mirror of https://github.com/msberends/AMR.git
312 lines
10 KiB
R
312 lines
10 KiB
R
# ==================================================================== #
|
|
# 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. #
|
|
# ==================================================================== #
|
|
|
|
#' Transform to bacteria ID
|
|
#'
|
|
#' Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
|
|
#' @param x a character vector or a dataframe with one or two columns
|
|
#' @rdname as.bactid
|
|
#' @details Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
|
|
#' \itemize{
|
|
#' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
|
|
#' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
|
|
#' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
|
|
#' \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
|
|
#' }
|
|
#' Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
|
|
#' For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
|
|
#' @export
|
|
#' @importFrom dplyr %>% filter pull
|
|
#' @return Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
|
|
#' @seealso \code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
|
|
#' @examples
|
|
#' # These examples all return "STAAUR", the ID of S. aureus:
|
|
#' as.bactid("stau")
|
|
#' as.bactid("STAU")
|
|
#' as.bactid("staaur")
|
|
#' as.bactid("S. aureus")
|
|
#' as.bactid("S aureus")
|
|
#' as.bactid("Staphylococcus aureus")
|
|
#' as.bactid("MRSA") # Methicillin Resistant S. aureus
|
|
#' as.bactid("VISA") # Vancomycin Intermediate S. aureus
|
|
#' as.bactid("VRSA") # Vancomycin Resistant S. aureus
|
|
#'
|
|
#' \dontrun{
|
|
#' df$bactid <- as.bactid(df$microorganism_name)
|
|
#'
|
|
#' # the select function of tidyverse is also supported:
|
|
#' library(dplyr)
|
|
#' df$bactid <- df %>%
|
|
#' select(microorganism_name) %>%
|
|
#' as.bactid()
|
|
#'
|
|
#' # and can even contain 2 columns, which is convenient for genus/species combinations:
|
|
#' df$bactid <- df %>%
|
|
#' select(genus, species) %>%
|
|
#' as.bactid()
|
|
#'
|
|
#' # same result:
|
|
#' df <- df %>%
|
|
#' mutate(bactid = paste(genus, species) %>%
|
|
#' as.bactid())
|
|
#' }
|
|
as.bactid <- function(x) {
|
|
|
|
failures <- character(0)
|
|
|
|
if (NCOL(x) == 2) {
|
|
# support tidyverse selection like: df %>% select(colA, colB)
|
|
# paste these columns together
|
|
x_vector <- vector("character", NROW(x))
|
|
for (i in 1:NROW(x)) {
|
|
x_vector[i] <- paste(pull(x[i,], 1), pull(x[i,], 2), sep = " ")
|
|
}
|
|
x <- x_vector
|
|
} else {
|
|
if (NCOL(x) > 2) {
|
|
stop('`x` can be 2 columns at most', call. = FALSE)
|
|
}
|
|
|
|
# support tidyverse selection like: df %>% select(colA)
|
|
if (!is.vector(x)) {
|
|
x <- pull(x, 1)
|
|
}
|
|
}
|
|
|
|
x.fullbackup <- x
|
|
# remove dots and other non-text in case of "E. coli" except spaces
|
|
x <- gsub("[^a-zA-Z0-9 ]+", "", x)
|
|
# but spaces before and after should be omitted
|
|
x <- trimws(x, which = "both")
|
|
x.backup <- x
|
|
# replace space by regex sign
|
|
x <- gsub(" ", ".*", x, fixed = TRUE)
|
|
# add start and stop
|
|
x_species <- paste(x, 'species')
|
|
x <- paste0('^', x, '$')
|
|
|
|
for (i in 1:length(x)) {
|
|
|
|
if (identical(x.backup[i], "")) {
|
|
# empty values
|
|
x[i] <- NA
|
|
failures <- c(failures, x.fullbackup[i])
|
|
next
|
|
}
|
|
if (x.fullbackup[i] %in% AMR::microorganisms$bactid) {
|
|
# is already a valid bactid
|
|
x[i] <- x.fullbackup[i]
|
|
next
|
|
}
|
|
if (x.backup[i] %in% AMR::microorganisms$bactid) {
|
|
# is already a valid bactid
|
|
x[i] <- x.backup[i]
|
|
next
|
|
}
|
|
|
|
if (tolower(x[i]) == '^e.*coli$') {
|
|
# avoid detection of Entamoeba coli in case of E. coli
|
|
x[i] <- 'ESCCOL'
|
|
next
|
|
}
|
|
if (tolower(x[i]) == '^h.*influenzae$') {
|
|
# avoid detection of Haematobacter influenzae in case of H. influenzae
|
|
x[i] <- 'HAEINF'
|
|
next
|
|
}
|
|
if (tolower(x[i]) == '^st.*au$'
|
|
| tolower(x[i]) == '^stau$'
|
|
| tolower(x[i]) == '^staaur$') {
|
|
# avoid detection of Staphylococcus auricularis in case of S. aureus
|
|
x[i] <- 'STAAUR'
|
|
next
|
|
}
|
|
if (tolower(x[i]) == '^p.*aer$') {
|
|
# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
|
|
x[i] <- 'PSEAER'
|
|
next
|
|
}
|
|
if (tolower(x[i]) %like% 'coagulase'
|
|
| tolower(x[i]) %like% 'cns'
|
|
| tolower(x[i]) %like% 'cons') {
|
|
