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speed improvement for as.mo, more old taxonomic names
This commit is contained in:
746
R/mo.R
746
R/mo.R
@ -60,7 +60,7 @@
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#' \code{guess_mo} is an alias of \code{as.mo}.
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#' @section ITIS:
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#' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
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#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
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# (source as section, so it can be inherited by mo_property:)
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#' @section Source:
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#' [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}
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@ -69,8 +69,6 @@
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#'
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#' [3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
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#' @export
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#' @importFrom dplyr %>% pull left_join
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#' @importFrom data.table as.data.table setkey
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#' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
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#' @seealso \code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
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#' The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
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@ -126,7 +124,25 @@
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#' mutate(mo = guess_mo(paste(genus, species)))
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE) {
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exec_as.mo(x = x, Becker = Becker, Lancefield = Lancefield,
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allow_uncertain = allow_uncertain, property = "mo")
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}
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#' @rdname as.mo
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#' @export
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is.mo <- function(x) {
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# bactid for older releases
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# remove when is.bactid will be removed
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identical(class(x), "mo") | identical(class(x), "bactid")
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}
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#' @rdname as.mo
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#' @export
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guess_mo <- as.mo
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#' @importFrom dplyr %>% pull left_join
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#' @importFrom data.table as.data.table setkey
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exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, property = "mo") {
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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@ -147,374 +163,362 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
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}
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}
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MOs <- as.data.table(AMR::microorganisms)
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setkey(MOs, prevalence, tsn)
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MOs_mostprevalent <- MOs[prevalence != 9999,]
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MOs_allothers <- NULL # will be set later, if needed
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MOs_old <- NULL # will be set later, if needed
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if (all(unique(x) %in% MOs[,mo])) {
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class(x) <- "mo"
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attr(x, 'package') <- 'AMR'
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attr(x, 'ITIS') <- TRUE
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return(x)
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}
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if (AMR::is.mo(x) & isTRUE(attributes(x)$ITIS)) {
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# check for new mo class, data coming from ITIS
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return(x)
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}
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failures <- character(0)
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x_input <- x
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# only check the uniques, which is way faster
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x <- unique(x)
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x_backup <- trimws(x, which = "both")
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x_species <- paste(x_backup, "species")
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# translate to English for supported languages of mo_property
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x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x)
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# remove 'empty' genus and species values
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x <- gsub("(no MO)", "", x, fixed = TRUE)
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# remove dots and other non-text in case of "E. coli" except spaces
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x <- gsub("[^a-zA-Z0-9/ \\-]+", "", x)
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# but spaces before and after should be omitted
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x <- trimws(x, which = "both")
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x_trimmed <- x
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x_trimmed_species <- paste(x_trimmed, "species")
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# replace space by regex sign
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x_withspaces <- gsub(" ", ".* ", x, fixed = TRUE)
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x <- gsub(" ", ".*", x, fixed = TRUE)
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# add start en stop regex
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x <- paste0('^', x, '$')
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x_withspaces_all <- x_withspaces
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x_withspaces_start <- paste0('^', x_withspaces)
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x_withspaces <- paste0('^', x_withspaces, '$')
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MOs <- NULL # will be set later, if needed
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MOs_mostprevalent <- NULL # will be set later, if needed
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MOs_allothers <- NULL # will be set later, if needed
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MOs_old <- NULL # will be set later, if needed
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# cat(paste0('x "', x, '"\n'))
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# cat(paste0('x_species "', x_species, '"\n'))
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# cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
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# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
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# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
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# cat(paste0('x_backup "', x_backup, '"\n'))
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# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
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# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
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if (all(x %in% AMR::microorganisms[, property])) {
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# already existing mo
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} else if (all(x %in% AMR::microorganisms.certe[, "certe"])) {
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# old Certe codes
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suppressWarnings(
