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AMR/R/eucast_rules.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# global variables
EUCAST_VERSION_BREAKPOINTS <- "10.0, 2020"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' Apply EUCAST rules
#'
#' @description
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
#'
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
#' @inheritSection lifecycle Maturing lifecycle
#' @param x data with antibiotic columns, like e.g. `AMX` and `AMC`
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using e.g. `options(AMR.eucast_rules = "all")`.
#' @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.
#' @param ... column name of an antibiotic, please see section *Antibiotics* below
#' @inheritParams first_isolate
#' @details
#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] 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.
#'
#' Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:
#' - Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
#' - Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
#' - Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;
#' - Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;
#' - Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;
#' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
#' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
#' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
#'
#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
#'
#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
#'
#' @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 used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format '**antimicrobial ID**: name ([ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted by name:
#'
#' **AMK**: amikacin ([J01GB06](https://www.whocc.no/atc_ddd_index/?code=J01GB06)),
#' **AMX**: amoxicillin ([J01CA04](https://www.whocc.no/atc_ddd_index/?code=J01CA04)),
#' **AMC**: amoxicillin/clavulanic acid ([J01CR02](https://www.whocc.no/atc_ddd_index/?code=J01CR02)),
#' **AMP**: ampicillin ([J01CA01](https://www.whocc.no/atc_ddd_index/?code=J01CA01)),
#' **SAM**: ampicillin/sulbactam ([J01CR01](https://www.whocc.no/atc_ddd_index/?code=J01CR01)),
#' **AZM**: azithromycin ([J01FA10](https://www.whocc.no/atc_ddd_index/?code=J01FA10)),
#' **AZL**: azlocillin ([J01CA09](https://www.whocc.no/atc_ddd_index/?code=J01CA09)),
#' **ATM**: aztreonam ([J01DF01](https://www.whocc.no/atc_ddd_index/?code=J01DF01)),
#' **CAP**: capreomycin ([J04AB30](https://www.whocc.no/atc_ddd_index/?code=J04AB30)),
#' **RID**: cefaloridine ([J01DB02](https://www.whocc.no/atc_ddd_index/?code=J01DB02)),
#' **CZO**: cefazolin ([J01DB04](https://www.whocc.no/atc_ddd_index/?code=J01DB04)),
#' **FEP**: cefepime ([J01DE01](https://www.whocc.no/atc_ddd_index/?code=J01DE01)),
#' **CTX**: cefotaxime ([J01DD01](https://www.whocc.no/atc_ddd_index/?code=J01DD01)),
#' **CTT**: cefotetan ([J01DC05](https://www.whocc.no/atc_ddd_index/?code=J01DC05)),
#' **FOX**: cefoxitin ([J01DC01](https://www.whocc.no/atc_ddd_index/?code=J01DC01)),
#' **CPT**: ceftaroline ([J01DI02](https://www.whocc.no/atc_ddd_index/?code=J01DI02)),
#' **CAZ**: ceftazidime ([J01DD02](https://www.whocc.no/atc_ddd_index/?code=J01DD02)),
#' **CRO**: ceftriaxone ([J01DD04](https://www.whocc.no/atc_ddd_index/?code=J01DD04)),
#' **CXM**: cefuroxime ([J01DC02](https://www.whocc.no/atc_ddd_index/?code=J01DC02)),
#' **CED**: cephradine ([J01DB09](https://www.whocc.no/atc_ddd_index/?code=J01DB09)),