# coerce S. coagulase negative, also as CNS and CoNS
|
|
x[i] <- 'STACNS'
|
|
next
|
|
}
|
|
|
|
# translate known trivial names to genus+species
|
|
if (!is.na(x.backup[i])) {
|
|
if (toupper(x.backup[i]) == 'MRSA'
|
|
| toupper(x.backup[i]) == 'VISA'
|
|
| toupper(x.backup[i]) == 'VRSA') {
|
|
x[i] <- 'STAAUR'
|
|
next
|
|
}
|
|
if (toupper(x.backup[i]) == 'MRSE') {
|
|
x[i] <- 'Staphylococcus epidermidis'
|
|
}
|
|
if (toupper(x.backup[i]) == 'VRE') {
|
|
x[i] <- 'ENC'
|
|
next
|
|
}
|
|
if (toupper(x.backup[i]) == 'MRPA') {
|
|
# multi resistant P. aeruginosa
|
|
x[i] <- 'PSEAER'
|
|
next
|
|
}
|
|
if (toupper(x.backup[i]) == 'PISP'
|
|
| toupper(x.backup[i]) == 'PRSP') {
|
|
# peni resistant S. pneumoniae
|
|
x[i] <- 'Streptococcus pneumoniae'
|
|
}
|
|
if (toupper(x.backup[i]) == 'VISP'
|
|
| toupper(x.backup[i]) == 'VRSP') {
|
|
# vanco resistant S. pneumoniae
|
|
x[i] <- 'Streptococcus pneumoniae'
|
|
}
|
|
}
|
|
|
|
# let's try the ID's first
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$bactid == x.backup[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# now try exact match
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname == x[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# try any match
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname %like% x[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# try exact match of only genus, with 'species' attached
|
|
# (e.g. this prevents Streptococcus for becoming Peptostreptococcus, since "p" < "s")
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname == x_species[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# try any match of only genus, with 'species' attached
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname %like% x_species[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# search for GLIMS code
|
|
found <- AMR::microorganisms.umcg[which(toupper(AMR::microorganisms.umcg$mocode) == toupper(x.backup[i])),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# try splitting of characters and then find ID
|
|
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
|
|
x_split <- x
|
|
x_length <- nchar(x.backup[i])
|
|
x_split[i] <- paste0(x.backup[i] %>% substr(1, x_length / 2) %>% trimws(),
|
|
'.* ',
|
|
x.backup[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname %like% paste0('^', x_split[i])),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
|
|
# try any match with text before and after original search string
|
|
# so "negative rods" will be "GNR"
|
|
if (x.backup[i] %like% "^Gram") {
|
|
x.backup[i] <- gsub("^Gram", "", x.backup[i], ignore.case = TRUE)
|
|
# remove leading and trailing spaces again
|
|
x.backup[i] <- trimws(x.backup[i], which = "both")
|
|
}
|
|
if (!is.na(x.backup[i])) {
|
|
found <- AMR::microorganisms[which(AMR::microorganisms$fullname %like% x.backup[i]),]$bactid
|
|
if (length(found) > 0) {
|
|
x[i] <- found[1L]
|
|
next
|
|
}
|
|
}
|
|
|
|
# not found
|
|
x[i] <- NA_character_
|
|
failures <- c(failures, x.fullbackup[i])
|
|
|
|
}
|
|
|
|
failures <- failures[!failures %in% c(NA, NULL, NaN)]
|
|
if (length(failures) > 0) {
|
|
warning("These values could not be coerced to a valid bactid: ",
|
|
paste('"', unique(failures), '"', sep = "", collapse = ', '),
|
|
".",
|
|
call. = FALSE)
|
|
}
|
|
class(x) <- "bactid"
|
|
attr(x, 'package') <- 'AMR'
|
|
x
|
|
}
|
|
|
|
#' @rdname as.bactid
|
|
#' @export
|
|
guess_bactid <- as.bactid
|
|
|
|
#' @rdname as.bactid
|
|
#' @export
|
|
is.bactid <- function(x) {
|
|
identical(class(x), "bactid")
|
|
}
|
|
|
|
#' @exportMethod print.bactid
|
|
#' @export
|
|
#' @noRd
|
|
print.bactid <- function(x, ...) {
|
|
cat("Class 'bactid'\n")
|
|
print.default(as.character(x), quote = FALSE)
|
|
}
|
|
|
|
#' @exportMethod as.data.frame.bactid
|
|
#' @export
|
|
#' @noRd
|
|
as.data.frame.bactid <- function (x, ...) {
|
|
# same as as.data.frame.character but with removed stringsAsFactors
|
|
nm <- paste(deparse(substitute(x), width.cutoff = 500L),
|
|
collapse = " ")
|
|
if (!"nm" %in% names(list(...))) {
|
|
as.data.frame.vector(x, ..., nm = nm)
|
|
} else {
|
|
as.data.frame.vector(x, ...)
|
|
}
|
|
}
|
|
|
|
#' @exportMethod pull.bactid
|
|
#' @export
|
|
#' @importFrom dplyr pull
|
|
#' @noRd
|
|
pull.bactid <- function(.data, ...) {
|
|
pull(as.data.frame(.data), ...)
|
|
}
|