i in seq_len(nrow(ab_enzyme))) {
|
|
# check if both base and base + enzyme inhibitor are part of the data set
|
|
if (all(c(ab_enzyme$base_ab[i], ab_enzyme$enzyme_ab[i]) %in% names(cols_ab), na.rm = TRUE)) {
|
|
col_base <- unname(cols_ab[ab_enzyme$base_ab[i]])
|
|
col_enzyme <- unname(cols_ab[ab_enzyme$enzyme_ab[i]])
|
|
|
|
# Set base to R where base + enzyme inhibitor is R ----
|
|
rule_current <- paste0(
|
|
ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
|
|
tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R"
|
|
)
|
|
if (isTRUE(info)) {
|
|
cat(word_wrap(rule_current,
|
|
width = getOption("width") - 30,
|
|
extra_indent = 6
|
|
))
|
|
}
|
|
run_changes <- edit_sir(
|
|
x = x,
|
|
to = "R",
|
|
rule = c(
|
|
rule_current, "Other rules", "",
|
|
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)
|
|
),
|
|
rows = which(as.sir_no_warning(x[, col_enzyme, drop = TRUE]) == "R"),
|
|
cols = col_base,
|
|
last_verbose_info = verbose_info,
|
|
original_data = x.bak,
|
|
warned = warned,
|
|
info = info,
|
|
verbose = verbose
|
|
)
|
|
n_added <- n_added + run_changes$added
|
|
n_changed <- n_changed + run_changes$changed
|
|
verbose_info <- run_changes$verbose_info
|
|
x <- run_changes$output
|
|
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
|
# Print number of new changes
|
|
if (isTRUE(info)) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
|
# and reset counters
|
|
n_added <- 0
|
|
n_changed <- 0
|
|
}
|
|
|
|
# Set base + enzyme inhibitor to S where base is S ----
|
|
rule_current <- paste0(
|
|
ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
|
|
tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S"
|
|
)
|
|
|
|
if (isTRUE(info)) {
|
|
cat(word_wrap(rule_current,
|
|
width = getOption("width") - 30,
|
|
extra_indent = 6
|
|
))
|
|
}
|
|
run_changes <- edit_sir(
|
|
x = x,
|
|
to = "S",
|
|
rule = c(
|
|
rule_current, "Other rules", "",
|
|
paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)
|
|
),
|
|
rows = which(as.sir_no_warning(x[, col_base, drop = TRUE]) == "S"),
|
|
cols = col_enzyme,
|
|
last_verbose_info = verbose_info,
|
|
original_data = x.bak,
|
|
warned = warned,
|
|
info = info,
|
|
verbose = verbose
|
|
)
|
|
n_added <- n_added + run_changes$added
|
|
n_changed <- n_changed + run_changes$changed
|
|
verbose_info <- run_changes$verbose_info
|
|
x <- run_changes$output
|
|
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
|
# Print number of new changes
|
|
if (isTRUE(info)) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
|
# and reset counters
|
|
n_added <- 0
|
|
n_changed <- 0
|
|
}
|
|
}
|
|
}
|
|
} else {
|
|
if (isTRUE(info)) {
|
|
cat("\n")
|
|
message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
|
|
}
|
|
}
|
|
|
|
if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) {
|
|
if (isTRUE(info)) {
|
|
message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
|
|
}
|
|
custom_rules <- NULL
|
|
}
|
|
|
|
# Official EUCAST rules ---------------------------------------------------
|
|
eucast_notification_shown <- FALSE
|
|
if (!is.null(list(...)$eucast_rules_df)) {
|
|
# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
|
|
eucast_rules_df <- list(...)$eucast_rules_df
|
|
} else {
|
|
# otherwise internal data file, created in data-raw/_pre_commit_checks.R
|
|
eucast_rules_df <- EUCAST_RULES_DF
|
|
}
|
|
|
|
