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new class bactid
This commit is contained in:
@ -16,37 +16,58 @@
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Find bacteria ID based on genus/species
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#' Transform to bacteria ID
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#'
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#' Use this function to determine a valid ID based on a genus (and species). This input could be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
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#' @param x character vector or a dataframe with one or two columns
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#' Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
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#' @param x a character vector or a dataframe with one or two columns
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#' @rdname as.bactid
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#' @details Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
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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}}
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#' \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
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#' \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
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#' }
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#' Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
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#' For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
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#' @export
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#' @importFrom dplyr %>% filter pull
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#' @return Character (vector).
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#' @return Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
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#' @seealso \code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
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#' @examples
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#' # These examples all return "STAAUR", the ID of S. aureus:
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#' guess_bactid("stau")
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#' guess_bactid("STAU")
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#' guess_bactid("staaur")
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#' guess_bactid("S. aureus")
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#' guess_bactid("S aureus")
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#' guess_bactid("Staphylococcus aureus")
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#' guess_bactid("MRSA") # Methicillin-resistant S. aureus
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#' guess_bactid("VISA") # Vancomycin Intermediate S. aureus
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#' as.bactid("stau")
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#' as.bactid("STAU")
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#' as.bactid("staaur")
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#' as.bactid("S. aureus")
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#' as.bactid("S aureus")
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#' as.bactid("Staphylococcus aureus")
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#' as.bactid("MRSA") # Methicillin Resistant S. aureus
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#' as.bactid("VISA") # Vancomycin Intermediate S. aureus
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#' as.bactid("VRSA") # Vancomycin Resistant S. aureus
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#'
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#' \dontrun{
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#' df$bactid <- guess_bactid(df$microorganism_name)
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#' df$bactid <- as.bactid(df$microorganism_name)
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#'
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#' # the select function of tidyverse is also supported:
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#' df$bactid <- df %>% select(microorganism_name) %>% guess_bactid()
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#' library(dplyr)
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#' df$bactid <- df %>%
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#' select(microorganism_name) %>%
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#' as.bactid()
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#'
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#' # and can even contain 2 columns, which is convenient for genus/species combinations:
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#' df$bactid <- df %>% select(genus, species) %>% guess_bactid()
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#' df$bactid <- df %>%
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#' select(genus, species) %>%
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#' as.bactid()
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#'
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#' # same result:
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#' df <- df %>% mutate(bactid = paste(genus, species)) %>% guess_bactid())
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#' df <- df %>%
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#' mutate(bactid = paste(genus, species) %>%
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#' as.bactid())
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#' }
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guess_bactid <- function(x) {
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as.bactid <- function(x) {
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failures <- character(0)
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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@ -60,17 +81,19 @@ guess_bactid <- function(x) {
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if (NCOL(x) > 2) {
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stop('`x` can be 2 columns at most', call. = FALSE)
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}
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# support tidyverse selection like: df %>% select(colA)
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if (!is.vector(x)) {
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x <- pull(x, 1)
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}
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}
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x.fullbackup <- x
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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-Z ]+", "", x)
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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.bak <- x
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x.backup <- x
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# replace space by regex sign
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x <- gsub(" ", ".*", x, fixed = TRUE)
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# add start and stop
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@ -96,42 +119,44 @@ guess_bactid <- function(x) {
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# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
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x[i] <- 'Pseudomonas aeruginosa'
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}
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if (tolower(x[i]) %like% 'coagulase') {
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# coerce S. coagulase negative
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if (tolower(x[i]) %like% 'coagulase'
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| tolower(x[i]) %like% 'cns'
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| tolower(x[i]) %like% 'cons') {
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# coerce S. coagulase negative, also as CNS and CoNS
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x[i] <- 'Coagulase Negative Staphylococcus (CNS)'
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}
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# translate known trivial names to genus+species
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if (!is.na(x.bak[i])) {
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if (toupper(x.bak[i]) == 'MRSA'
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| toupper(x.bak[i]) == 'VISA'
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| toupper(x.bak[i]) == 'VRSA') {
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if (!is.na(x.backup[i])) {
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if (toupper(x.backup[i]) == 'MRSA'
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| toupper(x.backup[i]) == 'VISA'
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| toupper(x.backup[i]) == 'VRSA') {
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x[i] <- 'Staphylococcus aureus'
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}
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if (toupper(x.bak[i]) == 'MRSE') {
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if (toupper(x.backup[i]) == 'MRSE') {
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x[i] <- 'Staphylococcus epidermidis'
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}