#' **CHL**: chloramphenicol ([J01BA01](https://www.whocc.no/atc_ddd_index/?code=J01BA01)),
#' **CIP**: ciprofloxacin ([J01MA02](https://www.whocc.no/atc_ddd_index/?code=J01MA02)),
#' **CLR**: clarithromycin ([J01FA09](https://www.whocc.no/atc_ddd_index/?code=J01FA09)),
#' **CLI**: clindamycin ([J01FF01](https://www.whocc.no/atc_ddd_index/?code=J01FF01)),
#' **COL**: colistin ([J01XB01](https://www.whocc.no/atc_ddd_index/?code=J01XB01)),
#' **DAP**: daptomycin ([J01XX09](https://www.whocc.no/atc_ddd_index/?code=J01XX09)),
#' **DOR**: doripenem ([J01DH04](https://www.whocc.no/atc_ddd_index/?code=J01DH04)),
#' **DOX**: doxycycline ([J01AA02](https://www.whocc.no/atc_ddd_index/?code=J01AA02)),
#' **ETP**: ertapenem ([J01DH03](https://www.whocc.no/atc_ddd_index/?code=J01DH03)),
#' **ERY**: erythromycin ([J01FA01](https://www.whocc.no/atc_ddd_index/?code=J01FA01)),
#' **ETH**: ethambutol ([J04AK02](https://www.whocc.no/atc_ddd_index/?code=J04AK02)),
#' **FLC**: flucloxacillin ([J01CF05](https://www.whocc.no/atc_ddd_index/?code=J01CF05)),
#' **FOS**: fosfomycin ([J01XX01](https://www.whocc.no/atc_ddd_index/?code=J01XX01)),
#' **FUS**: fusidic acid ([J01XC01](https://www.whocc.no/atc_ddd_index/?code=J01XC01)),
#' **GAT**: gatifloxacin ([J01MA16](https://www.whocc.no/atc_ddd_index/?code=J01MA16)),
#' **GEN**: gentamicin ([J01GB03](https://www.whocc.no/atc_ddd_index/?code=J01GB03)),
#' **GEH**: gentamicin-high (no ATC code),
#' **IPM**: imipenem ([J01DH51](https://www.whocc.no/atc_ddd_index/?code=J01DH51)),
#' **INH**: isoniazid ([J04AC01](https://www.whocc.no/atc_ddd_index/?code=J04AC01)),
#' **KAN**: kanamycin ([J01GB04](https://www.whocc.no/atc_ddd_index/?code=J01GB04)),
#' **LVX**: levofloxacin ([J01MA12](https://www.whocc.no/atc_ddd_index/?code=J01MA12)),
#' **LIN**: lincomycin ([J01FF02](https://www.whocc.no/atc_ddd_index/?code=J01FF02)),
#' **LNZ**: linezolid ([J01XX08](https://www.whocc.no/atc_ddd_index/?code=J01XX08)),
#' **MEM**: meropenem ([J01DH02](https://www.whocc.no/atc_ddd_index/?code=J01DH02)),
#' **MTR**: metronidazole ([J01XD01](https://www.whocc.no/atc_ddd_index/?code=J01XD01)),
#' **MEZ**: mezlocillin ([J01CA10](https://www.whocc.no/atc_ddd_index/?code=J01CA10)),
#' **MNO**: minocycline ([J01AA08](https://www.whocc.no/atc_ddd_index/?code=J01AA08)),
#' **MFX**: moxifloxacin ([J01MA14](https://www.whocc.no/atc_ddd_index/?code=J01MA14)),
#' **NAL**: nalidixic acid ([J01MB02](https://www.whocc.no/atc_ddd_index/?code=J01MB02)),
#' **NEO**: neomycin ([J01GB05](https://www.whocc.no/atc_ddd_index/?code=J01GB05)),
#' **NET**: netilmicin ([J01GB07](https://www.whocc.no/atc_ddd_index/?code=J01GB07)),
#' **NIT**: nitrofurantoin ([J01XE01](https://www.whocc.no/atc_ddd_index/?code=J01XE01)),
#' **NOR**: norfloxacin ([J01MA06](https://www.whocc.no/atc_ddd_index/?code=J01MA06)),
#' **NOV**: novobiocin ([QJ01XX95](https://www.whocc.no/atc_ddd_index/?code=QJ01XX95)),
#' **OFX**: ofloxacin ([J01MA01](https://www.whocc.no/atc_ddd_index/?code=J01MA01)),
#' **OXA**: oxacillin ([J01CF04](https://www.whocc.no/atc_ddd_index/?code=J01CF04)),
#' **PEN**: penicillin G ([J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01)),
#' **PIP**: piperacillin ([J01CA12](https://www.whocc.no/atc_ddd_index/?code=J01CA12)),
#' **TZP**: piperacillin/tazobactam ([J01CR05](https://www.whocc.no/atc_ddd_index/?code=J01CR05)),
#' **PLB**: polymyxin B ([J01XB02](https://www.whocc.no/atc_ddd_index/?code=J01XB02)),
#' **PRI**: pristinamycin ([J01FG01](https://www.whocc.no/atc_ddd_index/?code=J01FG01)),