# filter on user-set guideline versions ----
|
|
if (any(c("all", "breakpoints") %in% rules)) {
|
|
eucast_rules_df <- subset(
|
|
eucast_rules_df,
|
|
reference.rule_group %unlike% "breakpoint" |
|
|
(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
|
|
)
|
|
}
|
|
if (any(c("all", "expert") %in% rules)) {
|
|
eucast_rules_df <- subset(
|
|
eucast_rules_df,
|
|
reference.rule_group %unlike% "expert" |
|
|
(reference.rule_group %like% "expert" & reference.version == version_expertrules)
|
|
)
|
|
}
|
|
# filter out AmpC de-repressed cephalosporin-resistant mutants ----
|
|
# no need to filter on version number here - the rules contain these version number, so are inherently filtered
|
|
# cefotaxime, ceftriaxone, ceftazidime
|
|
if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
|
|
eucast_rules_df <- subset(
|
|
eucast_rules_df,
|
|
reference.rule %unlike% "ampc"
|
|
)
|
|
} else {
|
|
if (isTRUE(ampc_cephalosporin_resistance)) {
|
|
ampc_cephalosporin_resistance <- "R"
|
|
}
|
|
eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
|
|
}
|
|
|
|
# Go over all rules and apply them ----
|
|
for (i in seq_len(nrow(eucast_rules_df))) {
|
|
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
|
|
rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE]
|
|
rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE]
|
|
rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE]
|
|
rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE]
|
|
# don't apply rules if user doesn't want to apply them
|
|
if (rule_group_current %like% "breakpoint" && !any(c("all", "breakpoints") %in% rules)) {
|
|
next
|
|
}
|
|
if (rule_group_current %like% "expert" && !any(c("all", "expert") %in% rules)) {
|
|
next
|
|
}
|
|
|
|
if (isFALSE(info) || isFALSE(verbose)) {
|
|
rule_text <- ""
|
|
} else {
|
|
if (is.na(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE])) {
|
|
rule_text <- paste0("always report as '", eucast_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]))
|
|
} else {
|
|
rule_text <- paste0(
|
|
"report as '", eucast_rules_df[i, "to_value", drop = TRUE], "' when ",
|
|
format_antibiotic_names(
|
|
ab_names = get_antibiotic_names(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]),
|
|
ab_results = eucast_rules_df[i, "have_these_values", drop = TRUE]
|
|
), ": ",
|
|
get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])
|
|
)
|
|
}
|
|
}
|
|
if (i == 1) {
|
|
rule_previous <- ""
|
|
rule_group_previous <- ""
|
|
}
|
|
if (i == nrow(eucast_rules_df)) {
|
|
rule_next <- ""
|
|
}
|
|
|
|
if (isTRUE(info)) {
|
|
# Print EUCAST intro ------------------------------------------------------
|
|
if (rule_group_current %unlike% "other" && eucast_notification_shown == FALSE) {
|
|
cat(
|
|
paste0(
|
|
"\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n",
|
|
word_wrap("Rules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)")), "\n",
|
|
font_blue("https://eucast.org/"), "\n"
|
|
)
|
|
)
|
|
eucast_notification_shown <- TRUE
|
|
}
|
|
|
|
# Print rule (group) ------------------------------------------------------
|
|
if (rule_group_current != rule_group_previous) {
|
|
# is new rule group, one of Breakpoints, Expert Rules and Other
|
|
cat(font_bold(
|
|
ifelse(
|
|
rule_group_current %like% "breakpoint",
|
|
paste0(
|
|
"\n",
|
|
word_wrap(
|
|
breakpoints_info$title, " (",
|
|
font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n"