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x <- data.frame(certe = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms.certe, by = "certe") %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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} else if (all(x %in% AMR::microorganisms.umcg[, "umcg"])) {
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# old UMCG codes
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suppressWarnings(
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x <- data.frame(umcg = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms.umcg, by = "umcg") %>%
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left_join(AMR::microorganisms.certe, by = "certe") %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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} else {
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for (i in 1:length(x)) {
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if (identical(x_trimmed[i], "") | is.na(x_trimmed[i])) {
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# empty values
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x[i] <- NA
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next
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}
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MOs <- as.data.table(AMR::microorganisms)
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setkey(MOs, prevalence, tsn)
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MOs_mostprevalent <- MOs[prevalence != 9999,]
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# translate known trivial abbreviations to genus + species ----
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if (!is.na(x_trimmed[i])) {
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if (toupper(x_trimmed[i]) == 'MRSA'
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| toupper(x_trimmed[i]) == 'VISA'
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| toupper(x_trimmed[i]) == 'VRSA') {
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x[i] <- 'B_STPHY_AUR'
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next
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}
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if (toupper(x_trimmed[i]) == 'MRSE') {
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x[i] <- 'B_STPHY_EPI'
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next
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}
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if (toupper(x_trimmed[i]) == 'VRE') {
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x[i] <- 'B_ENTRC'
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next
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}
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if (toupper(x_trimmed[i]) == 'MRPA') {
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# multi resistant P. aeruginosa
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x[i] <- 'B_PDMNS_AER'
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next
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}
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if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
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# peni I, peni R, vanco I, vanco R: S. pneumoniae
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x[i] <- 'B_STRPTC_PNE'
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next
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}
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if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
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x[i] <- gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i])
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next
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}
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# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
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if (tolower(x[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
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# coerce S. coagulase negative
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x[i] <- 'B_STPHY_CNS'
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next
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}
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if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
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# coerce S. coagulase positive
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x[i] <- 'B_STPHY_CPS'
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next
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}
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}
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x_backup <- trimws(x, which = "both")
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x_species <- paste(x_backup, "species")
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# translate to English for supported languages of mo_property
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x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x)
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# remove 'empty' genus and species values
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x <- gsub("(no MO)", "", x, fixed = TRUE)
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# remove dots and other non-text in case of "E. coli" except spaces
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x <- gsub("[^a-zA-Z0-9/ \\-]+", "", x)
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# but spaces before and after should be omitted
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x <- trimws(x, which = "both")
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x_trimmed <- x
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x_trimmed_species <- paste(x_trimmed, "species")
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# replace space by regex sign
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x_withspaces <- gsub(" ", ".* ", x, fixed = TRUE)
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x <- gsub(" ", ".*", x, fixed = TRUE)
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# add start en stop regex
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x <- paste0('^', x, '$')
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x_withspaces_all <- x_withspaces
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x_withspaces_start <- paste0('^', x_withspaces)
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x_withspaces <- paste0('^', x_withspaces, '$')
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# FIRST TRY FULLNAMES AND CODES
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# if only genus is available, don't select species
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if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
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found <- MOs[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), mo]
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if (length(found) > 0) {
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x[i] <- found[1L]
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# cat(paste0('x "', x, '"\n'))
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# cat(paste0('x_species "', x_species, '"\n'))
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# cat(paste0('x_withspaces_all "', x_withspaces_all, '"\n'))
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# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
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# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
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# cat(paste0('x_backup "', x_backup, '"\n'))
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# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
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# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
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for (i in 1:length(x)) {
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if (identical(x_trimmed[i], "") | is.na(x_trimmed[i])) {
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# empty values
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x[i] <- NA
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next
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}
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if (nchar(x_trimmed[i]) > 4) {
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# not when abbr is esco, stau, klpn, etc.