#' **PZA**: pyrazinamide ([J04AK01](https://www.whocc.no/atc_ddd_index/?code=J04AK01)),
#' **QDA**: quinupristin/dalfopristin ([J01FG02](https://www.whocc.no/atc_ddd_index/?code=J01FG02)),
#' **RIB**: rifabutin ([J04AB04](https://www.whocc.no/atc_ddd_index/?code=J04AB04)),
#' **RIF**: rifampicin ([J04AB02](https://www.whocc.no/atc_ddd_index/?code=J04AB02)),
#' **RFP**: rifapentine ([J04AB05](https://www.whocc.no/atc_ddd_index/?code=J04AB05)),
#' **RXT**: roxithromycin ([J01FA06](https://www.whocc.no/atc_ddd_index/?code=J01FA06)),
#' **SIS**: sisomicin ([J01GB08](https://www.whocc.no/atc_ddd_index/?code=J01GB08)),
#' **STH**: streptomycin-high (no ATC code),
#' **TEC**: teicoplanin ([J01XA02](https://www.whocc.no/atc_ddd_index/?code=J01XA02)),
#' **TLV**: telavancin ([J01XA03](https://www.whocc.no/atc_ddd_index/?code=J01XA03)),
#' **TCY**: tetracycline ([J01AA07](https://www.whocc.no/atc_ddd_index/?code=J01AA07)),
#' **TIC**: ticarcillin ([J01CA13](https://www.whocc.no/atc_ddd_index/?code=J01CA13)),
#' **TCC**: ticarcillin/clavulanic acid ([J01CR03](https://www.whocc.no/atc_ddd_index/?code=J01CR03)),
#' **TGC**: tigecycline ([J01AA12](https://www.whocc.no/atc_ddd_index/?code=J01AA12)),
#' **TOB**: tobramycin ([J01GB01](https://www.whocc.no/atc_ddd_index/?code=J01GB01)),
#' **TMP**: trimethoprim ([J01EA01](https://www.whocc.no/atc_ddd_index/?code=J01EA01)),
#' **SXT**: trimethoprim/sulfamethoxazole ([J01EE01](https://www.whocc.no/atc_ddd_index/?code=J01EE01)),
#' **VAN**: vancomycin ([J01XA01](https://www.whocc.no/atc_ddd_index/?code=J01XA01)).
#' @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. \cr
#' <https://doi.org/10.1111/j.1469-0691.2011.03703.x>
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf>
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx>
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @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", # Penicillin G
#' FOX = "S", # Cefoxitin
#' stringsAsFactors = FALSE)
#'
#' a
#' # mo VAN AMX COL CAZ CXM PEN FOX
#' # 1 Staphylococcus aureus - - - - - S S
#' # 2 Enterococcus faecalis - - - - - S S
#' # 3 Escherichia coli - - - - - S S
#' # 4 Klebsiella pneumoniae - - - - - S S
#' # 5 Pseudomonas aeruginosa - - - - - S S
#'
#'
#' # apply EUCAST rules: 18 results are forced as R or S
#' b <- eucast_rules(a)
#'
#' b
#' # mo VAN AMX COL CAZ CXM PEN FOX
#' # 1 Staphylococcus aureus - S R R S S S
#' # 2 Enterococcus faecalis - - R R R S R
#' # 3 Escherichia coli R - - - - R S
#' # 4 Klebsiella pneumoniae R R - - - R S
#' # 5 Pseudomonas aeruginosa R R - - R R R
#'
#'
#' # do not apply EUCAST rules, but rather get a data.frame
#' # with 18 rows, containing all details about the transformations:
#' c <- eucast_rules(a, verbose = TRUE)
#' }
eucast_rules <- function(x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR.eucast_rules", default = c("breakpoints", "expert")),
verbose = FALSE,
...) {
check_dataset_integrity()
if (verbose == TRUE & interactive()) {
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?")
if ("rstudioapi" %in% rownames(utils::installed.packages())) {
showQuestion <- import_fn("showQuestion", "rstudioapi")
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")
return(x)
}
}
stop_ifnot(is.data.frame(x), "`x` must be a data frame")
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
}
stop_if(is.null(col_mo), "`col_mo` must be set")
stop_ifnot(all(rules %in% c("breakpoints", "expert", "other", "all")),
'`rules` must be one or more of: "breakpoints", "expert", "other", "all".')
