mirror of https://github.com/msberends/AMR.git
895 lines
40 KiB
R
Executable File
895 lines
40 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. #
|
||
# ==================================================================== #
|
||
|
||
#' Transform to microorganism ID
|
||
#'
|
||
#' Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms \emph{Bacteria}, \emph{Fungi} and \emph{Protozoa} (see Source), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
|
||
#' @param x a character vector or a \code{data.frame} with one or two columns
|
||
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
|
||
#'
|
||
#' This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".
|
||
#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
|
||
#'
|
||
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
|
||
#' @param allow_uncertain a logical to indicate whether the input should be checked for less possible results, see Details
|
||
#' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid \code{mo} as found in the \code{\link{microorganisms}} data set.
|
||
#' @rdname as.mo
|
||
#' @aliases mo
|
||
#' @keywords mo Becker becker Lancefield lancefield guess
|
||
#' @details
|
||
#' A microbial ID from this package (class: \code{mo}) typically looks like these examples:\cr
|
||
#' \preformatted{
|
||
#' Code Full name
|
||
#' --------------- --------------------------------------
|
||
#' B_KLBSL Klebsiella
|
||
#' B_KLBSL_PNE Klebsiella pneumoniae
|
||
#' B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
|
||
#' | | | |
|
||
#' | | | |
|
||
#' | | | ----> subspecies, a 3-4 letter acronym
|
||
#' | | ----> species, a 3-4 letter acronym
|
||
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
|
||
#' ----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
|
||
#' }
|
||
#'
|
||
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
|
||
#'
|
||
#' This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:
|
||
#' \itemize{
|
||
#' \item{Taxonomic kingdom: it first searches in bacteria, then fungi, then protozoa}
|
||
#' \item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones}
|
||
#' \item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
|
||
#' \item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
|
||
#' }
|
||
#'
|
||
#' A couple of effects because of these rules:
|
||
#' \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} for the same reason}
|
||
#' \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{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
|
||
#' }
|
||
#' This means that looking up human pathogenic microorganisms takes less time than looking up human \strong{non}-pathogenic microorganisms.
|
||
#'
|
||
#' When using \code{allow_uncertain = TRUE} (which is the default setting), it will use additional rules if all previous AI rules failed to get valid results. Examples:
|
||
#' \itemize{
|
||
#' \item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPTC_GRB}) needs review.}
|
||
#' \item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
|
||
#' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
|
||
#' }
|
||
#'
|
||
#' @inheritSection ITIS ITIS
|
||
# (source as a section, so it can be inherited by other man pages)
|
||
#' @section Source:
|
||
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
|
||
#'
|
||
#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
|
||
#'
|
||
#' [3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
|
||
#' @export
|
||
#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
|
||
#' @seealso \code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
|
||
#' The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
|
||
#' @inheritSection AMR Read more on our website!
