P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 04:02:19 +02:00
Code Releases Activity

(v1.4.0.9018) reference_data in as.rsi()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-11-11 18:54:03 +01:00
parent 01d9522434
commit f2edac3b67
15 changed files with 48 additions and 30 deletions
Download Patch File Download Diff File Expand all files Collapse all files

33
R/rsi.R
View File

@ -36,7 +36,7 @@
#' @param guideline defaults to the latest included EUCAST guideline, see Details for all options
#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the 'guideline' column in this data set must contain values set in the 'guideline' parameter of [as.rsi()].
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` parameter will be ignored when `reference_data` is manually set.
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: parameters passed on to methods.
#' @details
@ -67,7 +67,7 @@
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`.
#'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` parameter.
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline. You can set your own data set using the `reference_data` parameter. The `guideline` parameter will then be ignored.
#'
#' ## After interpretation
#'
@ -359,7 +359,10 @@ as.rsi.mic <- function(x,
message_("=> Interpreting MIC values of `", font_bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
" according to ", font_bold(guideline_coerced), " ... ",
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
" ... ",
appendLF = FALSE,
as_note = FALSE)
@ -445,9 +448,14 @@ as.rsi.disk <- function(x,
message_("=> Interpreting disk zones of `", font_bold(ab), "` (",
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE), ") using guideline ", font_bold(guideline_coerced), " ... ",
appendLF = FALSE,
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
" ... ",
appendLF = FALSE,
as_note = FALSE)
result <- exec_as.rsi(method = "disk",
x = x,
mo = mo_coerced,
@ -622,6 +630,9 @@ as.rsi.data.frame <- function(x,
}
get_guideline <- function(guideline, reference_data) {
if (!identical(reference_data, AMR::rsi_translation)) {
return(guideline)
}
guideline_param <- toupper(guideline)
if (guideline_param %in% c("CLSI", "EUCAST")) {
guideline_param <- rev(sort(subset(reference_data, guideline %like% guideline_param)$guideline))[1L]
@ -646,7 +657,8 @@ exec_as.rsi <- function(method,
guideline,
uti,
conserve_capped_values,
add_intrinsic_resistance) {
add_intrinsic_resistance,
reference_data) {
metadata_mo <- get_mo_failures_uncertainties_renamed()
@ -687,8 +699,13 @@ exec_as.rsi <- function(method,
new_rsi <- rep(NA_character_, length(x))
ab_param <- ab
trans <- reference_data %pm>%
subset(guideline == guideline_coerced & method == method_param & ab == ab_param)
if (identical(reference_data, AMR::rsi_translation)) {
trans <- reference_data %pm>%
subset(guideline == guideline_coerced & method == method_param & ab == ab_param)
} else {
trans <- reference_data %pm>%
subset(method == method_param & ab == ab_param)
}
trans$lookup <- paste(trans$mo, trans$ab)
lookup_mo <- paste(mo, ab)