DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9224
+Version: 2.1.1.9222
 Date: 2025-03-20
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NAMESPACE

@@ -2,7 +2,6 @@
 
 S3method("!=",amr_selector)
 S3method("&",amr_selector)
-S3method("+",ab)
 S3method("+",amr_selector)
 S3method("==",amr_selector)
 S3method("[",ab)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9224
+# AMR 2.1.1.9222
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

R/aa_helper_functions.R

@@ -539,7 +539,7 @@ word_wrap <- function(...,
     )
     # text starting with `?` must also lead to the help page
     parts[parts %like% "^[?]"] <- font_url(
-      url = paste0("ide:help:AMR::", gsub("?", "", parts[parts %like% "^[?]"], fixed = TRUE)),
+      url = paste0("ide:help:AMR::", parts[parts %like% "^[?]"]),
       txt = parts[parts %like% "^[?]"]
     )
     msg <- paste0(parts, collapse = "`")

R/ab.R

@@ -610,16 +610,6 @@ rep.ab <- function(x, ...) {
   y
 }
 
-#' @method + ab
-#' @export
-#' @noRd
-`+.ab` <- function(e1, e2) {
-  # this does not return ab class, it should just allow console usage of e.g., carbapenems() + c("", aminoglycosides())
-  out <- as.character(outer(e1, e2, paste, sep = " + "))
-  out <- gsub(" [+] $", "", out)
-  out
-}
-
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices

R/amr_selectors.R

@@ -954,10 +954,9 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
 #' @noRd
 `+.amr_selector` <- function(e1, e2) {
   # this is useful for `antibiogram()`: antibiogram(example_isolates, carbapenems() + c("", "GEN", "TOB"))
-  # this is also implemented for ab class, to allow direct console usage
-  out <- as.character(outer(e1, e2, paste, sep = " + "))
-  out <- gsub(" [+] $", "", out)
-  structure(out, class = c("amr_selector", "character"))
+  structure(as.character(outer(e1, e2, paste, sep = " + ")),
+    class = c("amr_selector", "character")
+  )
 }
 
 is_any <- function(el1) {

R/antibiogram.R

@@ -42,9 +42,8 @@
 #'     - `c(aminoglycosides(), "AMP", "AMC")`
 #'     - `c(aminoglycosides(), carbapenems())`
 #'   - Combination therapy, indicated by using `"+"`, with or without [antimicrobial selectors][antimicrobial_selectors], e.g.:
-#'     - `"cipro + genta"`
 #'     - `"TZP+TOB"`
-#'     - `c("TZP", "TZP+GEN", "TZP+TOB")`
+#'     - `"cipro + genta"`
 #'     - `carbapenems() + "GEN"`
 #'     - `carbapenems() + c("", "GEN")`
 #'     - `carbapenems() + c("", aminoglycosides())`

data-raw/_generate_python_wrapper.sh

@@ -73,23 +73,26 @@ if not isinstalled('AMR', lib_loc=r_lib_path):
     print(f"AMR: Installing latest AMR R package to {r_lib_path}...", flush=True)
     utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
 
-# # Retrieve Python AMR version
-# try:
-#     python_amr_version = metadata.version('AMR')
-# except metadata.PackageNotFoundError:
-#     python_amr_version = ''
-# 
-# # Retrieve R AMR version
-# r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')
-# r_amr_version = str(r_amr_version[0])
-# 
-# # Compare R and Python package versions
-# if r_amr_version != python_amr_version:
-#     try:
-#         print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
-#         utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
-#     except Exception as e:
-#         print(f"AMR: Could not update: {e}", flush=True)
+# Retrieve Python AMR version
+try:
+    python_amr_version = metadata.version('AMR')
+except metadata.PackageNotFoundError:
+    python_amr_version = ''
+
+# Retrieve R AMR version
+r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')
+r_amr_version = str(r_amr_version[0])
+
+print(python_amr_version)
+print(r_amr_version)
+
+# Compare R and Python package versions
+if r_amr_version != python_amr_version:
+    try:
+        print(f"AMR: Updating AMR package in {r_lib_path}...", flush=True)
+        utils.install_packages('AMR', repos='https://msberends.r-universe.dev', quiet=True)
+    except Exception as e:
+        print(f"AMR: Could not update: {e}", flush=True)
 
 print(f"AMR: Setting up R environment and AMR datasets...", flush=True)
 

data-raw/gpt_training_text_v2.1.1.9222.txt

@@ -1,6 +1,6 @@
 This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
 
-First and foremost, you are trained on version 2.1.1.9224. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9222. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
@@ -13,7 +13,6 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE':
 
