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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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26
R/guess_ab_col.R
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@ -33,7 +33,7 @@
#' @param x a [data.frame]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a [logical] to indicate whether additional info should be printed
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param only_sir_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (defaults to `FALSE`)
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic.
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
@ -57,11 +57,11 @@
#' guess_ab_col(df, "ampicillin")
#' guess_ab_col(df, "J01CR02")
#' guess_ab_col(df, as.ab("augmentin"))
guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_rsi_columns = FALSE) {
guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_sir_columns = FALSE) {
meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if (is.null(x) && is.null(search_string)) {
return(as.name("guess_ab_col"))
@ -70,7 +70,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
}
all_found <- get_column_abx(x,
info = verbose, only_rsi_columns = only_rsi_columns,
info = verbose, only_sir_columns = only_sir_columns,
verbose = verbose, fn = "guess_ab_col"
)
search_string.ab <- suppressWarnings(as.ab(search_string))
@ -102,7 +102,7 @@ get_column_abx <- function(x,
hard_dependencies = NULL,
verbose = FALSE,
info = TRUE,
only_rsi_columns = FALSE,
only_sir_columns = FALSE,
sort = TRUE,
reuse_previous_result = TRUE,
fn = NULL) {
@ -125,8 +125,8 @@ get_column_abx <- function(x,
new_cols <- colnames(x)[!colnames(x) %in% AMR_env$get_column_abx.checked_cols]
if (length(new_cols) > 0) {
# these columns did not exist in the last call, so add them
new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
current <- c(current, new_cols_rsi)
new_cols_sir <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
current <- c(current, new_cols_sir)
# order according to columns in current call
current <- current[match(colnames(x)[colnames(x) %in% current], current)]
}
@ -144,7 +144,7 @@ get_column_abx <- function(x,
meet_criteria(hard_dependencies, allow_class = "character", allow_NULL = TRUE)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(sort, allow_class = "logical", has_length = 1)
if (isTRUE(info)) {
@ -153,8 +153,8 @@ get_column_abx <- function(x,
x <- as.data.frame(x, stringsAsFactors = FALSE)
x.bak <- x
if (only_rsi_columns == TRUE) {
x <- x[, which(is.rsi(x)), drop = FALSE]
if (only_sir_columns == TRUE) {
x <- x[, which(is.sir(x)), drop = FALSE]
}
if (NROW(x) > 10000) {
@ -171,7 +171,7 @@ get_column_abx <- function(x,
}
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the 'rsi' class (as.rsi)
# or already have the 'sir' class (as.sir)
# and that they have no more than 50% invalid values
vectr_antibiotics <- unlist(AMR_env$AB_lookup$generalised_all)
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
@ -180,8 +180,8 @@ get_column_abx <- function(x,
colnames(x),
function(col, df = x) {
if (generalise_antibiotic_name(col) %in% vectr_antibiotics ||
is.rsi(x[, col, drop = TRUE]) ||
is.rsi.eligible(x[, col, drop = TRUE], threshold = 0.5)
is.sir(x[, col, drop = TRUE]) ||
is_sir_eligible(x[, col, drop = TRUE], threshold = 0.5)
) {
return(col)
} else {