mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:46:11 +01:00
498 lines
22 KiB
R
Executable File
498 lines
22 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# This R package was created for academic research and 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.gitab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Determine multidrug-resistant organisms (MDRO)
|
|
#'
|
|
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
|
|
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
|
|
#' @param country country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).
|
|
#' @param info print progress
|
|
#' @inheritParams eucast_rules
|
|
#' @param metr column name of an antibiotic, see Antibiotics
|
|
#' @param ... parameters that are passed on to methods
|
|
#' @inheritSection eucast_rules Antibiotics
|
|
#' @details When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
|
|
#' @return Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
|
|
#' @rdname mdro
|
|
#' @importFrom dplyr %>%
|
|
#' @importFrom crayon red blue bold
|
|
#' @export
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @examples
|
|
#' library(dplyr)
|
|
#'
|
|
#' septic_patients %>%
|
|
#' mutate(EUCAST = mdro(.),
|
|
#' BRMO = brmo(.))
|
|
mdro <- function(tbl,
|
|
country = NULL,
|
|
col_mo = NULL,
|
|
info = TRUE,
|
|
amcl = guess_ab(),
|
|
amik = guess_ab(),
|
|
amox = guess_ab(),
|
|
ampi = guess_ab(),
|
|
azit = guess_ab(),
|
|
aztr = guess_ab(),
|
|
cefa = guess_ab(),
|
|
cfra = guess_ab(),
|
|
cfep = guess_ab(),
|
|
cfot = guess_ab(),
|
|
cfox = guess_ab(),
|
|
cfta = guess_ab(),
|
|
cftr = guess_ab(),
|
|
cfur = guess_ab(),
|
|
chlo = guess_ab(),
|
|
cipr = guess_ab(),
|
|
clar = guess_ab(),
|
|
clin = guess_ab(),
|
|
clox = guess_ab(),
|
|
coli = guess_ab(),
|
|
czol = guess_ab(),
|
|
dapt = guess_ab(),
|
|
doxy = guess_ab(),
|
|
erta = guess_ab(),
|
|
eryt = guess_ab(),
|
|
fosf = guess_ab(),
|
|
fusi = guess_ab(),
|
|
gent = guess_ab(),
|
|
imip = guess_ab(),
|
|
kana = guess_ab(),
|
|
levo = guess_ab(),
|
|
linc = guess_ab(),
|
|
line = guess_ab(),
|
|
mero = guess_ab(),
|
|
metr = guess_ab(),
|
|
mino = guess_ab(),
|
|
moxi = guess_ab(),
|
|
nali = guess_ab(),
|
|
neom = guess_ab(),
|
|
neti = guess_ab(),
|
|
nitr = guess_ab(),
|
|
novo = guess_ab(),
|
|
norf = guess_ab(),
|
|
oflo = guess_ab(),
|
|
peni = guess_ab(),
|
|
pipe = guess_ab(),
|
|
pita = guess_ab(),
|
|
poly = guess_ab(),
|
|
qida = guess_ab(),
|
|
rifa = guess_ab(),
|
|
roxi = guess_ab(),
|
|
siso = guess_ab(),
|
|
teic = guess_ab(),
|
|
tetr = guess_ab(),
|
|
tica = guess_ab(),
|
|
tige = guess_ab(),
|
|
tobr = guess_ab(),
|
|
trim = guess_ab(),
|
|
trsu = guess_ab(),
|
|
vanc = guess_ab()) {
|
|
|
|
if (!is.data.frame(tbl)) {
|
|
stop("`tbl` must be a data frame.", call. = FALSE)
|
|
}
|
|
|
|
# try to find columns based on type
|
|
# -- mo
|
|
if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
|
|
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
|
|
message(blue(paste0("NOTE: Using column `", bold(col_mo), "` as input for `col_mo`.")))
