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AI improvements
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70
R/mo.R
70
R/mo.R
@ -26,7 +26,7 @@
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#' @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.
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#'
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#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
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#' @param allow_uncertain a logical to indicate whether empty results should be checked for only a part of the input string. When results are found, a warning will be given about the uncertainty and the result.
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#' @param allow_uncertain a logical to indicate whether the input should be checked for less possible results, see Details
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#' @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.
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#' @rdname as.mo
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#' @aliases mo
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@ -34,11 +34,11 @@
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#' @details
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#' A microbial ID from this package (class: \code{mo}) typically looks like these examples:\cr
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#' \preformatted{
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#' Code Full name
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#' --------------- --------------------------------------
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#' B_KLBSL Klebsiella
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#' B_KLBSL_PNE Klebsiella pneumoniae
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#' B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
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#' Code Full name
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#' --------------- --------------------------------------
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#' B_KLBSL Klebsiella
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#' B_KLBSL_PNE Klebsiella pneumoniae
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#' B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
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#' | | | |
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#' | | | |
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#' | | | ----> subspecies, a 3-4 letter acronym
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@ -57,7 +57,7 @@
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#' \item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
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#' }
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#'
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#' A couple of effects because of these rules
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#' A couple of effects because of these rules:
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#' \itemize{
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#' \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
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#' \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
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@ -66,6 +66,13 @@
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#' }
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#' This means that looking up human pathogenic microorganisms takes less time than looking up human \strong{non}-pathogenic microorganisms.
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#'
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#' 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:
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#' \itemize{
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#' \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.}
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#' \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.}
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#' \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.}
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#' }
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#'
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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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@ -94,6 +101,7 @@
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#' as.mo("S. aureus")
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#' as.mo("S aureus")
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#' as.mo("Staphylococcus aureus")
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#' as.mo("Staphylococcus aureus (MRSA)")
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#' as.mo("MRSA") # Methicillin Resistant S. aureus
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#' as.mo("VISA") # Vancomycin Intermediate S. aureus
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#' as.mo("VRSA") # Vancomycin Resistant S. aureus
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@ -136,7 +144,7 @@
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#' df <- df %>%
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#' mutate(mo = as.mo(paste(genus, species)))
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, reference_df = NULL) {
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = NULL) {
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mo <- mo_validate(x = x, property = "mo",
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Becker = Becker, Lancefield = Lancefield,
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allow_uncertain = allow_uncertain, reference_df = reference_df)
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@ -155,11 +163,11 @@ is.mo <- function(x) {
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#' @export
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guess_mo <- as.mo
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#' @importFrom dplyr %>% pull left_join n_distinct
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#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated
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#' @importFrom data.table data.table as.data.table setkey
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#' @importFrom crayon magenta red italic
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exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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allow_uncertain = FALSE, reference_df = NULL,
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allow_uncertain = TRUE, reference_df = NULL,
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property = "mo", clear_options = TRUE) {
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if (!"AMR" %in% base::.packages()) {
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@ -272,7 +280,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
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# cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n'))
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progress <- progress_estimated(n = length(x), min_time = 3)
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for (i in 1:length(x)) {
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progress$tick()$print()
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if (identical(x_trimmed[i], "")) {
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# empty values
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x[i] <- NA_character_
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@ -615,8 +628,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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} else {
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x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
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}
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warning(red(paste0("UNCERTAIN - '",
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x_backup[i], "' -> ", italic(found[1, name]))),
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warning(red(paste0('UNCERTAIN - "',
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x_backup[i], '" -> ', italic(found[1, name]))),
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call. = FALSE, immediate. = TRUE)
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renamed_note(name_old = found[1, name],
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name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
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@ -627,13 +640,17 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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}
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# (2) strip values between brackets ----
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found <- microorganismsDT[fullname %like% gsub("( [(].*[)]) ", " ", x_withspaces[i])
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| fullname %like% gsub("( [(].*[)]) ", " ", x_backup[i])
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| fullname %like% gsub("( [(].*[)]) ", " ", x[i]),]
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x_backup_stripped <- gsub("( [(].*[)])", "", x_backup[i])
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x_backup_stripped <- trimws(gsub(" ", " ", x_backup_stripped, fixed = TRUE))
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x_species_stripped <- gsub("( [(].*[)])", "", x_species[i])
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x_species_stripped <- trimws(gsub(" ", " ", x_species_stripped, fixed = TRUE))
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found <- microorganismsDT[fullname %like% x_backup_stripped
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| fullname %like% x_species_stripped,]
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if (NROW(found) > 0 & nchar(x_trimmed[i]) >= 6) {
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x[i] <- found[1, ..property][[1]]
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warning(red(paste0("UNCERTAIN - '",
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x_backup[i], "' -> ", italic(found[1, fullname][[1]]), " (", found[1, mo][[1]], ")")),
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warning(red(paste0('UNCERTAIN - "',
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x_backup[i], '" -> ', italic(found[1, fullname][[1]]), " (", found[1, mo][[1]], ")")),
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call. = FALSE, immediate. = TRUE)
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next
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}
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@ -647,8 +664,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE)))
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if (!is.na(found)) {
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found <- microorganismsDT[mo == found, ..property][[1]]
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warning(red(paste0("UNCERTAIN - '",
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z, "' -> ", italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
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warning(red(paste0('UNCERTAIN - "',
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z, '" -> ', italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
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call. = FALSE, immediate. = TRUE)
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return(found[1L])
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}
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@ -795,6 +812,21 @@ print.mo <- function(x, ...) {
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print.default(x, quote = FALSE)
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}
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#' @exportMethod summary.mo
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#' @export
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#' @noRd
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summary.mo <- function(object, ...) {
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# unique and top 1-3
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x <- object
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top_3 <- unname(top_freq(freq(x), 3))
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c("Class" = "mo",
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"<NA>" = length(x[is.na(x)]),
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"Unique" = dplyr::n_distinct(x[!is.na(x)]),
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"#1" = top_3[1],
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"#2" = top_3[2],
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"#3" = top_3[3])
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}
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#' @exportMethod as.data.frame.mo
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#' @export
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#' @noRd
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