|
||
#' @examples
|
||
#' # These examples all return "B_STPHY_AUR", the ID of S. aureus:
|
||
#' as.mo("stau")
|
||
#' as.mo("STAU")
|
||
#' as.mo("staaur")
|
||
#' as.mo("S. aureus")
|
||
#' as.mo("S aureus")
|
||
#' as.mo("Staphylococcus aureus")
|
||
#' as.mo("Staphylococcus aureus (MRSA)")
|
||
#' as.mo("MRSA") # Methicillin Resistant S. aureus
|
||
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
|
||
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
|
||
#' as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
|
||
#' # for the Integrated Taxonomic Information System (ITIS)
|
||
#'
|
||
#' as.mo("Streptococcus group A")
|
||
#' as.mo("GAS") # Group A Streptococci
|
||
#' as.mo("GBS") # Group B Streptococci
|
||
#'
|
||
#' as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
|
||
#' as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
|
||
#'
|
||
#' as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
|
||
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
|
||
#'
|
||
#' # Use mo_* functions to get a specific property based on `mo`
|
||
#' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
|
||
#' mo_genus(Ecoli) # returns "Escherichia"
|
||
#' mo_gramstain(Ecoli) # returns "Gram negative"
|
||
#' # but it uses as.mo internally too, so you could also just use:
|
||
#' mo_genus("E. coli") # returns "Escherichia"
|
||
#'
|
||
#'
|
||
#' \dontrun{
|
||
#' df$mo <- as.mo(df$microorganism_name)
|
||
#'
|
||
#' # the select function of tidyverse is also supported:
|
||
#' library(dplyr)
|
||
#' df$mo <- df %>%
|
||
#' select(microorganism_name) %>%
|
||
#' as.mo()
|
||
#'
|
||
#' # and can even contain 2 columns, which is convenient for genus/species combinations:
|
||
#' df$mo <- df %>%
|
||
#' select(genus, species) %>%
|
||
#' as.mo()
|
||
#' # although this works easier and does the same:
|
||
#' df <- df %>%
|
||
#' mutate(mo = as.mo(paste(genus, species)))
|
||
#' }
|
||
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = NULL) {
|
||
mo <- mo_validate(x = x, property = "mo",
|
||
Becker = Becker, Lancefield = Lancefield,
|
||
allow_uncertain = allow_uncertain, reference_df = reference_df)
|
||
structure(.Data = mo, class = "mo")
|
||
}
|
||
|
||
#' @rdname as.mo
|
||
#' @export
|
||
is.mo <- function(x) {
|
||
identical(class(x), "mo")
|
||
}
|
||
|
||
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated
|
||
#' @importFrom data.table data.table as.data.table setkey
|
||
#' @importFrom crayon magenta red italic
|
||
exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
|
||
allow_uncertain = TRUE, reference_df = NULL,
|
||
property = "mo", clear_options = TRUE) {
|
||
|
||
if (!"AMR" %in% base::.packages()) {
|
||
library("AMR")
|
||
# These data.tables are available as data sets when the AMR package is loaded:
|
||
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
|
||
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
|
||
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
|
||
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
|
||
}
|
||
|
||
if (clear_options == TRUE) {
|
||
options(mo_failures = NULL)
|
||
options(mo_renamed = NULL)
|
||
}
|
||
|
||
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)
|
||
}
|
||
x[is.null(x)] <- NA
|
||
|
||
# support tidyverse selection like: df %>% select(colA)
|
||
if (!is.vector(x) & !is.null(dim(x))) {
|
||
x <- pull(x, 1)
|
||
}
|
||
}
|
||
|
||
notes <- character(0)
|
||
failures <- character(0)
|
||
x_input <- x
|
||
# only check the uniques, which is way faster
|
||
x <- unique(x)
|
||
# remove empty values (to later fill them in again with NAs)
|
||
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
|
||
|
||
# defined df to check for
|
||
if (!is.null(reference_df)) {
|
||
if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
|
||
stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE)
|
||
}
|
||
# remove factors, just keep characters
|
||
suppressWarnings(
|
||
reference_df[] <- lapply(reference_df, as.character)
|
||
)
|
||
}
|
||
if (all(identical(trimws(x_input), "") | is.na(x_input))) {
|
||
# all empty
|
||
if (property == "mo") {
|
||
return(structure(rep(NA_character_, length(x_input)), class = "mo"))
|
||
} else if (property == "tsn") {
|
||
return(rep(NA_integer_, length(x_input)))
|
||
} else {
|
||
return(rep(NA_character_, length(x_input)))
|
||
}
|
||
} else if (all(x %in% microorganismsDT[["mo"]])) {
|
||
# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
|
||
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
|
||
} else if (!is.null(reference_df)
|
||
& all(x %in% reference_df[, 1])
|
||
& all(reference_df[, 2] %in% microorganismsDT[["mo"]])) {
|
||
# manually defined reference
|
||
colnames(reference_df)[1] <- "x"
|
||
colnames(reference_df)[2] <- "mo"
|
||
suppressWarnings(
|
||
x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
|
||
left_join(reference_df, by = "x") %>%
|
||
left_join(microorganisms, by = "mo") %>%
|
||
pull(property)
|
||
)
|
||
} else if (all(toupper(x) %in% microorganisms.certe[, "certe"])) {
|
||
# old Certe codes
|
||
y <- as.data.table(microorganisms.certe)[data.table(certe = toupper(x)), on = "certe", ]
|
||
x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
|
||
|
||
} else if (!all(x %in% microorganismsDT[[property]])) {
|
||
|
||
x_backup <- trimws(x, which = "both")
|
||
|
||
# remove spp and species
|
||
x <- trimws(gsub(" +(spp.?|ssp.?|subsp.?|species)", " ", x_backup, ignore.case = TRUE), which = "both")
|
||
x_species <- paste(x, "species")
|
||
# translate to English for supported languages of mo_property
|
||
x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE)
|
||
# remove 'empty' genus and species values
|
||
x <- gsub("(no MO)", "", x, fixed = TRUE)
|
||
# remove non-text in case of "E. coli" except dots and spaces
|
||
x <- gsub("[^.a-zA-Z0-9/ \\-]+", "", x)
|
||
|
||
# but spaces before and after should be omitted
|
||
x <- trimws(x, which = "both")
|
||
x_trimmed <- x
|
||
x_trimmed_species <- paste(x_trimmed, "species")
|
||
x_trimmed_without_group <- gsub(" group$", "", x_trimmed, ignore.case = TRUE)
|
||
# remove last part from "-" or "/"
|
||
x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
|
||
# replace space and dot by regex sign
|
||
x_withspaces <- gsub("[ .]+", ".* ", x)
|
||
x <- gsub("[ .]+", ".*", x)
|
||
# add start en stop regex
|
||
x <- paste0('^', x, '$')
|
||
x_withspaces_start <- paste0('^', x_withspaces)
|
||
x_withspaces <- paste0('^', x_withspaces, '$')
|
||
|
||
# cat(paste0('x "', x, '"\n'))
|
||
# cat(paste0('x_species "', x_species, '"\n'))
|
||
# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
|
||
# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
|
||
# cat(paste0('x_backup "', x_backup, '"\n'))
|
||
# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
|
||
# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
|
||
# cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n'))
|
||
|
||
progress <- progress_estimated(n = length(x), min_time = 3)
|
||
|
||
for (i in 1:length(x)) {
|
||
|
||
progress$tick()$print()
|
||
|
||
if (identical(x_trimmed[i], "")) {
|
||
# empty values
|
||
x[i] <- NA_character_
|
||
next
|
||
}
|
||
if (nchar(x_trimmed[i]) < 3) {
|
||
# check if search term was like "A. species", then return first genus found with ^A
|
||
if (x_backup[i] %like% "species" | x_backup[i] %like% "spp[.]?") {
|
||
# get mo code of first hit
|
||
found <- microorganismsDT[fullname %like% x_withspaces_start[i], mo]
|
||
if (length(found) > 0) {
|
||
mo_code <- found[1L] %>% strsplit("_") %>% unlist() %>% .[1:2] %>% paste(collapse = "_")
|
||
found <- microorganismsDT[mo == mo_code, ..property][[1]]