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found <- MOs[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), mo]
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# translate known trivial abbreviations to genus + species ----
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if (!is.na(x_trimmed[i])) {
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if (toupper(x_trimmed[i]) == 'MRSA'
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| toupper(x_trimmed[i]) == 'VISA'
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| toupper(x_trimmed[i]) == 'VRSA') {
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x[i] <- MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'MRSE') {
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x[i] <- MOs[mo == 'B_STPHY_EPI', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'VRE') {
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x[i] <- MOs[mo == 'B_ENTRC', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) == 'MRPA') {
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# multi resistant P. aeruginosa
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x[i] <- MOs[mo == 'B_PDMNS_AER', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
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# peni I, peni R, vanco I, vanco R: S. pneumoniae
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x[i] <- MOs[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
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next
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}
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if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
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x[i] <- MOs[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i]), ..property][[1]][1L]
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next
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}
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# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
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if (tolower(x[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
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# coerce S. coagulase negative
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x[i] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
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next
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}
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if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
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| tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
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# coerce S. coagulase positive
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x[i] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
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next
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}
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}
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# FIRST TRY FULLNAMES AND CODES
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# if only genus is available, don't select species
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if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
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found <- MOs[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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if (nchar(x_trimmed[i]) > 4) {
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# not when abbr is esco, stau, klpn, etc.
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found <- MOs[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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}
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}
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}
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# search for GLIMS code ----
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found <- AMR::microorganisms.umcg[which(toupper(AMR::microorganisms.umcg$umcg) == toupper(x_trimmed[i])),]$mo
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if (length(found) > 0) {
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x[i] <- MOs[mo.old == found, mo][1L]
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next
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}
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# TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
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# TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
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found <- MOs_mostprevalent[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
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# most probable: is exact match in fullname
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[tsn == x_trimmed[i], ..property][[1]]
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# is a valid TSN
