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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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12
R/mo_property.R
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@ -31,7 +31,7 @@
#'
#' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. See *Examples*.
#' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`
#' @inheritParams as.mo
#' @param ... other arguments passed on to [as.mo()], such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'
#' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
@ -900,12 +900,16 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
}
# get property reeaaally fast using match()
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
if (property == "snomed") {
x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)]))
} else {
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
}
if (property == "mo") {
return(set_clean_class(x, new_class = c("mo", "character")))
} else if (property == "snomed") {
return(sort(as.character(eval(parse(text = x)))))
return(x)
} else if (property == "prevalence") {
return(as.double(x))
} else {