|
||
# return first genus that begins with x_trimmed, e.g. when "E. spp."
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
}
|
||
}
|
||
# fewer than 3 chars and not looked for species, add as failure
|
||
x[i] <- NA_character_
|
||
failures <- c(failures, x_backup[i])
|
||
next
|
||
}
|
||
|
||
|
||
# translate known trivial abbreviations to genus + species ----
|
||
if (!is.na(x_trimmed[i])) {
|
||
if (toupper(x_trimmed[i]) == 'MRSA'
|
||
| toupper(x_trimmed[i]) == 'MSSA'
|
||
| toupper(x_trimmed[i]) == 'VISA'
|
||
| toupper(x_trimmed[i]) == 'VRSA') {
|
||
x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) == 'MRSE'
|
||
| toupper(x_trimmed[i]) == 'MSSE') {
|
||
x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) == "VRE"
|
||
| x_trimmed[i] %like% '(enterococci|enterokok|enterococo)[a-z]*?$') {
|
||
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) == 'MRPA') {
|
||
# multi resistant P. aeruginosa
|
||
x[i] <- microorganismsDT[mo == 'B_PDMNS_AER', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) == 'CRS'
|
||
| toupper(x_trimmed[i]) == 'CRSM') {
|
||
# co-trim resistant S. maltophilia
|
||
x[i] <- microorganismsDT[mo == 'B_STNTR_MAL', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
|
||
# peni I, peni R, vanco I, vanco R: S. pneumoniae
|
||
x[i] <- microorganismsDT[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
|
||
# Streptococci, like GBS = Group B Streptococci (B_STRPTC_GRB)
|
||
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) %like% '(streptococc|streptokok).* [ABCDFGHK]$') {
|
||
# Streptococci in different languages, like "estreptococos grupo B"
|
||
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPTC_GR\\2", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (toupper(x_trimmed[i]) %like% 'group [ABCDFGHK] (streptococ|streptokok|estreptococ)') {
|
||
# Streptococci in different languages, like "Group A Streptococci"
|
||
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
|
||
next
|
||
}
|
||
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
|
||
if (tolower(x[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
|
||
| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
|
||
| tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
|
||
# coerce S. coagulase negative
|
||
x[i] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
|
||
| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
|
||
| tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
|
||
# coerce S. coagulase positive
|
||
x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (tolower(x[i]) %like% 'gram[ -]?neg.*'
|
||
| tolower(x_trimmed[i]) %like% 'gram[ -]?neg.*') {
|
||
# coerce S. coagulase positive
|
||
x[i] <- microorganismsDT[mo == 'B_GRAMN', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (tolower(x[i]) %like% 'gram[ -]?pos.*'
|
||
| tolower(x_trimmed[i]) %like% 'gram[ -]?pos.*') {
|
||
# coerce S. coagulase positive
|
||
x[i] <- microorganismsDT[mo == 'B_GRAMP', ..property][[1]][1L]
|
||
next
|
||
}
|
||
if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_trimmed[i])) {
|
||
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
|
||
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
|
||
notes <- c(notes,
|
||
magenta(paste0("Note: ", italic(x_trimmed[i]),
|
||
" was considered (a subspecies of) ",
|
||
italic("Salmonella enterica"),
|
||
" (B_SLMNL_ENT)")))