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_rsi_class <- FALSE
txt_error <- function() {
if (info == TRUE) cat("", font_red_bg(font_white(" ERROR ")), "\n\n")
}
txt_warning <- function() {
if (warned == FALSE) {
if (info == TRUE) cat("", font_yellow_bg(font_black(" WARNING ")))
}
warned <<- TRUE
}
txt_ok <- function(no_added, no_changed) {
if (warned == FALSE) {
if (no_added + no_changed == 0) {
cat(font_subtle(" (no changes)\n"))
} else {
# opening
cat(font_grey(" ("))
# additions
if (no_added > 0) {
if (no_added == 1) {
cat(font_green("1 value added"))
} else {
cat(font_green(formatnr(no_added), "values added"))
}
}
# separator
if (no_added > 0 & no_changed > 0) {
cat(font_grey(", "))
}
# changes
if (no_changed > 0) {
if (no_changed == 1) {
cat(font_blue("1 value changed"))
} else {
cat(font_blue(formatnr(no_changed), "values changed"))
}
}
# closing
cat(font_grey(")\n"))
}
warned <<- FALSE
}
}
cols_ab <- get_column_abx(x = x,
soft_dependencies = c("AMC",
"AMK",
"AMX",
"AMP",
"AZM",
"AZL",
"ATM",
"RID",
"FEP",
"CTX",
"FOX",
"CED",
"CAZ",
"CRO",
"CXM",
"CHL",
"CIP",
"CLR",
"CLI",
"FLC",
"COL",
"CZO",
"DAP",
"DOX",
"ETP",
"ERY",
"FOS",
"FUS",
"GEN",
"IPM",
"KAN",
"LVX",
"LIN",
"LNZ",
"MEM",
"MEZ",
"MNO",
"MFX",
"NAL",
"NEO",
"NET",
"NIT",
"NOR",
"NOV",
"OFX",
"OXA",
"PEN",
"PIP",
"TZP",
"PLB",
"PRI",
"QDA",
"RIF",
"RXT",
"SIS",
"TEC",
"TCY",
"TIC",
"TGC",
"TOB",
"TMP",
"SXT",
"VAN"),
hard_dependencies = NULL,
verbose = verbose,
...)
# data preparation ----
message(font_blue("NOTE: Preparing data..."), appendLF = FALSE)
AMC <- cols_ab["AMC"]
AMK <- cols_ab["AMK"]
AMP <- cols_ab["AMP"]
AMX <- cols_ab["AMX"]
ATM <- cols_ab["ATM"]
AZL <- cols_ab["AZL"]
AZM <- cols_ab["AZM"]
CAZ <- cols_ab["CAZ"]
CED <- cols_ab["CED"]
CHL <- cols_ab["CHL"]
CIP <- cols_ab["CIP"]
CLI <- cols_ab["CLI"]
CLR <- cols_ab["CLR"]
COL <- cols_ab["COL"]
CRO <- cols_ab["CRO"]
CTX <- cols_ab["CTX"]
CXM <- cols_ab["CXM"]
CZO <- cols_ab["CZO"]
DAP <- cols_ab["DAP"]
DOX <- cols_ab["DOX"]
ERY <- cols_ab["ERY"]
ETP <- cols_ab["ETP"]
FEP <- cols_ab["FEP"]
FLC <- cols_ab["FLC"]
FOS <- cols_ab["FOS"]
FOX <- cols_ab["FOX"]
FUS <- cols_ab["FUS"]
GEN <- cols_ab["GEN"]
IPM <- cols_ab["IPM"]
KAN <- cols_ab["KAN"]
LIN <- cols_ab["LIN"]
LNZ <- cols_ab["LNZ"]
LVX <- cols_ab["LVX"]
MEM <- cols_ab["MEM"]
MEZ <- cols_ab["MEZ"]
MFX <- cols_ab["MFX"]
MNO <- cols_ab["MNO"]
NAL <- cols_ab["NAL"]
NEO <- cols_ab["NEO"]
NET <- cols_ab["NET"]
NIT <- cols_ab["NIT"]
NOR <- cols_ab["NOR"]
NOV <- cols_ab["NOV"]
OFX <- cols_ab["OFX"]
OXA <- cols_ab["OXA"]
PEN <- cols_ab["PEN"]
PIP <- cols_ab["PIP"]
PLB <- cols_ab["PLB"]
PRI <- cols_ab["PRI"]
QDA <- cols_ab["QDA"]
RID <- cols_ab["RID"]
RIF <- cols_ab["RIF"]
RXT <- cols_ab["RXT"]
SAM <- cols_ab["SAM"]
SIS <- cols_ab["SIS"]
SXT <- cols_ab["SXT"]
TCY <- cols_ab["TCY"]
TEC <- cols_ab["TEC"]
TGC <- cols_ab["TGC"]
TIC <- cols_ab["TIC"]
TMP <- cols_ab["TMP"]
TOB <- cols_ab["TOB"]
TZP <- cols_ab["TZP"]
VAN <- cols_ab["VAN"]
ab_missing <- function(ab) {
all(ab %in% c(NULL, NA))