 S3method("!=",amr_selector)
 S3method("&",amr_selector)
-S3method("+",ab)
 S3method("+",amr_selector)
 S3method("==",amr_selector)
 S3method("[",ab)
@@ -1714,9 +1713,8 @@ retrieve_wisca_parameters(wisca_model, ...)
 }
 \item Combination therapy, indicated by using \code{"+"}, with or without \link[=antimicrobial_selectors]{antimicrobial selectors}, e.g.:
 \itemize{
-\item \code{"cipro + genta"}
 \item \code{"TZP+TOB"}
-\item \code{c("TZP", "TZP+GEN", "TZP+TOB")}
+\item \code{"cipro + genta"}
 \item \code{carbapenems() + "GEN"}
 \item \code{carbapenems() + c("", "GEN")}
 \item \code{carbapenems() + c("", aminoglycosides())}

man/antibiogram.Rd

@@ -58,9 +58,8 @@ retrieve_wisca_parameters(wisca_model, ...)
 }
 \item Combination therapy, indicated by using \code{"+"}, with or without \link[=antimicrobial_selectors]{antimicrobial selectors}, e.g.:
 \itemize{
-\item \code{"cipro + genta"}
 \item \code{"TZP+TOB"}
-\item \code{c("TZP", "TZP+GEN", "TZP+TOB")}
+\item \code{"cipro + genta"}
 \item \code{carbapenems() + "GEN"}
 \item \code{carbapenems() + c("", "GEN")}
 \item \code{carbapenems() + c("", aminoglycosides())}

tests/testthat/test-_deprecated.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-_deprecated.R", {
-  skip_on_cran()
-
   expect_warning(example_isolates[, ab_class("mycobact")])
   expect_warning(example_isolates[, ab_selector(name %like% "trim")])
 })

tests/testthat/test-_misc.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-misc.R", {
-  skip_on_cran()
-
   expect_equal(AMR:::percentage(0.25), "25%")
   expect_equal(AMR:::percentage(0.5), "50%")
   expect_equal(AMR:::percentage(0.500, digits = 1), "50.0%")

tests/testthat/test-ab.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-ab.R", {
-  skip_on_cran()
-
   ab_reset_session()
 
   expect_equal(

tests/testthat/test-ab_from_text.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-ab_from_text.R", {
-  skip_on_cran()
-
   ab_reset_session()
 
   expect_identical(

tests/testthat/test-ab_property.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-ab_property.R", {
-  skip_on_cran()
-
   ab_reset_session()
 
   expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")

tests/testthat/test-age.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-age.R", {
-  skip_on_cran()
-
   expect_equal(
     age(
       x = c("1980-01-01", "1985-01-01", "1990-01-01"),

tests/testthat/test-amr_selectors.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-amr selectors.R", {
-  skip_on_cran()
-
   # antibiotic class selectors
   expect_equal(ncol(example_isolates[, aminoglycosides(), drop = FALSE]), 4, tolerance = 0.5)
   expect_equal(ncol(example_isolates[, aminopenicillins(), drop = FALSE]), 2, tolerance = 0.5)

tests/testthat/test-antibiogram.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-antibiogram.R", {
-  skip_on_cran()
-
   # Traditional antibiogram ----------------------------------------------
 
   ab1 <- antibiogram(example_isolates,

tests/testthat/test-atc_online.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-atc_online.R", {
-  skip_on_cran()
-
   if (AMR:::pkg_is_available("curl") &&
     AMR:::pkg_is_available("rvest") &&
     AMR:::pkg_is_available("xml2") &&

tests/testthat/test-av.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-av.R", {
-  skip_on_cran()
-
   expect_equal(
     as.character(as.av(c(
       "J05AB01",

tests/testthat/test-av_from_text.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-av_from_text.R", {
-  skip_on_cran()
-
   expect_identical(
     av_from_text("28/03/2020 regular aciclovir 500mg po tds")[[1]],
     as.av("Aciclovir")