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[mo == toupper(x_backup[i]), ..property][[1]]
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# is a valid mo
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), mo]
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# most probable: is exact match in fullname
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[tsn == x_trimmed[i], mo]
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# is a valid TSN
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[mo == toupper(x_backup[i]), mo]
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# is a valid mo
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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found <- MOs_mostprevalent[mo.old == toupper(x_backup[i])
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| (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
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| mo.old == substr(x_backup[i], 1, 3), mo]
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# is a valid old mo
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match keeping spaces ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match keeping spaces ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces[i], mo]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match keeping spaces, not ending with $ ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], ..property][[1]]
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# try any match keeping spaces, not ending with $ ----
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found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], mo]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
# try any match diregarding spaces ----
|
||||
found <- MOs_mostprevalent[fullname %like% x[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match diregarding spaces ----
|
||||
found <- MOs_mostprevalent[fullname %like% x[i], mo]
|
||||
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 <- MOs_mostprevalent[fullname %like% x_withspaces_start[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 <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], mo]
|
||||
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_trimmed[i])
|
||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||
'.* ',
|
||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||
found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||
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_trimmed[i])
|
||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||
'.* ',
|
||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||
found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), mo]
|
||||
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_trimmed[i] %like% "^Gram") {
|
||||
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
|
||||
# # remove leading and trailing spaces again
|
||||
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
|
||||
# }
|
||||
# if (!is.na(x_trimmed[i])) {
|
||||
# found <- MOs_mostprevalent[fullname %like% x_trimmed[i], ..property][[1]]
|
||||
# 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_trimmed[i] %like% "^Gram") {
|
||||
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
|
||||
# # remove leading and trailing spaces again
|
||||
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
|
||||
# }
|
||||
# if (!is.na(x_trimmed[i])) {
|
||||
# found <- MOs_mostprevalent[fullname %like% x_trimmed[i], mo]
|
||||
# if (length(found) > 0) {
|
||||
# x[i] <- found[1L]
|
||||
# next
|
||||
# }
|
||||
# }
|
||||
# THEN TRY ALL OTHERS ----
|
||||
if (is.null(MOs_allothers)) {
|
||||
MOs_allothers <- MOs[prevalence == 9999,]
|
||||
}
|
||||
|
||||
# THEN TRY ALL OTHERS ----
|
||||
if (is.null(MOs_allothers)) {
|
||||
MOs_allothers <- MOs[prevalence == 9999,]
|
||||
}
|
||||
found <- MOs_allothers[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 <- MOs_allothers[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 <- MOs_allothers[tsn == x_trimmed[i], ..property][[1]]
|
||||
# is a valid TSN
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[mo == toupper(x_backup[i]), ..property][[1]]
|
||||
# is a valid mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), mo]
|
||||
# most probable: is exact match in fullname
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[tolower(fullname) == tolower(x_trimmed[i]), mo]
|
||||
# most probable: is exact match in fullname
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[tsn == x_trimmed[i], mo]
|
||||
# is a valid TSN
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[mo == toupper(x_backup[i]), mo]
|
||||
# is a valid mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
found <- MOs_allothers[mo.old == toupper(x_backup[i])
|
||||
| (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
|
||||
| mo.old == substr(x_backup[i], 1, 3), mo]
|
||||
# is a valid old mo
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