}
verbose_info <- data.frame(row = integer(0),
col = character(0),
mo_fullname = character(0),
old = as.rsi(character(0)),
new = as.rsi(character(0)),
rule = character(0),
rule_group = character(0),
rule_name = character(0),
stringsAsFactors = FALSE)
# helper function for editing the table ----
edit_rsi <- function(to, rule, rows, cols) {
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
if (length(rows) > 0 & length(cols) > 0) {
before_df <- x_original
if (any(!sapply(x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) {
warn_lacking_rsi_class <<- TRUE
}
tryCatch(
# insert into original table
x_original[rows, cols] <<- to,
warning = function(w) {
if (w$message %like% "invalid factor level") {
xyz <- sapply(cols, function(col) {
x_original[, col] <<- factor(x = as.character(pull(x_original, col)), levels = c(to, levels(pull(x_original, col))))
x[, col] <<- factor(x = as.character(pull(x, col)), levels = c(to, levels(pull(x, col))))
invisible()
})
x_original[rows, cols] <<- to
warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call. = FALSE)
txt_warning()
warned <<- FALSE
} else {
warning(w$message, call. = FALSE)
txt_warning()
cat("\n") # txt_warning() does not append a "\n" on itself
}
},
error = function(e) {
txt_error()
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
ifelse(length(rows) > 10, "...", ""),
" while writing value '", to,
"' to column(s) `", paste(cols, collapse = "`, `"),
"`:\n", e$message),
call. = FALSE)
}
)
tryCatch(
x[rows, cols] <<- x_original[rows, cols],
error = function(e) {
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
"... while writing value '", to,
"' to column(s) `", paste(cols, collapse = "`, `"),
"`:\n", e$message), call. = FALSE)
}
)
# before_df might not be a data.frame, but a tibble or data.table instead
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows, ]
track_changes <- list(added = 0,
changed = 0)
for (i in seq_len(length(cols))) {
verbose_new <- data.frame(row = rows,
col = cols[i],
mo_fullname = x[rows, "fullname"],
old = as.rsi(as.character(old[, cols[i]]), warn = FALSE),
new = as.rsi(as.character(x[rows, cols[i]])),
rule = font_stripstyle(rule[1]),
rule_group = font_stripstyle(rule[2]),
rule_name = font_stripstyle(rule[3]),
stringsAsFactors = FALSE)
colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name")
verbose_new <- verbose_new %>% filter(old != new | is.na(old))
# save changes to data set 'verbose_info'
verbose_info <<- rbind(verbose_info, verbose_new)
# count adds and changes
track_changes$added <- track_changes$added + verbose_new %>% filter(is.na(old)) %>% nrow()
track_changes$changed <- track_changes$changed + verbose_new %>% filter(!is.na(old)) %>% nrow()
}
# after the applied changes: return list with counts of added and changed
return(track_changes)
}
# no changes were applied: return number of (new) changes: none.
return(list(added = 0,
changed = 0))
}
old_cols <- colnames(x)
old_attributes <- attributes(x)
x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc.