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if (toupper(x.bak[i]) == 'VRE') {
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if (toupper(x.backup[i]) == 'VRE') {
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x[i] <- 'Enterococcus'
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}
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if (toupper(x.bak[i]) == 'MRPA') {
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if (toupper(x.backup[i]) == 'MRPA') {
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# multi resistant P. aeruginosa
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x[i] <- 'Pseudomonas aeruginosa'
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}
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if (toupper(x.bak[i]) == 'PISP'
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| toupper(x.bak[i]) == 'PRSP') {
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if (toupper(x.backup[i]) == 'PISP'
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| toupper(x.backup[i]) == 'PRSP') {
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# peni resistant S. pneumoniae
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x[i] <- 'Streptococcus pneumoniae'
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}
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if (toupper(x.bak[i]) == 'VISP'
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| toupper(x.bak[i]) == 'VRSP') {
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if (toupper(x.backup[i]) == 'VISP'
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| toupper(x.backup[i]) == 'VRSP') {
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# vanco resistant S. pneumoniae
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x[i] <- 'Streptococcus pneumoniae'
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}
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}
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# let's try the ID's first
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found <- AMR::microorganisms %>% filter(bactid == x.bak[i])
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found <- AMR::microorganisms %>% filter(bactid == x.backup[i])
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if (nrow(found) == 0) {
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# now try exact match
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@ -152,38 +177,82 @@ guess_bactid <- function(x) {
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}
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if (nrow(found) == 0) {
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# search for GLIMS code
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if (toupper(x.bak[i]) %in% toupper(AMR::microorganisms.umcg$mocode)) {
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found <- AMR::microorganisms.umcg %>% filter(toupper(mocode) == toupper(x.bak[i]))
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if (toupper(x.backup[i]) %in% toupper(AMR::microorganisms.umcg$mocode)) {
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found <- AMR::microorganisms.umcg %>% filter(toupper(mocode) == toupper(x.backup[i]))
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}
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}
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if (nrow(found) == 0) {
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# try splitting of characters and then find ID
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# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
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x_split <- x
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x_length <- nchar(x.bak[i])
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x_split[i] <- paste0(x.bak[i] %>% substr(1, x_length / 2) %>% trimws(),
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x_length <- nchar(x.backup[i])
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x_split[i] <- paste0(x.backup[i] %>% substr(1, x_length / 2) %>% trimws(),
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'.* ',
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x.bak[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
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x.backup[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
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found <- AMR::microorganisms %>% filter(fullname %like% paste0('^', x_split[i]))
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}
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if (nrow(found) == 0) {
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# try any match with text before and after original search string
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# so "negative rods" will be "GNR"
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if (x.bak[i] %like% "^Gram") {
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x.bak[i] <- gsub("^Gram", "", x.bak[i], ignore.case = TRUE)
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if (x.backup[i] %like% "^Gram") {
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x.backup[i] <- gsub("^Gram", "", x.backup[i], ignore.case = TRUE)
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# remove leading and trailing spaces again
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x.bak[i] <- trimws(x.bak[i], which = "both")
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x.backup[i] <- trimws(x.backup[i], which = "both")
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}
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if (!is.na(x.bak[i])) {
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found <- AMR::microorganisms %>% filter(fullname %like% x.bak[i])
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if (!is.na(x.backup[i])) {
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found <- AMR::microorganisms %>% filter(fullname %like% x.backup[i])
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}
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}
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if (nrow(found) != 0) {
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if (nrow(found) != 0 & x.backup[i] != "") {
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x[i] <- as.character(found[1, 'bactid'])
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} else {
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x[i] <- ""
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x[i] <- NA_character_
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failures <- c(failures, x.fullbackup[i])
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}
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}
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failures <- failures[!failures %in% c(NA, NULL, NaN)]
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if (length(failures) > 0) {
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warning("These values could not be coerced to a valid bactid: ",
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paste('"', unique(failures), '"', sep = "", collapse = ', '),
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".",
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call. = FALSE)
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}
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class(x) <- "bactid"
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attr(x, 'package') <- 'AMR'
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attr(x, 'package.version') <- packageDescription('AMR')$Version
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x
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}
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#' @rdname as.bactid
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#' @export
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guess_bactid <- as.bactid
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#' @rdname as.bactid
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#' @export
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is.bactid <- function(x) {
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identical(class(x), "bactid")
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}
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#' @exportMethod print.bactid
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#' @export
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#' @noRd
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print.bactid <- function(x, ...) {
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cat("Class 'bactid'\n")
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print.default(as.character(x), quote = FALSE)
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}
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#' @exportMethod as.data.frame.bactid
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#' @export
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#' @noRd
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as.data.frame.bactid <- function (x, ...) {
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# same as as.data.frame.character but with removed stringsAsFactors
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nm <- paste(deparse(substitute(x), width.cutoff = 500L),
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collapse = " ")
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if (!"nm" %in% names(list(...))) {
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as.data.frame.vector(x, ..., nm = nm)
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} else {
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as.data.frame.vector(x, ...)