|
|
)
|
|
),
|
|
ifelse(
|
|
rule_group_current %like% "expert",
|
|
paste0(
|
|
"\n",
|
|
word_wrap(
|
|
expertrules_info$title, " (",
|
|
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"
|
|
)
|
|
),
|
|
""
|
|
)
|
|
)
|
|
), "\n")
|
|
}
|
|
# Print rule -------------------------------------------------------------
|
|
if (rule_current != rule_previous) {
|
|
# is new rule within group, print its name
|
|
cat(italicise_taxonomy(
|
|
word_wrap(rule_current,
|
|
width = getOption("width") - 30,
|
|
extra_indent = 6
|
|
),
|
|
type = "ansi"
|
|
))
|
|
warned <- FALSE
|
|
}
|
|
}
|
|
|
|
# Get rule from file ------------------------------------------------------
|
|
if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE])
|
|
like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE])
|
|
mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE])
|
|
|
|
# be sure to comprise all coagulase-negative/-positive staphylococci when they are mentioned
|
|
if (mo_value %like% "coagulase" && any(x$genus == "Staphylococcus", na.rm = TRUE)) {
|
|
if (mo_value %like% "negative") {
|
|
eucast_rules_df[i, "this_value"] <- paste0(
|
|
"^(", paste0(
|
|
all_staph[which(all_staph$CNS_CPS %like% "negative"),
|
|
"fullname",
|
|
drop = TRUE
|
|
],
|
|
collapse = "|"
|
|
),
|
|
")$"
|
|
)
|
|
} else {
|
|
eucast_rules_df[i, "this_value"] <- paste0(
|
|
"^(", paste0(
|
|
all_staph[which(all_staph$CNS_CPS %like% "positive"),
|
|
"fullname",
|
|
drop = TRUE
|
|
],
|
|
collapse = "|"
|
|
),
|
|
")$"
|
|
)
|
|
}
|
|
like_is_one_of <- "like"
|
|
}
|
|
# be sure to comprise all beta-haemolytic Streptococci (Lancefield groups A, B, C and G) when they are mentioned
|
|
if (mo_value %like% "group [ABCG]" && any(x$genus == "Streptococcus", na.rm = TRUE)) {
|
|
eucast_rules_df[i, "this_value"] <- paste0(
|
|
"^(", paste0(
|
|
all_strep[which(all_strep$Lancefield %like% "group [ABCG]"),
|
|
"fullname",
|
|
drop = TRUE
|
|
],
|
|
collapse = "|"
|
|
),
|
|
")$"
|
|
)
|
|
like_is_one_of <- "like"
|
|
}
|
|
|
|
if (like_is_one_of == "is") {
|
|
# so e.g. 'Enterococcus' will turn into '^Enterococcus$'
|
|
mo_value <- paste0("^", mo_value, "$")
|
|
} else if (like_is_one_of == "one_of") {
|
|
# so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$'
|
|
mo_value <- paste0(
|
|
"^(",
|
|
paste(trimws(unlist(strsplit(mo_value, ",", fixed = TRUE))),
|
|
collapse = "|"
|
|
),
|
|
")$"
|
|
)
|
|
} else if (like_is_one_of != "like") {
|
|
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
|
|
}
|
|
|
|
source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]
|
|
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
|
|
target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
|
|
target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
|
|
|
|
if (is.na(source_antibiotics)) {
|
|
rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
|
|
error = function(e) integer(0)
|
|
)
|
|
} else {
|
|
source_antibiotics <- get_ab_from_namespace(source_antibiotics, cols_ab)
|
|
if (length(source_value) == 1 && length(source_antibiotics) > 1) {
|
|
source_value <- rep(source_value, length(source_antibiotics))
|
|
}
|
|
if (length(source_antibiotics) == 0) {
|
|
rows <- integer(0)
|
|
} else if (length(source_antibiotics) == 1) {
|
|
rows <- tryCatch(
|
|
which(x[, if_mo_property, drop = TRUE] %like% mo_value &
|
|