# create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination)
x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]))), function(x) {
x[is.na(x)] <- "."
paste0(x, collapse = "")
})
# save original table, with the new .rowid column
x_original.bak <- x
# keep only unique rows for MO and ABx
x <- x %>% distinct(`.rowid`, .keep_all = TRUE)
x_original <- x
# join to microorganisms data set
x <- as.data.frame(x, stringsAsFactors = FALSE)
x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE])
x <- x %>%
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL)
x$genus_species <- paste(x$genus, x$species)
message(font_blue("OK."))
if (ab_missing(AMP) & !ab_missing(AMX)) {
# ampicillin column is missing, but amoxicillin is available
message(font_blue(paste0("NOTE: Using column `", font_bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
AMP <- AMX
}
# nolint start
# antibiotic classes ----
aminoglycosides <- c(TOB, GEN, KAN, NEO, NET, SIS)
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
polymyxins <- c(PLB, COL)
macrolides <- c(ERY, AZM, RXT, CLR) # since EUCAST v3.1 clinda is set apart
glycopeptides <- c(VAN, TEC)
streptogramins <- c(QDA, PRI) # should officially also be quinupristin/dalfopristin
aminopenicillins <- c(AMP, AMX)
cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
carbapenems <- c(ETP, IPM, MEM)
ureidopenicillins <- c(PIP, TZP, AZL, MEZ)
all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN)
fluoroquinolones <- c(OFX, CIP, NOR, LVX, MFX)
# nolint end
# help function to get available antibiotic column names ------------------
get_antibiotic_columns <- function(x, df) {
x <- trimws(unlist(strsplit(x, ",", fixed = TRUE)))
y <- character(0)
for (i in seq_len(length(x))) {
if (is.function(get(x[i]))) {
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
}
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
}
y[y != "" & y %in% colnames(df)]
}
get_antibiotic_names <- function(x) {
x <- x %>%
strsplit(",") %>%
unlist() %>%
trimws() %>%
sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
sort() %>%
paste(collapse = ", ")
x <- gsub("_", " ", x, fixed = TRUE)
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
x
}
format_antibiotic_names <- function(ab_names, ab_results) {
ab_names <- trimws(unlist(strsplit(ab_names, ",")))
ab_results <- trimws(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)
x <- paste(paste0(ab_names, collapse = " and "), "are all")
}
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.rsi_no_warning <- function(x) suppressWarnings(as.rsi(x))
no_added <- 0
no_changed <- 0
# Other rules: enzyme inhibitors ------------------------------------------
if (any(c("all", "other") %in% rules)) {
if (info == TRUE) {
cat(font_bold(paste0("\nRules by this AMR package (",
font_red(paste0("v", utils::packageVersion("AMR"), ", ",
format(utils::packageDate("AMR"), "%Y"))), "), see ?eucast_rules\n")))
}
ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")]
ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$name)
ab_enzyme$base_ab <- as.ab(ab_enzyme$base_name)
for (i in seq_len(nrow(ab_enzyme))) {
if (all(c(ab_enzyme[i, ]$ab, ab_enzyme[i, ]$base_ab) %in% names(cols_ab), na.rm = TRUE)) {
ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE)
ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE)
# Set base to R where base + enzyme inhibitor is R
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
if (info == TRUE) {
cat(rule_current)
}
run_changes <- edit_rsi(to = "R",
rule = c(rule_current, "Other rules", ""),
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"),
cols = cols_ab[ab_enzyme[i, ]$base_ab])
no_added <- no_added + run_changes$added
no_changed <- no_changed + run_changes$changed
# Print number of new changes
if (info == TRUE) {
# print only on last one of rules in this group
txt_ok(no_added = no_added, no_changed = no_changed)
# and reset counters
no_added <- 0
no_changed <- 0
}
# Set base + enzyme inhibitor to S where base is S
rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ",
ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S")
if (info == TRUE) {
cat(rule_current)
}
run_changes <- edit_rsi(to = "S",
rule = c(rule_current, "Other rules", ""),
rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"),
cols = cols_ab[ab_enzyme[i, ]$ab])
no_added <- no_added + run_changes$added
