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documentation, unit tests

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dr. M.S. (Matthijs) Berends
2023-01-24 10:20:27 +01:00
parent eef00069fd
commit 830c67f1bf
60 changed files with 45 additions and 7 deletions
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2
R/sir.R
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@ -36,7 +36,7 @@
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.sir()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate
#' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [clinical_breakpoints] data set), but can be set with the [option][options()] `AMR_guideline`. Supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
#' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [clinical_breakpoints] data set), but can be set with the option [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
#' @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 `r format_eucast_version_nr(3.3)`.
#' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to `TRUE`. Can also be set with the option [`AMR_include_PKPD`][AMR-options].

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R/sysdata.rda
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6
R/zz_deprecated.R
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@ -150,7 +150,7 @@ theme_rsi <- function(...) {
# will be exported using s3_register() in R/zzz.R
pillar_shaft.rsi <- pillar_shaft.sir
type_sum.rsi <- function(x, ...) {
deprecation_warning(extra_msg = "* Transform your old 'rsi' class to the new 'sir' class with `as.sir()` using e.g.:\n your_data %>% mutate_if(is.rsi, as.sir)")
deprecation_warning(extra_msg = "* The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns to 'sir' with `as.sir()`, e.g.:\n your_data %>% mutate_if(is.rsi, as.sir)")
paste0("rsi", font_bold(font_red("[!]")))
}
@ -158,7 +158,7 @@ type_sum.rsi <- function(x, ...) {
#' @export
#' @noRd
print.rsi <- function(x, ...) {
deprecation_warning(extra_msg = "Transform your old 'rsi' class to the new 'sir' class with `as.sir()`")
deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir' - transform your 'rsi' data with `as.sir()`")
cat("Class 'rsi'", font_bold(font_red("[!]\n")))
print(as.character(x), quote = FALSE)
}
@ -191,6 +191,8 @@ summary.rsi <- summary.sir
#' @export
unique.rsi <- unique.sir
# WHEN REMOVING RSI, DON'T FORGET TO REMOVE THE "rsi_df" CLASS FROM R/sir_calc.R
deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL) {
if (is.null(old)) {
warning_(extra_msg)