tests/testthat/test-av_property.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-ab_property.R", {
-  skip_on_cran()
-
   expect_identical(av_name("ACI", language = NULL), "Aciclovir")
   expect_identical(av_atc("ACI"), "J05AB01")
   expect_identical(av_cid("ACI"), as.integer(135398513))

tests/testthat/test-availability.R

@@ -28,7 +28,5 @@
 # ==================================================================== #
 
 test_that("test-availibility.R", {
-  skip_on_cran()
-
   expect_inherits(availability(example_isolates), "data.frame")
 })

tests/testthat/test-bug_drug_combinations.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-bug/drug.R", {
-  skip_on_cran()
-
   b <- suppressWarnings(bug_drug_combinations(example_isolates))
   expect_inherits(b, "bug_drug_combinations")
   expect_output(suppressMessages(print(b)))

tests/testthat/test-count.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-count.R", {
-  skip_on_cran()
-
   expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
   expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
   expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))

tests/testthat/test-custom_antimicrobials.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-custom ab.R", {
-  skip_on_cran()
-
   ab_reset_session()
 
   expect_message(as.ab("testab", info = TRUE))

tests/testthat/test-custom_microorganisms.R

@@ -29,8 +29,6 @@
 
 
 test_that("test-custom mo.R", {
-  skip_on_cran()
-
   expect_identical(
     as.mo("Enterobacter asburiae/cloacae"),
     as.mo("Enterobacter asburiae")

tests/testthat/test-data.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-data.R", {
-  skip_on_cran()
-
   # IDs should always be unique
   expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
   expect_identical(class(microorganisms$mo), c("mo", "character"))

tests/testthat/test-disk.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-disk.R", {
-  skip_on_cran()
-
   expect_true(as.disk(8) == as.disk("8"))
   expect_true(is.disk(as.disk(8)))
 

tests/testthat/test-eucast_rules.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-eucast_rules.R", {
-  skip_on_cran()
-
   # thoroughly check input table
   expect_equal(
     colnames(AMR:::EUCAST_RULES_DF),

tests/testthat/test-first_isolate.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-first_isolate.R", {
-  skip_on_cran()
-
   # all four methods
   expect_equal(
     sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),

tests/testthat/test-g.test.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-g.test.R", {
-  skip_on_cran()
-
   # GOODNESS-OF-FIT
 
   # example 1: clearfield rice vs. red rice

tests/testthat/test-get_episode.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-get_episode.R", {
-  skip_on_cran()
-
   x <- data.frame(dates = as.Date(c("2021-01-01", "2021-01-02", "2021-01-05", "2021-01-08", "2021-02-21", "2021-02-22", "2021-02-23", "2021-02-24", "2021-03-01", "2021-03-01")))
   x$absolute <- get_episode(x$dates, episode_days = 7)
   x$relative <- get_episode(x$dates, case_free_days = 7)

tests/testthat/test-ggplot_sir.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-ggplot_sir.R", {
-  skip_on_cran()
-
   if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE) &&
     AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
     pdf(NULL) # prevent Rplots.pdf being created

tests/testthat/test-guess_ab_col.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-guess_ab_col.R", {
-  skip_on_cran()
-
   expect_equal(
     guess_ab_col(example_isolates, "amox"),
     "AMX"

tests/testthat/test-italicise_taxonomy.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-italicise_taxonomy.R", {
-  skip_on_cran()
-
   expect_identical(
     italicise_taxonomy("test for E. coli"),
     "test for *E. coli*"

tests/testthat/test-join_microorganisms.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-join_microorganisms.R", {
-  skip_on_cran()
-
   unjoined <- example_isolates
   inner <- inner_join_microorganisms(example_isolates)
   left <- left_join_microorganisms(example_isolates)

tests/testthat/test-key_antimicrobials.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-key_antimicrobials.R", {
-  skip_on_cran()
-
   expect_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
   expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
   expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))

tests/testthat/test-kurtosis.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-kurtosis.R", {
-  skip_on_cran()
-
   expect_equal(kurtosis(example_isolates$age),
     5.227999,
     tolerance = 0.00001