|
||
next
|
||
}
|
||
}
|
||
|
||
# FIRST TRY FULLNAMES AND CODES
|
||
# if only genus is available, return only genus
|
||
if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
|
||
found <- microorganismsDT[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
if (nchar(x_trimmed[i]) > 4) {
|
||
# not when abbr is esco, stau, klpn, etc.
|
||
found <- microorganismsDT[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
}
|
||
}
|
||
|
||
# TRY OTHER SOURCES ----
|
||
if (toupper(x_backup[i]) %in% microorganisms.certe[, 1]) {
|
||
mo_found <- microorganisms.certe[toupper(x_backup[i]) == microorganisms.certe[, 1], 2][1L]
|
||
if (length(mo_found) > 0) {
|
||
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
|
||
next
|
||
}
|
||
}
|
||
if (x_backup[i] %in% microorganisms.umcg[, 1]) {
|
||
mo_umcg <- microorganisms.umcg[microorganisms.umcg[, 1] == x_backup[i], 2]
|
||
mo_found <- microorganisms.certe[microorganisms.certe[, 1] == mo_umcg, 2][1L]
|
||
if (length(mo_found) == 0) {
|
||
# not found
|
||
x[i] <- NA_character_
|
||
failures <- c(failures, x_backup[i])
|
||
} else {
|
||
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
|
||
}
|
||
next
|
||
}
|
||
if (!is.null(reference_df)) {
|
||
if (x_backup[i] %in% reference_df[, 1]) {
|
||
ref_mo <- reference_df[reference_df[, 1] == x_backup[i], 2]
|
||
if (ref_mo %in% microorganismsDT[, mo]) {
|
||
x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
|
||
next
|
||
} else {
|
||
warning("Value '", x_backup[i], "' was found in reference_df, but '", ref_mo, "' is not a valid MO code.", call. = FALSE)
|
||
}
|
||
}
|
||
}
|
||
|
||
# TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
|
||
found <- microorganisms.prevDT[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
|
||
# most probable: is exact match in fullname
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.prevDT[tsn == x_trimmed[i], ..property][[1]]
|
||
# is a valid TSN
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.prevDT[mo == toupper(x_backup[i]), ..property][[1]]
|
||
# is a valid mo
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.prevDT[tolower(fullname) == tolower(x_trimmed_without_group[i]), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
|
||
# try any match keeping spaces ----
|
||
found <- microorganisms.prevDT[fullname %like% x_withspaces[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
# try any match keeping spaces, not ending with $ ----
|
||
found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
# try any match diregarding spaces ----
|
||
found <- microorganisms.prevDT[fullname %like% x[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
|
||
# try splitting of characters in the middle and then find ID ----
|
||
# only when text length is 6 or lower
|
||
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
|
||
if (nchar(x_trimmed[i]) <= 6) {
|
||
x_length <- nchar(x_trimmed[i])
|
||
x[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2),
|
||
'.* ',
|
||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length))
|
||
found <- microorganisms.prevDT[fullname %like% paste0('^', x[i]), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
}
|
||
|
||
# try fullname without start and stop regex, to also find subspecies ----
|
||
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
|
||
found <- microorganisms.prevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
# THEN TRY ALL OTHERS ----
|
||
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
|
||
# most probable: is exact match in fullname
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_trimmed[i]), ..property][[1]]
|
||
# most probable: is exact match in fullname
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.unprevDT[tsn == x_trimmed[i], ..property][[1]]
|
||
# is a valid TSN
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.unprevDT[mo == toupper(x_backup[i]), ..property][[1]]
|
||
# is a valid mo
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_trimmed_without_group[i]), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
