(v2.1.1.9187) WISCA fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9186
+Version: 2.1.1.9187
 Date: 2025-03-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9186
+# AMR 2.1.1.9187
 
 *(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: 2.1.1.9186
+Version: 2.1.1.9187
 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='2.1.1.9186',
+    version='2.1.1.9187',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/antibiogram.R

@@ -606,9 +606,6 @@ antibiogram.default <- function(x,
     warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
     return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
   } else if (any(out$n_tested < minimum, na.rm = TRUE)) {
-    out <- out %pm>%
-      # also for WISCA, refrain from anything below 15 isolates:
-      subset(n_tested > 15)
     mins <- sum(out$n_tested < minimum, na.rm = TRUE)
     if (wisca == FALSE) {
       out <- out %pm>%
@@ -620,7 +617,6 @@ antibiogram.default <- function(x,
       warning_("Number of tested isolates per regimen should exceed ", minimum, " for each species. Coverage estimates might be inaccurate.", call = FALSE)
     }
   }
-
   if (NROW(out) == 0) {
     return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
   }
@@ -671,6 +667,7 @@ antibiogram.default <- function(x,
       out_wisca <- out %pm>%
         pm_group_by(ab)
     }
+
     out_wisca <- out_wisca %pm>%
       pm_summarise(
         coverage = NA_real_,
@@ -680,6 +677,7 @@ antibiogram.default <- function(x,
         n_tested = sum(n_tested, na.rm = TRUE),
         n_susceptible = sum(n_susceptible, na.rm = TRUE)
       )
+
     out_wisca$p_susceptible <- out_wisca$n_susceptible / out_wisca$n_tested
 
     if (isTRUE(has_syndromic_group)) {

R/data.R

@@ -74,7 +74,6 @@
 #' * European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
 #' @inheritSection WHOCC WHOCC
 #' @seealso [microorganisms], [intrinsic_resistant]
-#' @aliases antibiotics
 #' @examples
 #' antimicrobials
 #' antivirals

R/temp_file

@@ -1 +0,0 @@
-test_that("key_antimicrobials works", {

R/zz_deprecated.R

@@ -36,6 +36,7 @@
 NULL
 
 #' @rdname AMR-deprecated
+#' @usage NULL
 #' @export
 "antibiotics"
 

R/zzz.R

@@ -210,7 +210,9 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
 
   # deprecated antibiotics data set
   makeActiveBinding("antibiotics", function() {
+    if (interactive()) {
       deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE)
+    }
     AMR::antimicrobials
   }, env = asNamespace(pkgname))
 

data-raw/gpt_training_text_v2.1.1.9187.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 2.1.1.9186. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9187. 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.
 ----------------------------------------------------------------------------------------------------
@@ -735,8 +735,6 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/AMR-deprecated.Rd':
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 487 rows and 14 columns.
 }
 \usage{
-antibiotics
-
 ab_class(...)
 
 ab_selector(...)
@@ -2498,7 +2496,6 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/antimicrobials.Rd':
 \docType{data}
 \name{antimicrobials}
 \alias{antimicrobials}
-\alias{antibiotics}
 \alias{antivirals}
 \title{Data Sets with 607 Antimicrobial Drugs}
 \format{

man/AMR-deprecated.Rd

@@ -11,8 +11,6 @@
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 487 rows and 14 columns.
 }
 \usage{
-antibiotics
-
 ab_class(...)
 
 ab_selector(...)

man/antimicrobials.Rd

@@ -3,7 +3,6 @@
 \docType{data}
 \name{antimicrobials}
 \alias{antimicrobials}
-\alias{antibiotics}
 \alias{antivirals}
 \title{Data Sets with 607 Antimicrobial Drugs}
 \format{