as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
|
|
error = function(e) integer(0)
|
|
)
|
|
} else if (length(source_antibiotics) == 2) {
|
|
rows <- tryCatch(
|
|
which(x[, if_mo_property, drop = TRUE] %like% mo_value &
|
|
as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L] &
|
|
as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
|
error = function(e) integer(0)
|
|
)
|
|
# nolint start
|
|
# } else if (length(source_antibiotics) == 3) {
|
|
# rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
|
# & as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
|
# & as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
|
|
# & as.sir_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
|
|
# error = function(e) integer(0))
|
|
# nolint end
|
|
} else {
|
|
stop_("only 2 antibiotics supported for source_antibiotics")
|
|
}
|
|
}
|
|
|
|
cols <- get_ab_from_namespace(target_antibiotics, cols_ab)
|
|
|
|
# Apply rule on data ------------------------------------------------------
|
|
# this will return the unique number of changes
|
|
run_changes <- edit_sir(
|
|
x = x,
|
|
to = target_value,
|
|
rule = c(
|
|
rule_text, rule_group_current, rule_current,
|
|
ifelse(rule_group_current %like% "breakpoint",
|
|
paste0(breakpoints_info$title, " ", breakpoints_info$version_txt, ", ", breakpoints_info$year),
|
|
paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year)
|
|
)
|
|
),
|
|
rows = rows,
|
|
cols = cols,
|
|
last_verbose_info = verbose_info,
|
|
original_data = x.bak,
|
|
warned = warned,
|
|
info = info,
|
|
verbose = verbose
|
|
)
|
|
n_added <- n_added + run_changes$added
|
|
n_changed <- n_changed + run_changes$changed
|
|
verbose_info <- run_changes$verbose_info
|
|
x <- run_changes$output
|
|
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
|
# Print number of new changes ---------------------------------------------
|
|
if (isTRUE(info) && rule_next != rule_current) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
|
# and reset counters
|
|
n_added <- 0
|
|
n_changed <- 0
|
|
}
|
|
} # end of going over all rules
|
|
|
|
# Apply custom rules ----
|
|
if (!is.null(custom_rules)) {
|
|
if (isTRUE(info)) {
|
|
cat("\n")
|
|
cat(font_bold("Custom EUCAST rules, set by user"), "\n")
|
|
}
|
|
for (i in seq_len(length(custom_rules))) {
|
|
rule <- custom_rules[[i]]
|
|
rows <- which(eval(parse(text = rule$query), envir = x))
|
|
cols <- as.character(rule$result_group)
|
|
cols <- c(
|
|
cols[cols %in% colnames(x)], # direct column names
|
|
unname(cols_ab[names(cols_ab) %in% cols])
|
|
) # based on previous cols_ab finding
|
|
cols <- unique(cols)
|
|
target_value <- as.character(rule$result_value)
|
|
rule_text <- paste0(
|
|
"report as '", target_value, "' when ",
|
|
format_custom_query_rule(rule$query, colours = FALSE), ": ",
|
|
get_antibiotic_names(cols)
|
|
)
|
|
if (isTRUE(info)) {
|
|
# print rule
|
|
cat(italicise_taxonomy(
|
|
word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
|
|
width = getOption("width") - 30,
|
|
extra_indent = 6
|
|
),
|
|
type = "ansi"
|
|
))
|
|
warned <- FALSE
|
|
}
|
|
run_changes <- edit_sir(
|
|
x = x,
|
|
to = target_value,
|
|
rule = c(
|
|
rule_text,
|
|
"Custom EUCAST rules",
|
|
paste0("Custom EUCAST rule ", i),
|
|
paste0(
|
|
"Object '", deparse(substitute(custom_rules)),
|
|
"' consisting of ", length(custom_rules), " custom rules"
|
|
)
|
|
),
|
|
rows = rows,
|
|
cols = cols,
|
|
last_verbose_info = verbose_info,
|
|
original_data = x.bak,
|
|
warned = warned,
|
|
info = info,
|
|
verbose = verbose
|
|
)
|
|
n_added <- n_added + run_changes$added
|
|
n_changed <- n_changed + run_changes$changed
|
|
verbose_info <- run_changes$verbose_info
|
|
x <- run_changes$output
|
|
warn_lacking_sir_class <- c(warn_lacking_sir_class, run_changes$sir_warn)
|
|
# Print number of new changes ---------------------------------------------
|
|
if (isTRUE(info) && rule_next != rule_current) {
|
|
# print only on last one of rules in this group
|
|
txt_ok(n_added = n_added, n_changed = n_changed, warned = warned)
|
|
# and reset counters
|
|
n_added <- 0
|
|
n_changed <- 0
|
|
}
|
|
}
|
|
}
|
|
|
|
# Print overview ----------------------------------------------------------
|
|
if (isTRUE(info) || isTRUE(verbose)) {
|
|
verbose_info <- x.bak %pm>%
|
|
pm_mutate(row = pm_row_number()) %pm>%
|
|
pm_select(`.rowid`, row) %pm>%
|
|
pm_right_join(verbose_info,
|
|
by = c(".rowid" = "rowid")
|
|
) %pm>%
|
|
pm_select(-`.rowid`) %pm>%
|
|
pm_select(row, pm_everything()) %pm>%
|
|
pm_filter(!is.na(new) | is.na(new) & !is.na(old)) %pm>%
|
|
pm_arrange(row, rule_group, rule_name, col)
|
|
rownames(verbose_info) <- NULL
|
|
}
|
|
|
|
if (isTRUE(info)) {
|
|
if (isTRUE(verbose)) {
|
|
wouldve <- "would have "
|
|
} else {
|
|
wouldve <- ""
|
|
}
|
|
|
|
cat(paste0("\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
|
|
cat(word_wrap(paste0(
|
|
"The rules ", paste0(wouldve, "affected "),
|
|
font_bold(
|
|
formatnr(pm_n_distinct(verbose_info$row)),
|
|
"out of", formatnr(nrow(x.bak)),
|
|
"rows"
|
|
),
|
|
", making a total of ",
|
|
font_bold(formatnr(nrow(verbose_info)), "edits\n")
|
|
)))
|
|
|
|
total_n_added <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow()
|
|
total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow()
|
|
|
|
# print added values
|
|
if (total_n_added == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- font_green # is function
|
|
}
|
|
cat(colour(paste0(
|
|
"=> ", wouldve, "added ",
|
|
font_bold(formatnr(verbose_info %pm>%
|
|
pm_filter(is.na(old)) %pm>%
|
|
nrow()), "test results"),
|
|
"\n"
|
|
)))
|
|
if (total_n_added > 0) {
|
|
added_summary <- verbose_info %pm>%
|
|
pm_filter(is.na(old)) %pm>%
|
|
pm_count(new, name = "n")
|
|
cat(paste(" -",
|
|
paste0(
|
|
formatnr(added_summary$n), " test result", ifelse(added_summary$n > 1, "s", ""),
|
|
" added as ", paste0('"', added_summary$new, '"')
|
|
),
|
|
collapse = "\n"
|
|
))
|
|
}
|
|
|
|
# print changed values
|
|
if (total_n_changed == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- font_blue # is function
|
|
}
|
|
if (total_n_added + total_n_changed > 0) {
|
|
cat("\n")
|
|
}
|
|
cat(colour(paste0(
|
|
"=> ", wouldve, "changed ",
|
|
font_bold(formatnr(verbose_info %pm>%
|
|
pm_filter(!is.na(old)) %pm>%
|
|
nrow()), "test results"),
|
|
"\n"
|
|
)))
|
|
if (total_n_changed > 0) {
|
|
changed_summary <- verbose_info %pm>%
|
|
pm_filter(!is.na(old)) %pm>%
|
|
pm_mutate(new = ifelse(is.na(new), "NA", new)) %pm>%
|
|
pm_count(old, new, name = "n")
|
|
cat(paste(" -",
|
|
paste0(
|
|
formatnr(changed_summary$n), " test result", ifelse(changed_summary$n > 1, "s", ""), " changed from ",
|
|
paste0('"', changed_summary$old, '"'), " to ", paste0('"', changed_summary$new, '"')
|