# try any match keeping spaces ----
|
||
found <- microorganisms.unprevDT[fullname %like% x_withspaces[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
# try any match keeping spaces, not ending with $ ----
|
||
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
# try any match diregarding spaces ----
|
||
found <- microorganisms.unprevDT[fullname %like% x[i], ..property][[1]]
|
||
if (length(found) > 0 & nchar(x_trimmed[i]) >= 6) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
# try splitting of characters in the middle and then find ID ----
|
||
# only when text length is 6 or lower
|
||
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
|
||
if (nchar(x_trimmed[i]) <= 6) {
|
||
x_length <- nchar(x_trimmed[i])
|
||
x[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2),
|
||
'.* ',
|
||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length))
|
||
found <- microorganisms.unprevDT[fullname %like% paste0('^', x[i]), ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
}
|
||
|
||
# try fullname without start and stop regex, to also find subspecies ----
|
||
# like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
|
||
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||
if (length(found) > 0) {
|
||
x[i] <- found[1L]
|
||
next
|
||
}
|
||
|
||
# MISCELLANEOUS ----
|
||
|
||
# look for old taxonomic names ----
|
||
found <- microorganisms.oldDT[tolower(name) == tolower(x_backup[i])
|
||
| tsn == x_trimmed[i]
|
||
| name %like% x_withspaces[i],]
|
||
if (NROW(found) > 0) {
|
||
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
|
||
# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
|
||
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
|
||
if (property == "ref") {
|
||
x[i] <- found[1, ref]
|
||
} else {
|
||
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
|
||
}
|
||
notes <- c(notes,
|
||
renamed_note(name_old = found[1, name],
|
||
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
|
||
ref_old = found[1, ref],
|
||
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
|
||
mo = microorganismsDT[tsn == found[1, tsn_new], mo]))
|
||
next
|
||
}
|
||
|
||
# check for uncertain results ----
|
||
if (allow_uncertain == TRUE) {
|
||
|
||
uncertain_fn <- function(a.x_backup, b.x_trimmed, c.x_withspaces, d.x_withspaces_start, e.x) {
|
||
# (1) look again for old taxonomic names, now for G. species ----
|
||
found <- microorganisms.oldDT[name %like% c.x_withspaces
|
||
| name %like% d.x_withspaces_start
|
||
| name %like% e.x,]
|
||
if (NROW(found) > 0 & nchar(b.x_trimmed) >= 6) {
|
||
if (property == "ref") {
|
||
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
|
||
# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
|
||
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
|
||
x <- found[1, ref]
|
||
} else {
|
||
x <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
|
||
}
|
||
warning(red(paste0('UNCERTAIN - "',
|
||
a.x_backup, '" -> ', italic(found[1, name]))),
|
||
call. = FALSE, immediate. = FALSE)
|
||
notes <<- c(notes,
|
||
renamed_note(name_old = found[1, name],
|
||
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
|
||
ref_old = found[1, ref],
|
||
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
|
||
mo = microorganismsDT[tsn == found[1, tsn_new], mo]))
|
||
return(x)
|
||
}
|
||
|
||
# (2) strip values between brackets ----
|
||
a.x_backup_stripped <- gsub("( [(].*[)])", "", a.x_backup)
|
||
a.x_backup_stripped <- trimws(gsub(" ", " ", a.x_backup_stripped, fixed = TRUE))
|
||
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, clear_options = FALSE, allow_uncertain = FALSE)))
|
||
if (!is.na(found) & nchar(b.x_trimmed) >= 6) {
|
||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||
warning(red(paste0('UNCERTAIN - "',
|
||
a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
|
||
call. = FALSE, immediate. = FALSE)
|
||
return(found[1L])
|
||
}
|
||
|
||