no_changed <- no_changed + run_changes$changed
# Print number of new changes
if (info == TRUE) {
# print only on last one of rules in this group
txt_ok(no_added = no_added, no_changed = no_changed)
# and reset counters
no_added <- 0
no_changed <- 0
}
}
}
} else {
if (info == TRUE) {
cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n"))
}
}
# Official EUCAST rules ---------------------------------------------------
eucast_notification_shown <- FALSE
if (!is.null(list(...)$eucast_rules_df)) {
# this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
eucast_rules_df <- list(...)$eucast_rules_df
} else {
# otherwise internal data file, created in data-raw/internals.R
eucast_rules_df <- eucast_rules_file
}
for (i in seq_len(nrow(eucast_rules_df))) {
rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"]
rule_current <- eucast_rules_df[i, "reference.rule"]
rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule"]
rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group"]
rule_group_current <- eucast_rules_df[i, "reference.rule_group"]
if (is.na(eucast_rules_df[i, 4])) {
rule_text <- paste0("always report as '", eucast_rules_df[i, 7], "': ", get_antibiotic_names(eucast_rules_df[i, 6]))
} else {
rule_text <- paste0("report as '", eucast_rules_df[i, 7], "' when ",
format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, 4]),
ab_results = eucast_rules_df[i, 5]), ": ",
get_antibiotic_names(eucast_rules_df[i, 6]))
}
if (i == 1) {
rule_previous <- ""
rule_group_previous <- ""
}
if (i == nrow(eucast_rules_df)) {
rule_next <- ""
}
# 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 (info == TRUE & !rule_group_current %like% "other" & eucast_notification_shown == FALSE) {
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)),
"\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
"\n", font_blue("http://eucast.org/"), "\n"))
eucast_notification_shown <- TRUE
}
if (info == TRUE) {
# Print rule (group) ------------------------------------------------------
if (rule_group_current != rule_group_previous) {
# is new rule group, one of Breakpoints, Expert Rules and Other
cat(font_bold(
ifelse(
rule_group_current %like% "breakpoint",
paste0("\nEUCAST Clinical Breakpoints (",
font_red(paste0("v", EUCAST_VERSION_BREAKPOINTS)), ")\n"),
ifelse(
rule_group_current %like% "expert",
paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (",
font_red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"),
""))))
}
# Print rule -------------------------------------------------------------
if (rule_current != rule_previous) {
# is new rule within group, print its name
if (rule_current %in% c(microorganisms$family,
microorganisms$fullname)) {
cat(font_italic(rule_current))
} else {
cat(rule_current)
}
warned <- FALSE
}
}
# Get rule from file ------------------------------------------------------
col_mo_property <- eucast_rules_df[i, 1]
like_is_one_of <- eucast_rules_df[i, 2]
# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
if (eucast_rules_df[i, 3] %like% "coagulase") {
all_staph <- microorganisms[which(microorganisms$genus == "Staphylococcus"), ]
all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL))
if (eucast_rules_df[i, 3] %like% "coagulase") {
eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "negative"),
"fullname",
drop = TRUE],
collapse = "|"),
")$")
} else {
eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "positive"),
"fullname",
drop = TRUE],
collapse = "|"),
")$")
}
like_is_one_of <- "like"
}
if (like_is_one_of == "is") {
# so e.g. 'Enterococcus' will turn into '^Enterococcus$'
mo_value <- paste0("^", eucast_rules_df[i, 3], "$")
} else if (like_is_one_of == "one_of") {
# so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$'
mo_value <- paste0("^(",
paste(trimws(unlist(strsplit(eucast_rules_df[i, 3], ",", fixed = TRUE))),
collapse = "|"),
")$")
} else if (like_is_one_of == "like") {
mo_value <- eucast_rules_df[i, 3]
} else {
stop("invalid value for column 'like.is.one_of'", call. = FALSE)
}
source_antibiotics <- eucast_rules_df[i, 4]
source_value <- trimws(unlist(strsplit(eucast_rules_df[i, 5], ",", fixed = TRUE)))
target_antibiotics <- eucast_rules_df[i, 6]
target_value <- eucast_rules_df[i, 7]
if (is.na(source_antibiotics)) {
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value),
error = function(e) integer(0))
} else {