# try any match keeping spaces ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match keeping spaces ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces[i], mo]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
# try any match keeping spaces, not ending with $ ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces_start[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match keeping spaces, not ending with $ ----
|
||||
found <- MOs_allothers[fullname %like% x_withspaces_start[i], mo]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
# try any match diregarding spaces ----
|
||||
found <- MOs_allothers[fullname %like% x[i], ..property][[1]]
|
||||
if (length(found) > 0) {
|
||||
x[i] <- found[1L]
|
||||
next
|
||||
}
|
||||
|
||||
# try any match diregarding spaces ----
|
||||
found <- MOs_allothers[fullname %like% x[i], mo]
|
||||
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 <- MOs_allothers[fullname %like% x_withspaces_start[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 <- MOs_allothers[fullname %like% x_withspaces_start[i], mo]
|
||||
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_trimmed[i])
|
||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||
'.* ',
|
||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||
found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||
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_trimmed[i])
|
||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||
'.* ',
|
||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||
found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), mo]
|
||||
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_trimmed[i] %like% "^Gram") {
|
||||
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
|
||||
# # remove leading and trailing spaces again
|
||||
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
|
||||
# }
|
||||
# if (!is.na(x_trimmed[i])) {
|
||||
# found <- MOs_allothers[fullname %like% x_trimmed[i], ..property][[1]]
|
||||
# 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_trimmed[i] %like% "^Gram") {
|
||||
# x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
|
||||
# # remove leading and trailing spaces again
|
||||
# x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
|
||||
# }
|
||||
# if (!is.na(x_trimmed[i])) {
|
||||
# found <- MOs_allothers[fullname %like% x_trimmed[i], mo]
|
||||
# if (length(found) > 0) {
|
||||
# x[i] <- found[1L]
|
||||
# next
|
||||
# }
|
||||
# }
|
||||
# MISCELLANEOUS ----
|
||||
|
||||
# MISCELLANEOUS ----
|
||||
|
||||
# look for old taxonomic names ----
|
||||
if (is.null(MOs_old)) {
|
||||
MOs_old <- as.data.table(AMR::microorganisms.old)
|
||||
setkey(MOs_old, name, tsn_new)
|
||||
}
|
||||
found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
|
||||
tsn == x_trimmed[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], mo]
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
authors = found[1, authors],
|
||||
year = found[1, year])
|
||||
next
|
||||
}
|
||||
|
||||
# check for uncertain results ----
|
||||
if (allow_uncertain == TRUE) {
|
||||
# (1) look again for old taxonomic names, now for G. species ----
|
||||
found <- MOs_old[name %like% x_withspaces[i]
|
||||
| name %like% x_withspaces_start[i]
|
||||
| name %like% x[i],]
|
||||
# look for old taxonomic names ----
|
||||
if (is.null(MOs_old)) {
|
||||
MOs_old <- as.data.table(AMR::microorganisms.old)
|
||||
setkey(MOs_old, name, tsn_new)
|
||||
}
|
||||
found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
|
||||
tsn == x_trimmed[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], mo]
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", found[1, name], "'",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
authors = found[1, authors],
|
||||
year = found[1, year])
|
||||
|
||||
next
|
||||
}
|
||||
|
||||
# (2) try to strip off one element and check the remains
|
||||
x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
|
||||
x_strip <- x_strip[1:length(x_strip) - 1]
|
||||
x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
|
||||
if (!is.na(x[i])) {
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
next
|
||||
# check for uncertain results ----
|
||||
if (allow_uncertain == TRUE) {
|
||||
# (1) look again for old taxonomic names, now for G. species ----
|
||||
found <- MOs_old[name %like% x_withspaces[i]
|
||||
| name %like% x_withspaces_start[i]
|
||||
| name %like% x[i],]
|
||||
if (NROW(found) > 0) {
|
||||
x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", found[1, name], "'",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
renamed_note(name_old = found[1, name],
|
||||
name_new = MOs[tsn == found[1, tsn_new], fullname],
|
||||
authors = found[1, authors],
|
||||
year = found[1, year])
|
||||
|
||||
next
|
||||
}
|
||||
|
||||
# (2) try to strip off one element and check the remains
|
||||
x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
|
||||
x_strip <- x_strip[1:length(x_strip) - 1]
|
||||
x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
|
||||
if (!is.na(x[i])) {
|
||||
warning("Uncertain interpretation: '",
|
||||
x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
|
||||
call. = FALSE, immediate. = TRUE)