tests/testthat/test-like.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-like.R", {
-  skip_on_cran()
-
   expect_true(sum("test" %like% c("^t", "^s")) == 1)
 
   expect_true("test" %like% "test")

tests/testthat/test-mdro.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-mdro.R", {
-  skip_on_cran()
-
   expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
   expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
 

tests/testthat/test-mean_amr_distance.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-mean_amr_distance.R", {
-  skip_on_cran()
-
   vctr_disk <- as.disk(c(20:25))
   vctr_mic <- as.mic(2^c(0:5))
   vctr_sir <- as.sir(c("S", "S", "I", "I", "R", "R"))

tests/testthat/test-mic.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-mic.R", {
-  skip_on_cran()
-
   # used in multiple functions, also in plotting
   expect_true(all(as.mic(AMR:::COMMON_MIC_VALUES) %in% AMR:::VALID_MIC_LEVELS))
   expect_true(all(paste0("<=", as.mic(AMR:::COMMON_MIC_VALUES)) %in% AMR:::VALID_MIC_LEVELS))

tests/testthat/test-mo.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-mo.R", {
-  skip_on_cran()
-
   MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
   expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo, keep_synonyms = TRUE)))
 

tests/testthat/test-mo_property.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-mo_property.R", {
-  skip_on_cran()
-
   expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
   expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
   expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")

tests/testthat/test-pca.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-pca.R", {
-  skip_on_cran()
-
   resistance_data <- structure(
     list(
       order = c("Bacillales", "Enterobacterales", "Enterobacterales"),

tests/testthat/test-plotting.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-plotting.R", {
-  skip_on_cran()
-
   if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
     pdf(NULL) # prevent Rplots.pdf being created
 

tests/testthat/test-proportion.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-proportion.R", {
-  skip_on_cran()
-
   expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
   expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
   # AMX resistance in `example_isolates`

tests/testthat/test-random.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-random.R", {
-  skip_on_cran()
-
   expect_inherits(random_mic(100), "mic")
   expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae"), "mic")
   expect_inherits(random_mic(100, mo = "Klebsiella pneumoniae", ab = "meropenem"), "mic")

tests/testthat/test-resistance_predict.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-resistance_predict.R", {
-  skip_on_cran()
-
   if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
     expect_output(AMX_R <- example_isolates %>%
       filter(mo == "B_ESCHR_COLI") %>%

tests/testthat/test-sir.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-sir.R", {
-  skip_on_cran()
-
   # Existing SIR ------------------------------------------------------------
 
   # we must only have EUCAST and CLSI, because otherwise the rules in as.sir() will fail

tests/testthat/test-skewness.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-skewness.R", {
-  skip_on_cran()
-
   expect_equal(skewness(example_isolates$age),
     -1.212888,
     tolerance = 0.00001

tests/testthat/test-top_n_microorganisms.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-top_n_microorganisms.R", {
-  skip_on_cran()
-
   out1 <- top_n_microorganisms(example_isolates, n = 3)
   out2 <- top_n_microorganisms(example_isolates, n = 5, property = "genus")
   out3 <- top_n_microorganisms(example_isolates, n = 5, property = "genus", n_for_each = 3)

tests/testthat/test-translate.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-translate.R", {
-  skip_on_cran()
-
   expect_identical(mo_genus("B_GRAMP", language = "pt"), "(gênero desconhecido)")
 
   expect_identical(mo_fullname("CoNS", "cs"), "Koaguláza-negativní stafylokok (KNS)")

tests/testthat/test-vctrs.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-vctrs.R", {
-  skip_on_cran()
-
   # extra tests for {vctrs} pkg support
   if (AMR:::pkg_is_available("tibble")) {
     test <- tibble::tibble(

tests/testthat/test-zzz.R

@@ -28,8 +28,6 @@
 # ==================================================================== #
 
 test_that("test-zzz.R", {
-  skip_on_cran()
-
   # Check if these functions still exist in their package (all are in Suggests field)
   # Since GitHub Actions runs every night, we will get emailed when a dependency fails based on this unit test
 

tests/tinytest.R.old

@@ -43,7 +43,6 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
       code
     }
     expect_output <- tinytest::expect_stdout
-    skip_on_cran <- function() invisible(NULL)
     
     # set language
     set_AMR_locale("English")