(v2.1.1.9150) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9149
+Version: 2.1.1.9150
 Date: 2025-02-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9149
+# AMR 2.1.1.9150
 
 *(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: 2.1.1.9149
+Version: 2.1.1.9150
 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='2.1.1.9149',
+    version='2.1.1.9150',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/antibiogram.R

@@ -364,7 +364,7 @@
 #'
 #' ureido <- antibiogram(example_isolates,
 #'   antibiotics = ureidopenicillins(),
-#'   syndromic_group = "name",
+#'   syndromic_group = "ward",
 #'   wisca = TRUE)
 #'
 #' # in an Rmd file, you would just need to return `ureido` in a chunk,

data-raw/gpt_training_text_v2.1.1.9150.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 2.1.1.9149. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9150. 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.
 ----------------------------------------------------------------------------------------------------
@@ -2031,7 +2031,7 @@ antibiogram(example_isolates,
 
 ureido <- antibiogram(example_isolates,
   antibiotics = ureidopenicillins(),
-  syndromic_group = "name",
+  syndromic_group = "ward",
   wisca = TRUE)
 
 # in an Rmd file, you would just need to return `ureido` in a chunk,

man/antibiogram.Rd

@@ -400,7 +400,7 @@ antibiogram(example_isolates,
 
 ureido <- antibiogram(example_isolates,
   antibiotics = ureidopenicillins(),
-  syndromic_group = "name",
+  syndromic_group = "ward",
   wisca = TRUE)
 
 # in an Rmd file, you would just need to return `ureido` in a chunk,

tests/testthat/test-antibiogram.R

@@ -128,7 +128,9 @@ expect_silent(plot(ab5))
 expect_silent(plot(ab6))
 expect_silent(plot(ab7))
 expect_silent(plot(ab8))
-expect_silent(plot(ab9))
+if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
+  expect_silent(plot(ab9))
+}
 
 if (AMR:::pkg_is_available("ggplot2")) {
   expect_inherits(ggplot2::autoplot(ab1), "gg")
@@ -139,5 +141,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
   expect_inherits(ggplot2::autoplot(ab6), "gg")
   expect_inherits(ggplot2::autoplot(ab7), "gg")
   expect_inherits(ggplot2::autoplot(ab8), "gg")
-  expect_inherits(ggplot2::autoplot(ab9), "gg")
+  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
+    expect_inherits(ggplot2::autoplot(ab9), "gg")
+  }
 }