# (3) try to strip off one element and check the remains ----
|
||
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
|
||
if (length(x_strip) > 1 & nchar(b.x_trimmed) >= 6) {
|
||
for (i in 1:(length(x_strip) - 1)) {
|
||
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
|
||
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE, allow_uncertain = FALSE)))
|
||
if (!is.na(found)) {
|
||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||
warning(red(paste0('UNCERTAIN - "',
|
||
a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
|
||
call. = FALSE, immediate. = FALSE)
|
||
return(found[1L])
|
||
}
|
||
}
|
||
}
|
||
|
||
# (4) not yet implemented taxonomic changes in ITIS
|
||
found <- suppressMessages(suppressWarnings(exec_as.mo(temp_changes(b.x_trimmed), clear_options = FALSE, allow_uncertain = FALSE)))
|
||
if (!is.na(found)) {
|
||
found <- microorganismsDT[mo == found, ..property][[1]]
|
||
warning(red(paste0('UNCERTAIN - "',
|
||
a.x_backup, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
|
||
call. = FALSE, immediate. = FALSE)
|
||
return(found[1L])
|
||
}
|
||
|
||
# didn't found in uncertain results too
|
||
return(NA_character_)
|
||
}
|
||
|
||
x[i] <- uncertain_fn(x_backup[i], x_trimmed[i], x_withspaces[i], x_withspaces_start[i], x[i])
|
||
if (!is.na(x[i])) {
|
||
next
|
||
}
|
||
}
|
||
|
||
# not found ----
|
||
x[i] <- NA_character_
|
||
failures <- c(failures, x_backup[i])
|
||
|
||
}
|
||
}
|
||
|
||
failures <- failures[!failures %in% c(NA, NULL, NaN)]
|
||
if (length(failures) > 0) {
|
||
options(mo_failures = sort(unique(failures)))
|
||
if (n_distinct(failures) > 25) {
|
||
warning(n_distinct(failures), " different values could not be coerced to a valid MO code. See mo_failures() to review them.",
|
||
call. = FALSE)
|
||
} else {
|
||
warning(red(paste0("These ", length(failures) , " values could not be coerced to a valid MO code: ",
|
||
paste('"', unique(failures), '"', sep = "", collapse = ', '),
|
||
". See mo_failures() to review them.")),
|
||
call. = FALSE,
|
||
immediate. = TRUE) # thus will always be shown, even if >= warnings
|
||
}
|
||
}
|
||
|
||
# Becker ----
|
||
if (Becker == TRUE | Becker == "all") {
|
||
# See Source. It's this figure:
|
||
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
||
MOs_staph <- microorganismsDT[genus == "Staphylococcus"]
|
||
setkey(MOs_staph, species)
|
||
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
||
"caprae", "carnosus", "cohnii", "condimenti",
|
||
"devriesei", "epidermidis", "equorum",
|
||
"fleurettii", "gallinarum", "haemolyticus",
|
||
"hominis", "jettensis", "kloosii", "lentus",
|
||
"lugdunensis", "massiliensis", "microti",
|
||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||
"pettenkoferi", "piscifermentans", "rostri",
|
||
"saccharolyticus", "saprophyticus", "sciuri",
|
||
"stepanovicii", "simulans", "succinus",
|
||
"vitulinus", "warneri", "xylosus"), ..property][[1]]
|
||
CoPS <- MOs_staph[species %in% c("simiae", "agnetis", "chromogenes",
|
||
"delphini", "felis", "lutrae",
|
||
"hyicus", "intermedius",
|
||
"pseudintermedius", "pseudointermedius",
|
||
"schleiferi"), ..property][[1]]
|
||
x[x %in% CoNS] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
|
||
x[x %in% CoPS] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||
if (Becker == "all") {
|
||
x[x == microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||
}
|
||
}
|
||
|
||
# Lancefield ----
|
||
if (Lancefield == TRUE | Lancefield == "all") {
|
||
# group A - S. pyogenes
|
||
x[x == microorganismsDT[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
||
# group B - S. agalactiae
|
||
x[x == microorganismsDT[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
|
||
# group C
|
||
S_groupC <- microorganismsDT %>% filter(genus == "Streptococcus",
|
||
species %in% c("equisimilis", "equi",
|
||
"zooepidemicus", "dysgalactiae")) %>%
|
||
pull(property)
|
||
x[x %in% S_groupC] <- microorganismsDT[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