|
),
|
|
collapse = "\n"
|
|
))
|
|
cat("\n")
|
|
}
|
|
|
|
cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
|
|
|
|
if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
|
|
cat("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
|
|
} else if (isTRUE(verbose)) {
|
|
cat("\n", word_wrap("Used 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data."), "\n\n", sep = "")
|
|
}
|
|
}
|
|
|
|
if (length(warn_lacking_sir_class) > 0) {
|
|
warn_lacking_sir_class <- unique(warn_lacking_sir_class)
|
|
# take order from original data set
|
|
warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
|
|
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
|
|
warning_(
|
|
"in `eucast_rules()`: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
|
|
" - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
|
|
warn_lacking_sir_class,
|
|
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
|
|
), ")\n",
|
|
" - ", x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)\n",
|
|
" - ", x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"
|
|
)
|
|
}
|
|
|
|
# Return data set ---------------------------------------------------------
|
|
if (isTRUE(verbose)) {
|
|
as_original_data_class(verbose_info, old_attributes$class) # will remove tibble groups
|
|
} else {
|
|
# x was analysed with only unique rows, so join everything together again
|
|
x <- x[, c(cols_ab, ".rowid"), drop = FALSE]
|
|
x.bak <- x.bak[, setdiff(colnames(x.bak), cols_ab), drop = FALSE]
|
|
x.bak <- x.bak %pm>%
|
|
pm_left_join(x, by = ".rowid")
|
|
x.bak <- x.bak[, old_cols, drop = FALSE]
|
|
# reset original attributes
|
|
attributes(x.bak) <- old_attributes
|
|
x.bak <- as_original_data_class(x.bak, old_class = class(x.bak)) # will remove tibble groups
|
|
x.bak
|
|
}
|
|
}
|
|
|
|
# helper function for editing the table ----
|
|
edit_sir <- function(x,
|
|
to,
|
|
rule,
|
|
rows,
|
|
cols,
|
|
last_verbose_info,
|
|
original_data,
|
|
warned,
|
|
info,
|
|
verbose) {
|
|
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
|
|
|
# for Verbose Mode, keep track of all changes and return them
|
|
track_changes <- list(
|
|
added = 0,
|
|
changed = 0,
|
|
output = x,
|
|
verbose_info = last_verbose_info,
|
|
sir_warn = character(0)
|
|
)
|
|
|
|
txt_error <- function() {
|
|
if (isTRUE(info)) cat("", font_red_bg(" ERROR "), "\n\n")
|
|
}
|
|
txt_warning <- function() {
|
|
if (warned == FALSE) {
|
|
if (isTRUE(info)) cat(" ", font_orange_bg(" WARNING "), sep = "")
|
|
}
|
|
warned <<- TRUE
|
|
}
|
|
|
|
if (length(rows) > 0 && length(cols) > 0) {
|
|
new_edits <- x
|
|
if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
|
|
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
|
|
}
|
|
tryCatch(
|
|
# insert into original table
|
|
new_edits[rows, cols] <- to,
|
|
warning = function(w) {
|
|
if (w$message %like% "invalid factor level") {
|
|
xyz <- vapply(FUN.VALUE = logical(1), cols, function(col) {
|
|
new_edits[, col] <<- factor(
|
|
x = as.character(pm_pull(new_edits, col)),
|
|
levels = unique(c(to, levels(pm_pull(new_edits, col))))
|
|
)
|
|
TRUE
|
|
})
|
|
suppressWarnings(new_edits[rows, cols] <<- to)
|
|
warning_(
|
|
"in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
|
|
ifelse(length(cols) == 1, "", "s"),
|
|
" ", vector_and(cols, quotes = "`", sort = FALSE),
|
|
" because this value was not an existing factor level."
