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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

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dr. M.S. (Matthijs) Berends
2021-11-28 23:01:26 +01:00
parent 9a2c431e16
commit 694cf5ba77
72 changed files with 780 additions and 669 deletions
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24
R/key_antimicrobials.R
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@ -250,16 +250,16 @@ generate_antimcrobials_string <- function(df) {
if (NROW(df) == 0) {
return(character(0))
}
out <- tryCatch(
tryCatch({
do.call(paste0,
lapply(as.list(df),
function(x) {
x <- toupper(as.character(x))
x[!x %in% c("R", "S", "I")] <- "."
paste(x)
})),
error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
out
}))
},
error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
}
#' @rdname key_antimicrobials
@ -279,10 +279,20 @@ antimicrobials_equal <- function(y,
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
key2rsi <- function(val) {
as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
val <- strsplit(val, "")[[1L]]
val.int <- rep(NA_real_, length(val))
val.int[val == "S"] <- 1
val.int[val == "I"] <- 2
val.int[val == "R"] <- 3
val.int
}
y <- lapply(y, key2rsi)
z <- lapply(z, key2rsi)
# only run on uniques
uniq <- unique(c(y, z))
uniq_list <- lapply(uniq, key2rsi)
names(uniq_list) <- uniq
y <- uniq_list[match(y, names(uniq_list))]
z <- uniq_list[match(z, names(uniq_list))]
determine_equality <- function(a, b, type, points_threshold, ignore_I) {
if (length(a) != length(b)) {