|
||||
next
|
||||
}
|
||||
}
|
||||
|
||||
# not found ----
|
||||
x[i] <- NA_character_
|
||||
failures <- c(failures, x_backup[i])
|
||||
|
||||
}
|
||||
|
||||
# not found ----
|
||||
x[i] <- NA_character_
|
||||
failures <- c(failures, x_backup[i])
|
||||
|
||||
}
|
||||
|
||||
failures <- failures[!failures %in% c(NA, NULL, NaN)]
|
||||
@ -529,6 +533,10 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
if (Becker == TRUE | Becker == "all") {
|
||||
# See Source. It's this figure:
|
||||
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
||||
if (is.null(MOs)) {
|
||||
MOs <- as.data.table(AMR::microorganisms)
|
||||
setkey(MOs, prevalence, tsn)
|
||||
}
|
||||
MOs_staph <- MOs[genus == "Staphylococcus"]
|
||||
setkey(MOs_staph, species)
|
||||
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
||||
@ -541,65 +549,66 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
|
||||
"pettenkoferi", "piscifermentans", "rostri",
|
||||
"saccharolyticus", "saprophyticus", "sciuri",
|
||||
"stepanovicii", "simulans", "succinus",
|
||||
"vitulinus", "warneri", "xylosus"), mo]
|
||||
"vitulinus", "warneri", "xylosus"), ..property][[1]]
|
||||
CoPS <- MOs_staph[species %in% c("simiae", "agnetis", "chromogenes",
|
||||
"delphini", "felis", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schleiferi"), mo]
|
||||
x[x %in% CoNS] <- "B_STPHY_CNS"
|
||||
x[x %in% CoPS] <- "B_STPHY_CPS"
|
||||
"schleiferi"), ..property][[1]]
|
||||
x[x %in% CoNS] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
|
||||
x[x %in% CoPS] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
if (Becker == "all") {
|
||||
x[x == "B_STPHY_AUR"] <- "B_STPHY_CPS"
|
||||
x[x == MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
|
||||
}
|
||||
}
|
||||
|
||||
# Lancefield ----
|
||||
if (Lancefield == TRUE | Lancefield == "all") {
|
||||
# group A
|
||||
x[x == "B_STRPTC_PYO"] <- "B_STRPTC_GRA" # S. pyogenes
|
||||
# group B
|
||||
x[x == "B_STRPTC_AGA"] <- "B_STRPTC_GRB" # S. agalactiae
|
||||
if (is.null(MOs)) {
|
||||
MOs <- as.data.table(AMR::microorganisms)
|
||||
setkey(MOs, prevalence, tsn)
|
||||
}
|
||||
# group A - S. pyogenes
|
||||
x[x == MOs[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
||||
# group B - S. agalactiae
|
||||
x[x == MOs[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
|
||||
# group C
|
||||
S_groupC <- MOs %>% filter(genus == "Streptococcus",
|
||||
species %in% c("equisimilis", "equi",
|
||||
"zooepidemicus", "dysgalactiae")) %>%
|
||||
pull(mo)
|
||||
x[x %in% S_groupC] <- "B_STRPTC_GRC" # S. agalactiae
|
||||
pull(property)
|
||||
x[x %in% S_groupC] <- MOs[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
|
||||
if (Lancefield == "all") {
|
||||
x[substr(x, 1, 7) == "B_ENTRC"] <- "B_STRPTC_GRD" # all Enterococci
|
||||
# all Enterococci
|
||||
x[x %like% "^(Enterococcus|B_ENTRC)"] <- MOs[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
|
||||
}
|
||||
# group F
|
||||
x[x == "B_STRPTC_ANG"] <- "B_STRPTC_GRF" # S. anginosus
|
||||
# group H
|
||||
x[x == "B_STRPTC_SAN"] <- "B_STRPTC_GRH" # S. sanguinis
|
||||
# group K
|
||||
x[x == "B_STRPTC_SAL"] <- "B_STRPTC_GRK" # S. salivarius
|
||||
# group F - S. anginosus
|
||||
x[x == MOs[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
|
||||
# group H - S. sanguinis
|
||||
x[x == MOs[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
|
||||
# group K - S. salivarius
|
||||
x[x == MOs[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
|
||||
}
|
||||
|
||||
# left join the found results to the original input values (x_input)
|
||||
DT_found <- data.table(input = as.character(unique(x_input)),
|
||||
df_found <- data.frame(input = as.character(unique(x_input)),
|
||||
found = x,
|
||||
key = "input",
|
||||
stringsAsFactors = FALSE)
|
||||
DT_input <- data.table(input = as.character(x_input),
|
||||
key = "input",
|
||||
df_input <- data.frame(input = as.character(x_input),
|
||||
stringsAsFactors = FALSE)
|
||||
x <- DT_found[DT_input, on = "input", found]
|
||||
x <- df_input %>%
|
||||
left_join(df_found,
|
||||
by = "input") %>%
|
||||
pull(found)
|
||||
|
||||
# df_found <- data.frame(input = as.character(unique(x_input)),
|
||||
# found = 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"
|
||||
attr(x, 'package') <- 'AMR'
|
||||
attr(x, 'ITIS') <- TRUE
|
||||
} else if (property == "tsn") {
|
||||
x <- as.integer(x)
|
||||
}
|
||||
|
||||
class(x) <- "mo"
|
||||
attr(x, 'package') <- 'AMR'
|
||||
attr(x, 'ITIS') <- TRUE
|
||||
x
|
||||
}
|
||||
|
||||
@ -614,19 +623,6 @@ renamed_note <- function(name_old, name_new, authors, year) {
|
||||
base::message(msg)
|
||||
}
|
||||
|
||||
|
||||
#' @rdname as.mo
|
||||
#' @export
|
||||
is.mo <- function(x) {
|
||||
# bactid for older releases
|
||||
# remove when is.bactid will be removed
|
||||
identical(class(x), "mo") | identical(class(x), "bactid")
|
||||
}
|
||||
|
||||
#' @rdname as.mo
|
||||
#' @export
|
||||
guess_mo <- as.mo
|
||||
|
||||
#' @exportMethod print.mo
|
||||
#' @export
|
||||
#' @noRd
|
||||
|
||||
Reference in New Issue
Block a user