|
|
)
|
|
txt_warning()
|
|
warned <- FALSE
|
|
} else {
|
|
warning_("in `eucast_rules()`: ", w$message)
|
|
txt_warning()
|
|
}
|
|
},
|
|
error = function(e) {
|
|
txt_error()
|
|
stop(
|
|
paste0(
|
|
"In row(s) ", paste(rows[seq_len(min(length(rows), 10))], collapse = ","),
|
|
ifelse(length(rows) > 10, "...", ""),
|
|
" while writing value '", to,
|
|
"' to column(s) `", paste(cols, collapse = "`, `"),
|
|
"`:\n", e$message
|
|
),
|
|
call. = FALSE
|
|
)
|
|
}
|
|
)
|
|
|
|
track_changes$output <- new_edits
|
|
if ((isTRUE(info) || isTRUE(verbose)) && !isTRUE(all.equal(x, track_changes$output))) {
|
|
get_original_rows <- function(rowids) {
|
|
as.integer(rownames(original_data[which(original_data$.rowid %in% rowids), , drop = FALSE]))
|
|
}
|
|
for (i in seq_len(length(cols))) {
|
|
verbose_new <- data.frame(
|
|
rowid = new_edits[rows, ".rowid", drop = TRUE],
|
|
col = cols[i],
|
|
mo_fullname = new_edits[rows, "fullname", drop = TRUE],
|
|
old = x[rows, cols[i], drop = TRUE],
|
|
new = to,
|
|
rule = font_stripstyle(rule[1]),
|
|
rule_group = font_stripstyle(rule[2]),
|
|
rule_name = font_stripstyle(rule[3]),
|
|
rule_source = font_stripstyle(rule[4]),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
colnames(verbose_new) <- c(
|
|
"rowid", "col", "mo_fullname", "old", "new",
|
|
"rule", "rule_group", "rule_name", "rule_source"
|
|
)
|
|
verbose_new <- verbose_new %pm>% pm_filter(old != new | is.na(old) | is.na(new) & !is.na(old))
|
|
# save changes to data set 'verbose_info'
|
|
track_changes$verbose_info <- rbind_AMR(
|
|
track_changes$verbose_info,
|
|
verbose_new
|
|
)
|
|
# count adds and changes
|
|
track_changes$added <- track_changes$added + verbose_new %pm>%
|
|
pm_filter(is.na(old)) %pm>%
|
|
pm_pull(rowid) %pm>%
|
|
get_original_rows() %pm>%
|
|
length()
|
|
track_changes$changed <- track_changes$changed + verbose_new %pm>%
|
|
pm_filter(!is.na(old)) %pm>%
|
|
pm_pull(rowid) %pm>%
|
|
get_original_rows() %pm>%
|
|
length()
|
|
}
|
|
}
|
|
}
|
|
return(track_changes)
|
|
}
|
|
|
|
#' @rdname eucast_rules
|
|
#' @export
|
|
eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 12.0) {
|
|
meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor"))
|
|
meet_criteria(administration, allow_class = "character", is_in = dosage$administration[!is.na(dosage$administration)], has_length = 1)
|
|
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
|
|
|
|
# show used version_breakpoints number once per session (AMR_env will reload every session)
|
|
if (message_not_thrown_before("eucast_dosage", "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
|
|
message_(
|
|
"Dosages for antimicrobial drugs, as meant for ",
|
|
format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
|
|
font_red("This note will be shown once per session.")
|
|
)
|
|
}
|
|
|
|
ab <- as.ab(ab)
|
|
lst <- vector("list", length = length(ab))
|
|
for (i in seq_len(length(ab))) {
|
|
df <- AMR::dosage[which(AMR::dosage$ab == ab[i] & AMR::dosage$administration == administration), , drop = FALSE]
|
|
lst[[i]] <- list(
|
|
ab = "",
|
|
name = "",
|
|
standard_dosage = ifelse("standard_dosage" %in% df$type,
|
|
df[which(df$type == "standard_dosage"), "original_txt", drop = TRUE],
|
|
NA_character_
|
|
),
|
|
high_dosage = ifelse("high_dosage" %in% df$type,
|
|
df[which(df$type == "high_dosage"), "original_txt", drop = TRUE],
|
|
NA_character_
|
|
)
|
|
)
|
|
}
|
|
out <- do.call(rbind_AMR, lapply(lst, as.data.frame, stringsAsFactors = FALSE))
|
|
rownames(out) <- NULL
|
|
out$ab <- ab
|
|
out$name <- ab_name(ab, language = NULL)
|
|
if (pkg_is_available("tibble")) {
|
|
import_fn("as_tibble", "tibble")(out)
|
|
} else {
|
|
out
|
|
}
|
|
}
|