(v3.0.1.9020) unit test fixes

2026-02-09 21:52:53 +01:00 · 2026-02-09 13:16:36 +01:00
parent ba4c159154
commit 499c830ee7
9 changed files with 42 additions and 30 deletions
--- a/4
+++ b/4
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9019
-Date: 2026-02-08
+Version: 3.0.1.9020
+Date: 2026-02-09
 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
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9019
+# AMR 3.0.1.9020

 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -498,11 +498,6 @@ word_wrap <- function(...,
      url = paste0("ide:help:AMR::", gsub("()", "", parts[cmds & parts %like% "[.]"], fixed = TRUE)),
      txt = parts[cmds & parts %like% "[.]"]
    )
-    # otherwise, give a 'click to run' popup
-    parts[cmds & parts %unlike% "[.]"] <- font_url(
-      url = paste0("ide:run:AMR::", parts[cmds & parts %unlike% "[.]"]),
-      txt = parts[cmds & parts %unlike% "[.]"]
-    )
    # datasets should give help page as well
    parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")] <- font_url(
      url = paste0("ide:help:AMR::", gsub("()", "", parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")], fixed = TRUE)),
--- a/R/interpretive_rules.R
+++ b/R/interpretive_rules.R
@@ -164,9 +164,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
 interpretive_rules <- function(x,
                               col_mo = NULL,
-                               guideline = getOption("AMR_guideline", "EUCAST"),
                               info = interactive(),
                               rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
+                               guideline = getOption("AMR_guideline", "EUCAST"),
                               verbose = FALSE,
                               version_breakpoints = 15.0,
                               version_expected_phenotypes = 1.2,
@@ -190,6 +190,11 @@ interpretive_rules <- function(x,
  meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
  meet_criteria(overwrite, allow_class = "logical", has_length = 1)

+  stop_if(
+    guideline == "CLSI",
+    "CLSI guideline is not yet supported."
+  )
+
  stop_if(
    !is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
    "For the `ampc_cephalosporin_resistance` argument to work, the `rules` argument must contain `\"expert\"` or `\"all\"`."
@@ -1103,20 +1108,24 @@ interpretive_rules <- function(x,
 #' @rdname interpretive_rules
 #' @export
 eucast_rules <- function(x,
+                         col_mo = NULL,
+                         info = interactive(),
                         rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                         ...) {
  if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
    warning_("The global option `AMR_eucastrules` that you have set is now invalid was ignored - set `AMR_interpretive_rules` instead. See `?AMR-options`.")
  }
-  interpretive_rules(x = x, guideline = "EUCAST", rules = rules, ...)
+  interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
 }

 #' @rdname interpretive_rules
 #' @export
 clsi_rules <- function(x,
+                       col_mo = NULL,
+                       info = interactive(),
                       rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                       ...) {
-  interpretive_rules(x = x, guideline = "CLSI", rules = rules, ...)
+  interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "CLSI", ...)
 }

 # helper function for editing the table ----
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@@ -314,7 +314,9 @@ antimicrobials_equal <- function(y,

  key2sir <- function(val) {
    val <- strsplit(val, "", fixed = TRUE)[[1L]]
-    as.double(as.sir(val))
+    val.int <- rep(NA_real_, length(val))
+    val.int[val %in% VALID_SIR_LEVELS] <- as.double(as.sir(val[val %in% VALID_SIR_LEVELS]))
+    val.int
  }
  # only run on uniques
  uniq <- unique(c(y, z))
--- a/data/example_isolates.rda
+++ b/data/example_isolates.rda
--- a/man/interpretive_rules.Rd
+++ b/man/interpretive_rules.Rd
@@ -21,19 +21,21 @@ Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility test
 }
 }
 \usage{
-interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline",
-  "EUCAST"), info = interactive(),
+interpretive_rules(x, col_mo = NULL, info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
-  "expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
+  "expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
+  verbose = FALSE, version_breakpoints = 15,
  version_expected_phenotypes = 1.2, version_expertrules = 3.3,
  ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
  custom_rules = NULL, overwrite = FALSE, ...)

-eucast_rules(x, rules = getOption("AMR_interpretive_rules", default =
-  c("breakpoints", "expected_phenotypes")), ...)
+eucast_rules(x, col_mo = NULL, info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), ...)

-clsi_rules(x, rules = getOption("AMR_interpretive_rules", default =
-  c("breakpoints", "expected_phenotypes")), ...)
+clsi_rules(x, col_mo = NULL, info = interactive(),
+  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
+  "expected_phenotypes")), ...)

 eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 }
@@ -42,12 +44,12 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)

 \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}

-\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}
-
 \item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.}

 \item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}

+\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}
+
 \item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}

 \item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "11.0", or "10.0".}
--- a/tests/testthat/test-sir.R
+++ b/tests/testthat/test-sir.R
@@ -354,11 +354,11 @@ test_that("test-sir.R", {
    mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1])
  )

-  out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
+  out_vet <- suppressWarnings(as.sir(vet, host = vet$animal, guideline = "CLSI 2023"))
  # give host column name instead of values
  expect_identical(
    out_vet,
-    as.sir(vet, host = "animal", guideline = "CLSI 2023")
+    suppressWarnings(as.sir(vet, host = "animal", guideline = "CLSI 2023"))
  )

  # check outcomes
@@ -384,8 +384,12 @@ test_that("test-sir.R", {
  # ECOFF -----------------------------------------------------------------

  expect_equal(
-    suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF")),
-    as.sir("S")
+    suppressMessages(as.sir(as.mic(c(2, 32)), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF")),
+    as.sir(c("WT", "NWT")) # since ECOFF returns WT/NWT at default
+  )
+  expect_equal(
+    suppressMessages(as.sir(as.mic(c(2, 32)), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF", as_wt_nwt = FALSE)),
+    as.sir(c("S", "R"))
  )
  # old method
  expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
@@ -397,10 +401,10 @@ test_that("test-sir.R", {
  out2 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "conservative")
  out3 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "standard")
  out4 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "lenient")
-  expect_equal(out1, as.sir(c("R", "R", "R")))
-  expect_equal(out2, as.sir(c("R", "NI", "R")))
-  expect_equal(out3, as.sir(c("R", "S", "R")))
-  expect_equal(out4, as.sir(c("R", "S", "R")))
+  expect_equal(out1, as.sir(c("NWT", "NWT", "NWT")))
+  expect_equal(out2, as.sir(c("NWT", "NI", "NWT")))
+  expect_equal(out3, as.sir(c("NWT", "WT", "NWT")))
+  expect_equal(out4, as.sir(c("NWT", "WT", "NWT")))

  # Parallel computing ----------------------------------------------------

--- a/tests/testthat/test-translate.R
+++ b/tests/testthat/test-translate.R
@@ -40,7 +40,7 @@ test_that("test-translate.R", {
  expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
  expect_identical(mo_fullname("CoNS", "fi"), "Koagulaasinegatiivinen stafylokokki (KNS)")
  expect_identical(mo_fullname("CoNS", "fr"), "Staphylococcus à coagulase négative (CoNS)")
-  expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
+  expect_identical(mo_fullname("CoNS", "it"), "Stafilococco coagulasi-negativo (CoNS)")
  expect_identical(mo_fullname("CoNS", "ja"), "コアグラーゼ陰性ブドウ球菌 (グラム陰性)")
  expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
  expect_identical(mo_fullname("CoNS", "no"), "Koagulase-negative stafylokokker (KNS)")