|
|
}
|
|
if (is.null(col_mo)) {
|
|
stop("`col_mo` must be set.", call. = FALSE)
|
|
}
|
|
|
|
# strip whitespaces
|
|
if (length(country) > 1) {
|
|
stop('`country` must be a length one character string.', call. = FALSE)
|
|
}
|
|
|
|
if (is.null(country)) {
|
|
country <- 'EUCAST'
|
|
}
|
|
country <- trimws(country)
|
|
if (tolower(country) != 'eucast' & !country %like% '^[a-z]{2}$') {
|
|
stop('This is not a valid ISO 3166-1 alpha-2 country code: "', country, '". Please see ?mdro.', call. = FALSE)
|
|
}
|
|
|
|
# create list and make country code case-independent
|
|
guideline <- list(country = list(code = tolower(country)))
|
|
|
|
if (guideline$country$code == 'eucast') {
|
|
guideline$country$name <- '(European guidelines)'
|
|
guideline$name <- 'EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables"'
|
|
guideline$version <- 'Version 3.1'
|
|
guideline$source <- 'http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'
|
|
# support per country:
|
|
} else if (guideline$country$code == 'de') {
|
|
guideline$country$name <- 'Germany'
|
|
guideline$name <- ''
|
|
guideline$version <- ''
|
|
guideline$source <- ''
|
|
} else if (guideline$country$code == 'nl') {
|
|
guideline$country$name <- 'The Netherlands'
|
|
guideline$name <- 'WIP-Richtlijn BRMO'
|
|
guideline$version <- 'Revision of December 2017'
|
|
guideline$source <- 'https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'
|
|
# add here more countries like this:
|
|
# } else if (country$code == 'xx') {
|
|
# country$name <- 'country name'
|
|
} else {
|
|
stop('This country code is currently unsupported: ', guideline$country$code, call. = FALSE)
|
|
}
|
|
|
|
if (info == TRUE) {
|
|
cat("Determining multidrug-resistant organisms (MDRO), according to:\n",
|
|
"Guideline: ", red(paste0(guideline$name, ", ", guideline$version, "\n")),
|
|
"Country : ", red(paste0(guideline$country$name, "\n")),
|
|
"Source : ", blue(paste0(guideline$source, "\n")),
|
|
"\n", sep = "")
|
|
}
|
|
|
|
# check columns
|
|
if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = info) }
|
|
if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = info) }
|
|
if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = info) }
|
|
if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = info) }
|
|
if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = info) }
|
|
if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = info) }
|
|
if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = info) }
|
|
if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = info) }
|
|
if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = info) }
|
|
if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = info) }
|
|
if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = info) }
|
|
if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = info) }
|
|
if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = info) }
|
|
if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = info) }
|
|
if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = info) }
|
|
if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = info) }
|
|
if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = info) }
|
|
if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = info) }
|
|
if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = info) }
|
|
if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = info) }
|
|
if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = info) }
|
|
if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = info) }
|
|
if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = info) }
|
|
if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = info) }
|
|
if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = info) }
|
|
if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = info) }
|
|
if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = info) }
|
|
if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = info) }
|
|
if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = info) }
|
|
if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = info) }
|
|
if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = info) }
|
|
if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = info) }
|
|
if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = info) }
|
|
if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = info) }
|
|
if (identical(metr, as.name("guess_ab"))) { metr <- guess_ab(tbl, "metr", verbose = info) }
|
|
if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = info) }
|
|
if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = info) }
