documentation, unit tests

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9099
+Version: 1.8.2.9100
-Date: 2023-01-23
+Date: 2023-01-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9099
+# AMR 1.8.2.9100
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/sir.R

@@ -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].

R/zz_deprecated.R

@@ -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)

inst/tinytest/test-_deprecated.R

@@ -26,3 +26,39 @@
 # Visit our website for the full manual and a complete tutorial about  #
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
+
+sir <- random_sir(100)
+rsi <- sir
+class(rsi) <- gsub("sir", "rsi", class(rsi))
+mic <- random_mic(100)
+disk <- random_disk(100)
+
+expect_identical(summary(sir), summary(rsi))
+expect_identical(c(sir), c(rsi))
+
+expect_identical(suppressWarnings(suppressMessages(as.rsi(as.character(rsi)))),
+                 suppressWarnings(suppressMessages(as.sir(as.character(sir)))))
+expect_identical(suppressWarnings(suppressMessages(as.rsi(mic, mo = "Escherichia coli", ab = "CIP"))),
+                 suppressWarnings(suppressMessages(as.sir(mic, mo = "Escherichia coli", ab = "CIP"))))
+expect_identical(suppressWarnings(suppressMessages(as.rsi(disk, mo = "Escherichia coli", ab = "CIP"))),
+                 suppressWarnings(suppressMessages(as.sir(disk, mo = "Escherichia coli", ab = "CIP"))))
+expect_identical(suppressWarnings(suppressMessages(as.rsi(data.frame(CIP = mic, mo = "Escherichia coli")))),
+                 suppressWarnings(suppressMessages(as.sir(data.frame(CIP = mic, mo = "Escherichia coli")))))
+
+expect_identical(suppressWarnings(n_rsi(example_isolates$CIP)),
+                 suppressWarnings(n_sir(example_isolates$CIP)))
+
+expect_identical(suppressWarnings(rsi_df(example_isolates$CIP)),
+                 suppressWarnings(sir_df(example_isolates$CIP)))
+
+expect_identical(suppressWarnings(is.rsi.eligible(example_isolates)),
+                 suppressWarnings(is_sir_eligible(example_isolates)))
+
+if (pkg_is_available("ggplot2", also_load = FALSE)) {
+  expect_identical(suppressWarnings(ggplot_rsi(example_isolates[, c("CIP", "GEN", "TOB")])),
+                   suppressWarnings(ggplot_sir(example_isolates[, c("CIP", "GEN", "TOB")])))
+  
+  p <- ggplot2::ggplot(example_isolates[, c("CIP", "GEN", "TOB")])
+  expect_equal(suppressWarnings(p + geom_rsi() + scale_rsi_colours() + labels_rsi_count() + facet_rsi() + theme_rsi()),
+                   suppressWarnings(p + geom_sir() + scale_sir_colours() + labels_sir_count() + facet_sir() + theme_sir()))
+}

man/as.sir.Rd

@@ -82,7 +82,7 @@ sir_interpretation_history(clean = FALSE)
 
 \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
 
-\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=options]{option} \code{AMR_guideline}. Supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}.}
+\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}.}
 
 \item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{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 \emph{Examples}.}