(v3.0.0.9027) skimr update and as.ab warning - fixes #234, fixes #232

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9026
-Date: 2025-09-04
+Version: 3.0.0.9027
+Date: 2025-09-10
 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

NAMESPACE

@@ -388,6 +388,7 @@ if(getRversion() >= "3.0.0") S3method(pillar::type_sum, av)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mic)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mo)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, sir)
+if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.0.9026
+# AMR 3.0.0.9027
 
 This is a bugfix release following the release of v3.0.0 in June 2025.
 
@@ -13,8 +13,10 @@ This is a bugfix release following the release of v3.0.0 in June 2025.
 * Fixed a bug the `antimicrobials` data set to remove statins (#229)
 * Fixed a bug in `mdro()` to make sure all genes specified in arguments are acknowledged
 * Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
+* Fixed skimmers (`skimr` package) of class `ab`, `sir`, and `disk` (#234)
 * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
 * Fixed some specific Dutch translations for antimicrobials
+* Added a warning to `as.ab()` if input resembles antiviral codes or names (#232)
 * Added all reasons in verbose output of `mdro()` (#227)
 * Added `names` to `age_groups()` so that custom names can be given (#215)
 * Added note to `as.sir()` to make it explicit when higher-level taxonomic breakpoints are used (#218)

R/ab.R

@@ -202,6 +202,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   if (sum(already_known) < length(x)) {
     progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
     on.exit(close(progress))
+    if (any(x_new[!already_known] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
+      warning_("in `as.ab()`: some input seem to resemble antiviral drugs - use `as.av()` or e.g. `av_name()` for these, not `as.ab()` or e.g. `ab_name()`.")
+    }
   }
 
   for (i in which(!already_known)) {
@@ -448,7 +451,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
   if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
-      "in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
+      "in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
       vector_and(x_unknown), "."
     )
   }
@@ -627,6 +630,20 @@ rep.ab <- function(x, ...) {
   out
 }
 
+# this prevents the requirement for putting the dependency in Imports:
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
+get_skimmers.ab <- function(column) {
+  ab <- as.ab(column, info = FALSE)
+  ab <- ab[!is.na(ab)]
+  skimr::sfl(
+    skim_type = "ab",
+    n_unique = ~ length(unique(ab)),
+    top_ab = ~ names(sort(-table(ab)))[1L],
+    top_ab_name = ~ names(sort(-table(ab_name(ab, info = FALSE))))[1L],
+    top_group = ~ names(sort(-table(ab_group(ab, info = FALSE))))[1L]
+  )
+}
+
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices

R/disk.R

@@ -236,12 +236,14 @@ rep.disk <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 get_skimmers.disk <- function(column) {
+  column <- as.integer(column)
   skimr::sfl(
     skim_type = "disk",
-    min = ~ min(as.double(.), na.rm = TRUE),
-    max = ~ max(as.double(.), na.rm = TRUE),
-    median = ~ stats::median(as.double(.), na.rm = TRUE),
-    n_unique = ~ length(unique(stats::na.omit(.))),
-    hist = ~ skimr::inline_hist(stats::na.omit(as.double(.)))
+    p0 = ~ stats::quantile(column, probs = 0, na.rm = TRUE, names = FALSE),
+    p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
+    p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
+    p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
+    p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
+    hist = ~ skimr::inline_hist(stats::na.omit(column), 10)
   )
 }

R/mic.R

@@ -596,12 +596,12 @@ get_skimmers.mic <- function(column) {
   column <- as.mic(column) # make sure that currently implemented MIC levels are used
   skimr::sfl(
     skim_type = "mic",
-    p0 = ~ stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
-    p25 = ~ stats::quantile(., probs = 0.25, na.rm = TRUE, names = FALSE),
-    p50 = ~ stats::quantile(., probs = 0.5, na.rm = TRUE, names = FALSE),
-    p75 = ~ stats::quantile(., probs = 0.75, na.rm = TRUE, names = FALSE),
-    p100 = ~ stats::quantile(., probs = 1, na.rm = TRUE, names = FALSE),
-    hist = ~ skimr::inline_hist(log2(stats::na.omit(.)), 5)
+    p0 = ~ stats::quantile(column, probs = 0, na.rm = TRUE, names = FALSE),
+    p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
+    p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
+    p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
+    p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
+    hist = ~ skimr::inline_hist(log2(stats::na.omit(column)), 10)
   )
 }
 

