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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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12
R/mo.R
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@ -164,6 +164,8 @@ as.mo <- function(x,
language <- validate_language(language)
meet_criteria(info, allow_class = "logical", has_length = 1)
add_MO_lookup_to_AMR_env()
if (tryCatch(all(x %in% c(AMR_env$MO_lookup$mo, NA)) &&
isFALSE(Becker) &&
isFALSE(Lancefield), error = function(e) FALSE)) {
@ -492,6 +494,7 @@ mo_uncertainties <- function() {
#' @rdname as.mo
#' @export
mo_renamed <- function() {
add_MO_lookup_to_AMR_env()
x <- AMR_env$mo_renamed
x$new <- synonym_mo_to_accepted_mo(x$old)
@ -547,6 +550,7 @@ mo_cleaning_regex <- function() {
# will be exported using s3_register() in R/zzz.R
pillar_shaft.mo <- function(x, ...) {
add_MO_lookup_to_AMR_env()
out <- format(x)
# grey out the kingdom (part until first "_")
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
@ -664,6 +668,7 @@ get_skimmers.mo <- function(column) {
#' @export
#' @noRd
print.mo <- function(x, print.shortnames = FALSE, ...) {
add_MO_lookup_to_AMR_env()
cat("Class 'mo'\n")
x_names <- names(x)
if (is.null(x_names) & print.shortnames == TRUE) {
@ -704,6 +709,7 @@ summary.mo <- function(object, ...) {
#' @export
#' @noRd
as.data.frame.mo <- function(x, ...) {
add_MO_lookup_to_AMR_env()
if (!all(x %in% c(AMR_env$MO_lookup$mo, NA))) {
warning_(
"The data contains old MO codes (from a previous AMR package version). ",
@ -741,6 +747,7 @@ as.data.frame.mo <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(i)
# must only contain valid MOs
add_MO_lookup_to_AMR_env()
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
}
#' @method [[<- mo
@ -750,6 +757,7 @@ as.data.frame.mo <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(i)
# must only contain valid MOs
add_MO_lookup_to_AMR_env()
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
}
#' @method c mo
@ -759,6 +767,7 @@ c.mo <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
attributes(y) <- attributes(x)
add_MO_lookup_to_AMR_env()
return_after_integrity_check(y, "microorganism code", as.character(AMR_env$MO_lookup$mo))
}
@ -788,6 +797,8 @@ print.mo_uncertainties <- function(x, ...) {
cat(word_wrap("No uncertainties to show. Only uncertainties of the last call of `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
return(invisible(NULL))
}
add_MO_lookup_to_AMR_env()
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
if (has_colour()) {
@ -1049,6 +1060,7 @@ replace_old_mo_codes <- function(x, property) {
# B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% AMR_env$MO_lookup$mo
if (any(ind, na.rm = TRUE)) {
add_MO_lookup_to_AMR_env()
# get the ones that match
affected <- x[ind]
affected_unique <- unique(affected)