|
||
if (Lancefield == "all") {
|
||
# all Enterococci
|
||
x[x %like% "^(Enterococcus|B_ENTRC)"] <- microorganismsDT[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
|
||
}
|
||
# group F - S. anginosus
|
||
x[x == microorganismsDT[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
|
||
# group H - S. sanguinis
|
||
x[x == microorganismsDT[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
|
||
# group K - S. salivarius
|
||
x[x == microorganismsDT[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
|
||
}
|
||
|
||
# comply to x, which is also unique and without empty values
|
||
x_input_unique_nonempty <- unique(x_input[!is.na(x_input) & !is.null(x_input) & !identical(x_input, "")])
|
||
|
||
# left join the found results to the original input values (x_input)
|
||
df_found <- data.frame(input = as.character(x_input_unique_nonempty),
|
||
found = as.character(x),
|
||
stringsAsFactors = FALSE)
|
||
df_input <- data.frame(input = as.character(x_input),
|
||
stringsAsFactors = FALSE)
|
||
x <- df_input %>%
|
||
left_join(df_found,
|
||
by = "input") %>%
|
||
pull(found)
|
||
|
||
if (property == "mo") {
|
||
class(x) <- "mo"
|
||
} else if (property == "tsn") {
|
||
x <- as.integer(x)
|
||
}
|
||
|
||
if (length(notes > 0)) {
|
||
notes <- sort(notes)
|
||
for (i in 1:length(notes)) {
|
||
base::message(notes[i])
|
||
}
|
||
}
|
||
|
||
x
|
||
}
|
||
|
||
temp_changes <- function(x) {
|
||
x[x %like% 'Cutibacterium'] <- gsub('Cutibacterium', 'Propionibacterium', x[x %like% 'Cutibacterium'])
|
||
}
|
||
|
||
#' @importFrom crayon blue italic
|
||
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "") {
|
||
if (!is.na(ref_old)) {
|
||
ref_old <- paste0(" (", ref_old, ")")
|
||
} else {
|
||
ref_old <- ""
|
||
}
|
||
if (!is.na(ref_new)) {
|
||
ref_new <- paste0(" (", ref_new, ")")
|
||
} else {
|
||
ref_new <- ""
|
||
}
|
||
if (!is.na(mo)) {
|
||
mo <- paste0(" (", mo, ")")
|
||
} else {
|
||
mo <- ""
|
||
}
|
||
msg <- paste0(italic(name_old), ref_old, " was renamed ", italic(name_new), ref_new, mo)
|
||
msg <- gsub("et al.", italic("et al."), msg)
|
||
msg_plain <- paste0(name_old, ref_old, " -> ", name_new, ref_new)
|
||
msg_plain <- c(getOption("mo_renamed", character(0)), msg_plain)
|
||
options(mo_renamed = sort(msg_plain))
|
||
return(blue(paste("Note:", msg)))
|
||
}
|
||
|
||
#' @exportMethod print.mo
|
||
#' @export
|
||
#' @noRd
|
||
print.mo <- function(x, ...) {
|
||
cat("Class 'mo'\n")
|
||
x_names <- names(x)
|
||
x <- as.character(x)
|
||
names(x) <- x_names
|
||
print.default(x, quote = FALSE)
|
||
}
|
||
|
||
#' @exportMethod summary.mo
|
||
#' @export
|
||
#' @noRd
|
||
summary.mo <- function(object, ...) {
|
||
# unique and top 1-3
|
||
x <- object
|
||
top_3 <- unname(top_freq(freq(x), 3))
|
||
c("Class" = "mo",
|
||
"<NA>" = length(x[is.na(x)]),
|
||
"Unique" = dplyr::n_distinct(x[!is.na(x)]),
|
||
"#1" = top_3[1],
|
||
"#2" = top_3[2],
|
||
"#3" = top_3[3])
|
||
}
|
||
|
||
#' @exportMethod as.data.frame.mo
|
||
#' @export
|
||
#' @noRd
|
||
as.data.frame.mo <- function (x, ...) {
|
||
# same as as.data.frame.character but with removed stringsAsFactors, since it will be class "mo"
|
||
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.mo
|
||
#' @export
|
||
#' @importFrom dplyr pull
|
||
#' @noRd
|
||
pull.mo <- function(.data, ...) {
|
||
pull(as.data.frame(.data), ...)
|
||
}
|
||
|
||
#' Vector of failed coercion attempts
|
||
#'
|
||
#' Returns a vector of all failed attempts to coerce values to a valid MO code with \code{\link{as.mo}}.
|
||
#' @seealso \code{\link{as.mo}}
|
||
#' @export
|
||
mo_failures <- function() {
|
||
getOption("mo_failures")
|
||
}
|
||
|
||
#' Vector of taxonomic renamed items
|
||
#'
|
||
#' Returns a vector of all renamed items of the last coercion to valid MO codes with \code{\link{as.mo}}.
|
||
#' @seealso \code{\link{as.mo}}
|
||
#' @export
|
||
mo_renamed <- function() {
|
||
getOption("mo_renamed")
|
||
}
|