|
|
if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = info) }
|
|
if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = info) }
|
|
if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = info) }
|
|
if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = info) }
|
|
if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = info) }
|
|
if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = info) }
|
|
if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = info) }
|
|
if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = info) }
|
|
if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = info) }
|
|
if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = info) }
|
|
if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = info) }
|
|
if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = info) }
|
|
if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = info) }
|
|
if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = info) }
|
|
if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = info) }
|
|
if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = info) }
|
|
if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = info) }
|
|
if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = info) }
|
|
if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = info) }
|
|
if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = info) }
|
|
if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = info) }
|
|
if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = info) }
|
|
if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = info) }
|
|
col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot,
|
|
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
|
|
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
|
|
levo, linc, line, mero, metr, mino, moxi, nali, neom, neti,
|
|
nitr, novo, norf, oflo, peni, pipe, pita, poly, qida, rifa,
|
|
roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
|
|
if (length(col.list) < 60) {
|
|
warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
|
|
immediate. = TRUE,
|
|
call. = FALSE)
|
|
}
|
|
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
|
|
amcl <- col.list[amcl]
|
|
amik <- col.list[amik]
|
|
amox <- col.list[amox]
|
|
ampi <- col.list[ampi]
|
|
azit <- col.list[azit]
|
|
aztr <- col.list[aztr]
|
|
cefa <- col.list[cefa]
|
|
cfra <- col.list[cfra]
|
|
cfep <- col.list[cfep]
|
|
cfot <- col.list[cfot]
|
|
cfox <- col.list[cfox]
|
|
cfta <- col.list[cfta]
|
|
cftr <- col.list[cftr]
|
|
cfur <- col.list[cfur]
|
|
chlo <- col.list[chlo]
|
|
cipr <- col.list[cipr]
|
|
clar <- col.list[clar]
|
|
clin <- col.list[clin]
|
|
clox <- col.list[clox]
|
|
coli <- col.list[coli]
|
|
czol <- col.list[czol]
|
|
dapt <- col.list[dapt]
|
|
doxy <- col.list[doxy]
|
|
erta <- col.list[erta]
|
|
eryt <- col.list[eryt]
|
|
fosf <- col.list[fosf]
|
|
fusi <- col.list[fusi]
|
|
gent <- col.list[gent]
|
|
imip <- col.list[imip]
|
|
kana <- col.list[kana]
|
|
levo <- col.list[levo]
|
|
linc <- col.list[linc]
|
|
line <- col.list[line]
|
|
mero <- col.list[mero]
|
|
metr <- col.list[metr]
|
|
mino <- col.list[mino]
|
|
moxi <- col.list[moxi]
|
|
nali <- col.list[nali]
|
|
neom <- col.list[neom]
|
|
neti <- col.list[neti]
|
|
nitr <- col.list[nitr]
|
|
novo <- col.list[novo]
|
|
norf <- col.list[norf]
|
|
oflo <- col.list[oflo]
|
|
peni <- col.list[peni]
|
|
pipe <- col.list[pipe]
|
|
pita <- col.list[pita]
|
|
poly <- col.list[poly]
|
|
qida <- col.list[qida]
|
|
rifa <- col.list[rifa]
|
|
roxi <- col.list[roxi]
|
|
siso <- col.list[siso]
|
|
teic <- col.list[teic]
|
|
tetr <- col.list[tetr]
|
|
tica <- col.list[tica]
|
|
tige <- col.list[tige]
|
|
tobr <- col.list[tobr]
|
|
trim <- col.list[trim]
|
|
trsu <- col.list[trsu]
|
|
vanc <- col.list[vanc]
|
|
|
|
# antibiotic classes
|
|
aminoglycosides <- c(tobr, gent) # can also be kana but that one is often intrinsic R
|
|
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
|
|
cephalosporins_3rd <- c(cfot, cftr, cfta)
|
|
carbapenems <- c(erta, imip, mero)
|
|
fluoroquinolones <- c(oflo, cipr, levo, moxi)
|
|
|
|
# helper function for editing the table
|
|
trans_tbl <- function(to, rows, cols, any_all) {
|
|
cols <- cols[!is.na(cols)]
|
|
if (length(rows) > 0 & length(cols) > 0) {
|
|
if (any_all == "any") {
|
|
col_filter <- which(tbl[, cols] == 'R')
|
|
} else if (any_all == "all") {
|
|
col_filter <- tbl %>%
|
|
mutate(index = 1:nrow(.)) %>%
|
|
filter_at(vars(cols), all_vars(. == "R")) %>%
|
|
pull((index))
|
|
}
|
|
rows <- rows[rows %in% col_filter]
|
|
tbl[rows, 'MDRO'] <<- to
|
|
}