R/mo.R

@@ -747,13 +747,17 @@ freq.mo <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
 get_skimmers.mo <- function(column) {
+  mo <- as.mo(column, keep_synonyms = TRUE, language = NULL, info = FALSE)
+  mo <- mo[!is.na(mo)]
+  spp <- mo[mo_species(mo, keep_synonyms = TRUE, language = NULL, info = FALSE) != ""]
   skimr::sfl(
     skim_type = "mo",
-    unique_total = ~ length(unique(stats::na.omit(.))),
-    gram_negative = ~ sum(mo_is_gram_negative(.), na.rm = TRUE),
-    gram_positive = ~ sum(mo_is_gram_positive(.), na.rm = TRUE),
-    top_genus = ~ names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
-    top_species = ~ names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
+    n_unique = ~ length(unique(mo)),
+    gram_negative = ~ sum(mo_is_gram_negative(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    gram_positive = ~ sum(mo_is_gram_positive(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    yeast = ~ sum(mo_is_yeast(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
+    top_genus = ~ names(sort(-table(mo_genus(mo, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
+    top_species = ~ names(sort(-table(mo_name(spp, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
   )
 }
 

R/sir.R

@@ -1974,33 +1974,18 @@ freq.sir <- function(x, ...) {
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, sir)
 get_skimmers.sir <- function(column) {
-  # get the variable name 'skim_variable'
-  name_call <- function(.data) {
-    calls <- sys.calls()
-    frms <- sys.frames()
-    calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
-    if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
-      ind <- which(calls_txt %like% "skim_variable")[1L]
-      vars <- tryCatch(eval(parse(text = ".data$skim_variable$sir"), envir = frms[[ind]]),
-        error = function(e) NULL
-      )
-      tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL, info = FALSE),
-        error = function(e) NA_character_
-      )
-    } else {
-      NA_character_
-    }
-  }
-
+  # TODO add here in AMR 3.1.0 details about guideline
   skimr::sfl(
     skim_type = "sir",
-    ab_name = name_call,
-    count_R = count_R,
-    count_S = count_susceptible,
+    # guideline = function(x) "EUCAST 2025", # or "Multiple"
+    # origin = function(x) "MIC", # or "Multiple"
+    count_S = count_S,
     count_I = count_I,
-    prop_R = ~ proportion_R(., minimum = 0),
-    prop_S = ~ susceptibility(., minimum = 0),
-    prop_I = ~ proportion_I(., minimum = 0)
+    count_R = count_R,
+    prop_S = ~ round(proportion_S(., minimum = 0) * 100, 1),
+    prop_I = ~ round(proportion_I(., minimum = 0) * 100, 1),
+    prop_R = ~ round(proportion_R(., minimum = 0) * 100, 1),
+    hist = ~ skimr::inline_hist(as.double(stats::na.omit(.)), 3)
   )
 }
 

tests/testthat/test-ab.R

@@ -96,6 +96,14 @@ test_that("test-ab.R", {
     rep("GEH", 8)
   )
 
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(clinical_breakpoints$ab),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "ab.n_unique", "ab.top_ab", "ab.top_ab_name", "ab.top_group")
+    )
+  }
+
   # assigning and subsetting
   x <- AMR::antimicrobials$ab
   expect_inherits(x[1], "ab")

tests/testthat/test-disk.R

@@ -60,4 +60,12 @@ test_that("test-disk.R", {
   if (AMR:::pkg_is_available("tibble")) {
     expect_output(print(tibble::tibble(d = as.disk(12))))
   }
+
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(random_disk(100)),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "disk.p0", "disk.p25", "disk.p50", "disk.p75", "disk.p100", "disk.hist")
+    )
+  }
 })

tests/testthat/test-mic.R

@@ -81,6 +81,14 @@ test_that("test-mic.R", {
     expect_output(print(tibble::tibble(m = as.mic(2:4))))
   }
 
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(random_mic(100)),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "mic.p0", "mic.p25", "mic.p50", "mic.p75", "mic.p100", "mic.hist")
+    )
+  }
+
   # all mathematical operations
   x <- random_mic(50)
   x_double <- as.double(gsub("[<=>]+", "", as.character(x)))

tests/testthat/test-mo.R

@@ -321,4 +321,12 @@ test_that("test-mo.R", {
   if (AMR:::pkg_is_available("cleaner")) {
     expect_inherits(cleaner::freq(example_isolates$mo), "freq")
   }
+
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(example_isolates$mo),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species")
+    )
+  }
 })

tests/testthat/test-sir.R

@@ -103,22 +103,13 @@ test_that("test-sir.R", {
       pull(MEM) %>%
       is.sir())
   }
+
+  # skimr
   if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
-    expect_inherits(
-      skim(example_isolates),
-      "data.frame"
+    expect_named(
+      skim(example_isolates$PEN),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "sir.count_S", "sir.count_I", "sir.count_R", "sir.prop_S", "sir.prop_I", "sir.prop_R", "sir.hist")
     )
-    if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
-      expect_inherits(
-        example_isolates %>%
-          mutate(
-            m = as.mic(2),
-            d = as.disk(20)
-          ) %>%
-          skim(),
-        "data.frame"
-      )
-    }
   }
 
   expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))