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}
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}
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@ -201,9 +201,10 @@ EUCAST_rules <- function(tbl,
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}
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# join to microorganisms table
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joinby <- colnames(AMR::microorganisms)[1]
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names(joinby) <- col_bactid
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tbl <- tbl %>% left_join(y = AMR::microorganisms, by = joinby, suffix = c("_tempmicroorganisms", ""))
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if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
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tbl[, col_bactid] <- tbl %>% pull(col_bactid) %>% as.bactid()
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}
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tbl <- tbl %>% left_join_microorganisms(by = col_bactid, suffix = c("_tempmicroorganisms", ""))
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# antibiotic classes
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aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
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@ -22,7 +22,7 @@
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#' @param tbl a \code{data.frame} containing isolates.
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#' @param col_date column name of the result date (or date that is was received on the lab)
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#' @param col_patient_id column name of the unique IDs of the patients
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#' @param col_bactid column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset). Get your bactid's with the function \code{\link{guess_bactid}}, that takes microorganism names as input.
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#' @param col_bactid column name of the unique IDs of the microorganisms: \code{bactid}'s. If this column has another class than \code{"bactid"}, values will be coerced using \code{\link{as.bactid}}.
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#' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
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#' @param col_specimen column name of the specimen type or group
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#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)
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@ -126,7 +126,7 @@ first_isolate <- function(tbl,
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# bactid OR genus+species must be available
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if (is.na(col_bactid) & (is.na(col_genus) | is.na(col_species))) {
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stop('`col_bactid or both `col_genus` and `col_species` must be available.')
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stop('`col_bactid` or both `col_genus` and `col_species` must be available.')
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}
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# check if columns exist
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@ -152,6 +152,9 @@ first_isolate <- function(tbl,
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check_columns_existance(col_keyantibiotics)
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if (!is.na(col_bactid)) {
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if (!tbl %>% pull(col_bactid) %>% is.bactid()) {
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tbl[, col_bactid] <- tbl %>% pull(col_bactid) %>% as.bactid()
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}
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tbl <- tbl %>% left_join_microorganisms(by = col_bactid)
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col_genus <- "genus"
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col_species <- "species"
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3
R/freq.R
3
R/freq.R
@ -273,8 +273,11 @@ frequency_tbl <- function(x,
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} else {
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NAs <- x[is.na(x)]
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}
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if (na.rm == TRUE) {
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x_class <- class(x)
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x <- x[!x %in% NAs]
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class(x) <- x_class
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}
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if (missing(sort.count) & 'factor' %in% class(x)) {
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@ -26,8 +26,8 @@
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#' df2 <- left_join_microorganisms(df, "bacteria_id")
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#' colnames(df2)
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inner_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
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if (any(class(x) %in% c('character', 'factor'))) {
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x <- data.frame(bactid = x, stringsAsFactors = FALSE)
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if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
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x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
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}
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# no name set to `by` parameter
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if (is.null(names(by))) {
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@ -36,7 +36,9 @@ inner_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
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} else {
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joinby <- by
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}
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join <- dplyr::inner_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
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join <- suppressWarnings(
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dplyr::inner_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('the newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original')
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}
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@ -46,8 +48,8 @@ inner_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
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#' @rdname join
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#' @export
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left_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
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if (any(class(x) %in% c('character', 'factor'))) {
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x <- data.frame(bactid = x, stringsAsFactors = FALSE)
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if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
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x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
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}
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# no name set to `by` parameter
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if (is.null(names(by))) {
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@ -56,7 +58,9 @@ left_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
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} else {
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joinby <- by
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}
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join <- dplyr::left_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
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join <- suppressWarnings(
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dplyr::left_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
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)
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if (nrow(join) > nrow(x)) {
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warning('the newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original')
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}
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@ -66,8 +70,8 @@ left_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
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#' @rdname join
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#' @export
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right_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
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if (any(class(x) %in% c('character', 'factor'))) {
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x <- data.frame(bactid = x, stringsAsFactors = FALSE)
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if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
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x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
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}
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# no name set to `by` parameter
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if (is.null(names(by))) {
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@ -76,7 +80,9 @@ right_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
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} else {
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joinby <- by
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}
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join <- dplyr::right_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
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join <- suppressWarnings(
|
||||
dplyr::right_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
|
||||
)
|
||||
if (nrow(join) > nrow(x)) {
|
||||
warning('the newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original')
|
||||
}
|
||||
@ -86,8 +92,8 @@ right_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...