source_antibiotics <- get_antibiotic_columns(source_antibiotics, x)
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[, col_mo_property] %like% mo_value
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
error = function(e) integer(0))
} else if (length(source_antibiotics) == 2) {
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
error = function(e) integer(0))
} else if (length(source_antibiotics) == 3) {
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
& as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
& as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
& as.rsi_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
error = function(e) integer(0))
} else {
stop("only 3 antibiotics supported for source_antibiotics ", call. = FALSE)
}
}
cols <- get_antibiotic_columns(target_antibiotics, x)
# Apply rule on data ------------------------------------------------------
# this will return the unique number of changes
run_changes <- edit_rsi(to = target_value,
rule = c(rule_text, rule_group_current, rule_current),
rows = rows,
cols = cols)
no_added <- no_added + run_changes$added
no_changed <- no_changed + run_changes$changed
# Print number of new changes ---------------------------------------------
if (info == TRUE & rule_next != rule_current) {
# print only on last one of rules in this group
txt_ok(no_added = no_added, no_changed = no_changed)
# and reset counters
no_added <- 0
no_changed <- 0
}
}
# Print overview ----------------------------------------------------------
if (info == TRUE) {
if (verbose == TRUE) {
wouldve <- "would have "
} else {
wouldve <- ""
}
verbose_info <- verbose_info %>%
arrange(row, rule_group, rule_name, col)
cat(paste0("\n", font_grey(strrep("-", options()$width - 1)), "\n"))
cat(font_bold(paste("The rules", paste0(wouldve, "affected"),
formatnr(n_distinct(verbose_info$row)),
"out of", formatnr(nrow(x_original)),
"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
n_added <- verbose_info %>% filter(is.na(old)) %>% nrow()
n_changed <- verbose_info %>% filter(!is.na(old)) %>% nrow()
# print added values ----
if (n_added == 0) {
colour <- cat # is function
} else {
colour <- font_green # is function
}
cat(colour(paste0("=> ", wouldve, "added ",
font_bold(formatnr(verbose_info %>%
filter(is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (n_added > 0) {
added_summary <- verbose_info %>%
filter(is.na(old)) %>%
group_by(new) %>%
summarise(n = n())
cat(paste(" -",
paste0(formatnr(added_summary$n), " test result", ifelse(added_summary$n > 1, "s", ""),
" added as ", added_summary$new), collapse = "\n"))
}
# print changed values ----
if (n_changed == 0) {
colour <- cat # is function
} else {
colour <- font_blue # is function
}
if (n_added + n_changed > 0) {
cat("\n")
}
cat(colour(paste0("=> ", wouldve, "changed ",
font_bold(formatnr(verbose_info %>%
filter(!is.na(old)) %>%
nrow()), "test results"),
"\n")))
if (n_changed > 0) {
changed_summary <- verbose_info %>%
filter(!is.na(old)) %>%
group_by(old, new) %>%
summarise(n = n())
cat(paste(" -",
paste0(formatnr(changed_summary$n), " test result", ifelse(changed_summary$n > 1, "s", ""), " changed from ",
changed_summary$old, " to ", changed_summary$new), collapse = "\n"))
cat("\n")
}
cat(paste0(font_grey(strrep("-", options()$width - 1)), "\n"))
if (verbose == FALSE & nrow(verbose_info) > 0) {
cat(paste("\nUse", font_bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
} else if (verbose == TRUE) {
cat(paste0("\nUsed '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"))
}
}
if (isTRUE(warn_lacking_rsi_class)) {
warning("Not all columns with antimicrobial results are of class <rsi>.\n",
"Transform eligible columns to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)",
call. = FALSE)
}
# Return data set ---------------------------------------------------------
if (verbose == TRUE) {
rownames(verbose_info) <- NULL
verbose_info
} else {
# reset original attributes
x_original <- x_original[, c(col_mo, cols_ab, ".rowid"), drop = FALSE]
x_original.bak <- x_original.bak[, setdiff(colnames(x_original.bak), c(col_mo, cols_ab)), drop = FALSE]
x_original.bak <- x_original.bak %>%
left_join(x_original, by = ".rowid")
x_original.bak <- x_original.bak[, old_cols, drop = FALSE]
attributes(x_original.bak) <- old_attributes
x_original.bak
}
}
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