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AMR/R/key_antibiotics.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Key antibiotics for first \emph{weighted} isolates
#'
#' These function can be used to determine first isolates (see \code{\link{first_isolate}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
#' @param tbl table with antibiotics coloms, like \code{amox} and \code{amcl}.
#' @param x,y characters to compare
#' @inheritParams first_isolate
#' @param amcl,amox,cfot,cfta,cfur,cipr,coli,eryt,gent,mero,oxac,pita,rifa,teic,tetr,tobr,trsu,vanc column names of antibiotics, case-insensitive
#' @details The function \code{key_antibiotics} returns a character vector with antibiotic results.
#'
#' The antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
#' amox, amcl, cfur, pita, cipr, trsu, vanc, teic, tetr, eryt, oxac, rifa.
#'
#' The antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
#' amox, amcl, cfur, pita, cipr, trsu, gent, tobr, coli, cfot, cfta, mero.
#'
#'
#' The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
#' @inheritSection first_isolate Key antibiotics
#' @rdname key_antibiotics
#' @export
#' @importFrom dplyr %>% mutate if_else
#' @seealso \code{\link{first_isolate}}
#' @examples
#' \dontrun{
#' # set key antibiotics to a new variable
#' tbl$keyab <- key_antibiotics(tbl)
#'
#' # add regular first isolates
#' tbl$first_isolate <-
#' first_isolate(tbl)
#'
#' # add first WEIGHTED isolates using key antibiotics
#' tbl$first_isolate_weighed <-
#' first_isolate(tbl,
#' col_keyantibiotics = 'keyab')
#' }
key_antibiotics <- function(tbl,
col_bactid = "bactid",
amcl = "amcl",
amox = "amox",
cfot = "cfot",
cfta = "cfta",
cfur = "cfur",
cipr = "cipr",
coli = "coli",
eryt = "eryt",
gent = "gent",
mero = "mero",
oxac = "oxac",
pita = "pita",
rifa = "rifa",
teic = "teic",
tetr = "tetr",
tobr = "tobr",
trsu = "trsu",
vanc = "vanc",
info = TRUE) {
if (!col_bactid %in% colnames(tbl)) {
stop('Column ', col_bactid, ' not found.', call. = FALSE)
}
# check columns
col.list <- c(amcl, amox, cfot, cfta, cfur, cipr,
coli, eryt, gent, mero, oxac, pita,
rifa, teic, tetr, tobr, trsu, vanc)
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
amcl <- col.list[amcl]
amox <- col.list[amox]
cfot <- col.list[cfot]
cfta <- col.list[cfta]
cfur <- col.list[cfur]
cipr <- col.list[cipr]
coli <- col.list[coli]
eryt <- col.list[eryt]
gent <- col.list[gent]
mero <- col.list[mero]
oxac <- col.list[oxac]
pita <- col.list[pita]
rifa <- col.list[rifa]
teic <- col.list[teic]
tetr <- col.list[tetr]
tobr <- col.list[tobr]
trsu <- col.list[trsu]
vanc <- col.list[vanc]
gram_positive = c(amox, amcl, cfur, pita, cipr, trsu,
# specific for G+:
vanc, teic, tetr, eryt, oxac, rifa)
gram_positive <- gram_positive[!is.na(gram_positive)]
gram_negative = c(amox, amcl, cfur, pita, cipr, trsu,
# specific for G-:
gent, tobr, coli, cfot, cfta, mero)
gram_negative <- gram_negative[!is.na(gram_negative)]
# join microorganisms
tbl <- tbl %>% left_join_microorganisms(col_bactid)
tbl$key_ab <- NA_character_
# Gram +
tbl <- tbl %>% mutate(key_ab =
if_else(gramstain %like% '^Positive ',
apply(X = tbl[, gram_positive],
MARGIN = 1,
FUN = function(x) paste(x, collapse = "")),
key_ab))
# Gram -
tbl <- tbl %>% mutate(key_ab =
if_else(gramstain %like% '^Negative ',
apply(X = tbl[, gram_negative],
MARGIN = 1,
FUN = function(x) paste(x, collapse = "")),
key_ab))
# format
key_abs <- tbl %>%
pull(key_ab) %>%
gsub('(NA|NULL)', '-', .)
key_abs
}
#' @importFrom dplyr progress_estimated %>%
#' @rdname key_antibiotics
#' @export
key_antibiotics_equal <- function(x,
y,
type = c("keyantibiotics", "points"),
ignore_I = TRUE,
points_threshold = 2,
info = FALSE) {
# x is active row, y is lag
type <- type[1]
if (length(x) != length(y)) {
stop('Length of `x` and `y` must be equal.')
}
result <- logical(length(x))
if (type == "keyantibiotics") {
if (ignore_I == TRUE) {
# evaluation using regular expression will treat '?' as any character
# so I is actually ignored then
x <- gsub('I', '?', x, ignore.case = TRUE)
y <- gsub('I', '?', y, ignore.case = TRUE)
}
for (i in 1:length(x)) {
result[i] <- grepl(x = x[i],
pattern = y[i],
ignore.case = TRUE) |
grepl(x = y[i],
pattern = x[i],
ignore.case = TRUE)
}
return(result)
} else {
if (info == TRUE) {
p <- dplyr::progress_estimated(length(x))
}
for (i in 1:length(x)) {
if (info == TRUE) {
p$tick()$print()
}
if (is.na(x[i])) {
x[i] <- ''
}
if (is.na(y[i])) {
y[i] <- ''
}
if (nchar(x[i]) != nchar(y[i])) {
result[i] <- FALSE
} else if (x[i] == '' & y[i] == '') {
result[i] <- TRUE
} else {
x2 <- strsplit(x[i], "")[[1]]
y2 <- strsplit(y[i], "")[[1]]
if (type == 'points') {
# count points for every single character:
# - no change is 0 points
# - I <-> S|R is 0.5 point
# - S|R <-> R|S is 1 point
# use the levels of as.rsi (S = 1, I = 2, R = 3)
suppressWarnings(x2 <- x2 %>% as.rsi() %>% as.double())
suppressWarnings(y2 <- y2 %>% as.rsi() %>% as.double())
points <- (x2 - y2) %>% abs() %>% sum(na.rm = TRUE)
result[i] <- ((points / 2) >= points_threshold)
} else {
stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
}
}
}
if (info == TRUE) {
cat('\n')
}
result
}
}
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