|
|
}
|
|
|
|
tbl <- tbl %>%
|
|
mutate_at(vars(col_mo), as.mo) %>%
|
|
# join to microorganisms data set
|
|
left_join_microorganisms(by = col_mo) %>%
|
|
# add unconfirmed to where genus is available
|
|
mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_))
|
|
|
|
if (guideline$country$code == 'eucast') {
|
|
# EUCAST ------------------------------------------------------------------
|
|
# Table 5
|
|
trans_tbl(3,
|
|
which(tbl$family == 'Enterobacteriaceae'
|
|
| tbl$fullname %like% '^Pseudomonas aeruginosa'
|
|
| tbl$genus == 'Acinetobacter'),
|
|
coli,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Salmonella Typhi'),
|
|
c(carbapenems, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Haemophilus influenzae'),
|
|
c(cephalosporins_3rd, carbapenems, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Moraxella catarrhalis'),
|
|
c(cephalosporins_3rd, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Neisseria meningitidis'),
|
|
c(cephalosporins_3rd, fluoroquinolones),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Neisseria gonorrhoeae'),
|
|
azit,
|
|
"any")
|
|
# Table 6
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
|
|
c(vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Corynebacterium'),
|
|
c(vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Streptococcus pneumoniae'),
|
|
c(carbapenems, vanc, teic, dapt, line, qida, tige, rifa),
|
|
"any")
|
|
trans_tbl(3, # Sr. groups A/B/C/G
|
|
which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|equisimilis|equi|zooepidemicus|dysgalactiae|anginosus)'),
|
|
c(peni, cephalosporins, vanc, teic, dapt, line, qida, tige),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Enterococcus'),
|
|
c(dapt, line, tige, teic),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Enterococcus faecalis'),
|
|
c(ampi, amox),
|
|
"any")
|
|
# Table 7
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Bacteroides'),
|
|
metr,
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Clostridium difficile'),
|
|
c(metr, vanc),
|
|
"any")
|
|
}
|
|
|
|
if (guideline$country$code == 'de') {
|
|
# Germany -----------------------------------------------------------------
|
|
stop("We are still working on German guidelines in this beta version.", call. = FALSE)
|
|
}
|
|
|
|
if (guideline$country$code == 'nl') {
|
|
# Netherlands -------------------------------------------------------------
|
|
aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
|
|
fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
|
|
carbapenems <- carbapenems[!is.na(carbapenems)]
|
|
|
|
# Table 1
|
|
trans_tbl(3,
|
|
which(tbl$family == 'Enterobacteriaceae'),
|
|
c(aminoglycosides, fluoroquinolones),
|
|
"all")
|
|
|
|
trans_tbl(2,
|
|
which(tbl$family == 'Enterobacteriaceae'),
|
|
c(carbapenems),
|
|
"any")
|
|
|
|
# Table 2
|
|
trans_tbl(2,
|
|
which(tbl$genus == 'Acinetobacter'),
|
|
c(carbapenems),
|
|
"any")
|
|
trans_tbl(3,
|
|
which(tbl$genus == 'Acinetobacter'),
|
|
c(aminoglycosides, fluoroquinolones),
|
|
"all")
|
|
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
|
|
trsu,
|
|
"all")
|
|
|
|
if (!is.na(mero) & !is.na(imip)
|
|
& !is.na(gent) & !is.na(tobr)
|
|
& !is.na(cipr)
|
|
& !is.na(cfta)
|
|
& !is.na(pita) ) {
|
|
tbl <- tbl %>% mutate(
|
|
psae = 0,
|
|
psae = ifelse(mero == "R" | imip == "R", psae + 1, psae),
|
|
psae = ifelse(gent == "R" & tobr == "R", psae + 1, psae),
|
|
psae = ifelse(cipr == "R", psae + 1, psae),
|
|
psae = ifelse(cfta == "R", psae + 1, psae),
|
|
psae = ifelse(pita == "R", psae + 1, psae),
|
|
psae = ifelse(is.na(psae), 0, psae)
|
|
)
|
|
} else {
|
|
tbl$psae <- 0
|
|
}
|
|
tbl[which(
|
|
tbl$fullname %like% 'Pseudomonas aeruginosa'
|
|
& tbl$psae >= 3
|
|
), 'MDRO'] <- 3
|
|
|
|
# Table 3
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
|
peni,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Streptococcus pneumoniae'),
|
|
vanc,
|
|
"all")
|
|
trans_tbl(3,
|
|
which(tbl$fullname %like% 'Enterococcus faecium'),
|
|
c(peni, vanc),
|
|
"all")
|
|
}
|
|
|
|
factor(x = tbl$MDRO,
|
|
levels = 1:3,
|
|
labels = c('Negative', 'Positive, unconfirmed', 'Positive'),
|
|
ordered = TRUE)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
brmo <- function(..., country = "nl") {
|
|
mdro(..., country = "nl")
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
mrgn <- function(tbl, country = "de", ...) {
|
|
mdro(tbl = tbl, country = "de", ...)
|
|
}
|
|
|
|
#' @rdname mdro
|
|
#' @export
|
|
eucast_exceptional_phenotypes <- function(tbl, country = "EUCAST", ...) {
|
|
mdro(tbl = tbl, country = "EUCAST", ...)
|
|
}
|