|
||||
#' @rdname join
|
||||
#' @export
|
||||
full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
|
||||
if (any(class(x) %in% c('character', 'factor'))) {
|
||||
x <- data.frame(bactid = x, stringsAsFactors = FALSE)
|
||||
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
|
||||
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
|
||||
}
|
||||
# no name set to `by` parameter
|
||||
if (is.null(names(by))) {
|
||||
@ -96,7 +102,9 @@ full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
|
||||
} else {
|
||||
joinby <- by
|
||||
}
|
||||
join <- dplyr::full_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
|
||||
join <- suppressWarnings(
|
||||
dplyr::full_join(x = x, y = AMR::microorganisms, by = joinby, suffix = c("2", ""), ...)
|
||||
)
|
||||
if (nrow(join) > nrow(x)) {
|
||||
warning('the newly joined tbl contains ', nrow(join) - nrow(x), ' rows more that its original')
|
||||
}
|
||||
@ -106,8 +114,8 @@ full_join_microorganisms <- function(x, by = 'bactid', suffix = c("2", ""), ...)
|
||||
#' @rdname join
|
||||
#' @export
|
||||
semi_join_microorganisms <- function(x, by = 'bactid', ...) {
|
||||
if (any(class(x) %in% c('character', 'factor'))) {
|
||||
x <- data.frame(bactid = x, stringsAsFactors = FALSE)
|
||||
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
|
||||
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
|
||||
}
|
||||
# no name set to `by` parameter
|
||||
if (is.null(names(by))) {
|
||||
@ -116,14 +124,16 @@ semi_join_microorganisms <- function(x, by = 'bactid', ...) {
|
||||
} else {
|
||||
joinby <- by
|
||||
}
|
||||
dplyr::semi_join(x = x, y = AMR::microorganisms, by = joinby, ...)
|
||||
suppressWarnings(
|
||||
dplyr::semi_join(x = x, y = AMR::microorganisms, by = joinby, ...)
|
||||
)
|
||||
}
|
||||
|
||||
#' @rdname join
|
||||
#' @export
|
||||
anti_join_microorganisms <- function(x, by = 'bactid', ...) {
|
||||
if (any(class(x) %in% c('character', 'factor'))) {
|
||||
x <- data.frame(bactid = x, stringsAsFactors = FALSE)
|
||||
if (!any(class(x) %in% c("bactid", "data.frame", "matrix"))) {
|
||||
x <- data.frame(bactid = as.bactid(x), stringsAsFactors = FALSE)
|
||||
}
|
||||
# no name set to `by` parameter
|
||||
if (is.null(names(by))) {
|
||||
@ -132,5 +142,7 @@ anti_join_microorganisms <- function(x, by = 'bactid', ...) {
|
||||
} else {
|
||||
joinby <- by
|
||||
}
|
||||
dplyr::anti_join(x = x, y = AMR::microorganisms, by = joinby, ...)
|
||||
suppressWarnings(
|
||||
dplyr::anti_join(x = x, y = AMR::microorganisms, by = joinby, ...)
|
||||
)
|
||||
}
|
||||
Reference in New Issue
Block a user