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(v1.7.0.9001) CLSI 2020 guideline

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dr. M.S. (Matthijs) Berends
2021-06-01 15:33:06 +02:00
parent f406319503
commit bef0f42f66
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52
R/mo.R
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@ -23,9 +23,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Transform Input to a Microorganism ID
#' Transform Input to a Microorganism Code
#'
#' Use this function to determine a valid microorganism ID ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
#' Use this function to determine a valid microorganism code ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
#' @inheritSection lifecycle Stable Lifecycle
#' @param x a [character] vector or a [data.frame] with one or two columns
#' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
@ -46,7 +46,7 @@
#' @details
#' ## General Info
#'
#' A microorganism ID from this package (class: [`mo`]) is human readable and typically looks like these examples:
#' A microorganism (MO) code from this package (class: [`mo`]) is human readable and typically looks like these examples:
#' ```
#' Code Full name
#' --------------- --------------------------------------
@ -2050,7 +2050,7 @@ parse_and_convert <- function(x) {
}
replace_old_mo_codes <- function(x, property) {
ind <- x %like% "[A-Z_]" & !x %in% MO_lookup$mo
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
if (any(ind)) {
# get the ones that match
affected <- x[ind]
@ -2059,31 +2059,43 @@ replace_old_mo_codes <- function(x, property) {
# find their new codes, once per code
solved_unique <- unlist(lapply(strsplit(affected_unique, ""),
function(m) {
m <- m[3:length(m)]
m <- m[m != "_"]
m <- tolower(paste0(m, ".*", collapse = ""))
out <- MO_lookup$mo[MO_lookup$fullname_lower %like_case% m]
if (length(out) > 1) {
kingdom <- paste0("^", m[1])
name <- m[3:length(m)]
name[name == "_"] <- " "
name <- tolower(paste0(name, ".*", collapse = ""))
name <- gsub(" .*", " ", name, fixed = TRUE)
name <- paste0("^", name)
results <- MO_lookup$mo[MO_lookup$kingdom %like_case% kingdom &
MO_lookup$fullname_lower %like_case% name]
if (length(results) > 1) {
all_direct_matches <<- FALSE
}
out[1L]
results[1L]
}), use.names = FALSE)
solved <- solved_unique[match(affected, affected_unique)]
# assign on places where a match was found
x[ind] <- solved
n_matched <- length(affected[!is.na(affected)])
n_unique <- length(affected_unique[!is.na(affected_unique)])
if (property != "mo") {
message_(font_blue(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, " unique, from a previous AMR package version). Please update your MO codes with `as.mo()` to increase speed.")))
if (n_unique < n_matched) {
n_unique <- paste0(n_unique, " unique, ")
} else {
message_(font_blue(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, " unique, from a previous AMR package version) ",
ifelse(n_matched == 1, "was", "were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_matched == 1, "a ", ""),
"currently used MO code", ifelse(n_matched == 1, "", "s"), ".")))
n_unique <- ""
}
if (property != "mo") {
warning_(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed."),
call = FALSE)
} else {
warning_(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version) ",
ifelse(n_matched == 1, "was", "were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_matched == 1, "a ", ""),
"currently used MO code", ifelse(n_matched == 1, "", "s"), "."),
call = FALSE)
}
}
x