(v2.1.1.9160) cleanup

.github/workflows/lintr.yaml

@@ -53,7 +53,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::lintr
+          extra-packages: |
+            any::lintr
+            any::cyclocomp
 
       - name: Lint
         run: |
@@ -63,6 +65,7 @@ jobs:
           linters <- sort(linters[grepl("_linter$", linters)])
           # lose deprecated
           linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)]
+          linters <- linters[linters != "linter"]
           # and the ones we find unnnecessary
           linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)]
           # put the functions in a list

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9159
+Version: 2.1.1.9160
 Date: 2025-02-26
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9159
+# AMR 2.1.1.9160
 
 *(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).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9159
+Version: 2.1.1.9160
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9159',
+    version='2.1.1.9160',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/ab.R

@@ -106,10 +106,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
     ))
   }
   
-  loop_time <- list(...)$loop_time
-  if (is.null(loop_time)) {
-    loop_time <- 1
-  }
   already_regex <- isTRUE(list(...)$already_regex)
   fast_mode <- isTRUE(list(...)$fast_mode)
   
@@ -134,8 +130,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_unknown_ATCs <- character(0)
   
   note_if_more_than_one_found <- function(found, index, from_text) {
-    if (loop_time == 1 && isTRUE(length(from_text) > 1)) {
-      abnames <- ab_name(from_text, tolower = TRUE, loop_time = loop_time + 1)
+    if (isTRUE(length(from_text) > 1)) {
+      abnames <- ab_name(from_text, tolower = TRUE)
       if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|(avi|tazo|mono|vabor)bactam)") {
         abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam", "tazobactam", "vaborbactam", "monobactam")]
       }
@@ -190,15 +186,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_new[is.na(x)] <- NA
   already_known[is.na(x)] <- FALSE
   
-  if (loop_time == 1 && sum(already_known) < length(x)) {
+  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))
   }
   
   for (i in which(!already_known)) {
-    if (loop_time == 1) {
     progress$tick()
-    }
     
     if (is.na(x[i]) || is.null(x[i])) {
       next
@@ -218,7 +212,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
     }
     
     if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
-      from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 1, translate_ab = FALSE)[[1]]),
+      from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
                             error = function(e) character(0)
       )
     } else {
@@ -331,9 +325,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       next
     }
     
-    # INITIAL SEARCH - More uncertain results ----
-    if (loop_time == 1 && fast_mode == FALSE) {
-      # only run on first and second try
+    # More uncertain results ----
+    if (fast_mode == FALSE) {
       
       ab_df <- AMR_env$AB_lookup
       ab_df$length_name <- nchar(ab_df$generalised_name)
@@ -391,12 +384,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }
   
-  if (loop_time == 1 && sum(already_known) < length(x)) {
+  if (sum(already_known) < length(x)) {
     close(progress)
   }
   
   # save to package env to save time for next time
-  if (loop_time == 1) {
   AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
   AMR_env$ab_previously_coerced <- unique(rbind_AMR(
     AMR_env$ab_previously_coerced,
@@ -407,7 +399,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       stringsAsFactors = FALSE
     )
   ))
-  }
   
   # take failed ATC codes apart from rest
   if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {

R/custom_antimicrobials.R

@@ -69,11 +69,8 @@
 #' @export
 #' @examples
 #' \donttest{
-#'
-#' # returns NA and throws a warning (which is suppressed here):
-#' suppressWarnings(
+#' # returns a wildly guessed result:
 #' as.ab("testab")
-#' )
 #'
 #' # now add a custom entry - it will be considered by as.ab() and
 #' # all ab_*() functions
@@ -109,6 +106,7 @@
 #' ab_name("J01CR50")
 #'
 #' # even antimicrobial selectors work
+#' # see ?amr_selector
 #' x <- data.frame(
 #'   random_column = "some value",
 #'   coflu = as.sir("S"),
@@ -155,7 +153,7 @@ add_custom_antimicrobials <- function(x) {
   }
   AMR_env$AB_lookup <- unique(rbind_AMR(AMR_env$AB_lookup, new_df))
 
-  AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% x$ab), , drop = FALSE]
+  AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE]
   class(AMR_env$AB_lookup$ab) <- c("ab", "character")
   message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
 }

data-raw/gpt_training_text_v2.1.1.9160.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 2.1.1.9159. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9160. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the  file, the  file, and all the  files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
@@ -1324,11 +1324,8 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to
 }
 \examples{
 \donttest{
-
-# returns NA and throws a warning (which is suppressed here):
-suppressWarnings(
+# returns a wildly guessed result:
 as.ab("testab")
-)
 
 # now add a custom entry - it will be considered by as.ab() and
 # all ab_*() functions
@@ -1364,6 +1361,7 @@ ab_atc("Co-fluampicil")
 ab_name("J01CR50")
 
 # even antimicrobial selectors work
+# see ?amr_selector
 x <- data.frame(
   random_column = "some value",
   coflu = as.sir("S"),

man/add_custom_antimicrobials.Rd

@@ -50,11 +50,8 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to
 }
 \examples{
 \donttest{
-
-# returns NA and throws a warning (which is suppressed here):
-suppressWarnings(
+# returns a wildly guessed result:
 as.ab("testab")
-)
 
 # now add a custom entry - it will be considered by as.ab() and
 # all ab_*() functions
@@ -90,6 +87,7 @@ ab_atc("Co-fluampicil")
 ab_name("J01CR50")
 
 # even antimicrobial selectors work
+# see ?amr_selector
 x <- data.frame(
   random_column = "some value",
   coflu = as.sir("S"),

tests/testthat/test-amr_selectors.R

@@ -59,7 +59,7 @@ expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, toleran
 expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5)
 expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5)
 
-expect_message(carbapenems())
+expect_message(expect_stdout(print(carbapenems())))
 expect_error(administrable_per_os())
 
 # Examples: