(v2.1.1.9229) unit tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9228
+Version: 2.1.1.9229
 Date: 2025-03-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9228
+# AMR 2.1.1.9229
 
 *(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).)*
 

data-raw/gpt_training_text_v2.1.1.9229.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 2.1.1.9228. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9229. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
@@ -9972,7 +9972,7 @@ download_txt <- function(filename) {
     trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
     ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
   )
-  github_base <- "https://github.com/msberends/AMR/raw/main/"
+  github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/"
   local_filename <- paste0("../data-raw/datasets/", filename)
   rds <- paste0(local_filename, ".rds")
   txt <- paste0(local_filename, ".txt")
@@ -9984,7 +9984,7 @@ download_txt <- function(filename) {
   create_txt <- function(filename, type, software, exists) {
     if (isTRUE(exists)) {
       paste0(
-        "* Download as [", software, "](", github_base, filename, ") (",
+        "* Download as [", software, "](", github_base, basename(filename), ") (",
         AMR:::formatted_filesize(filename), ")  \n"
       )
     } else {

pkgdown/extra.css

@@ -130,6 +130,10 @@ input[type="search"] {
 .template-home .endorse_img {
   width: 150px;
 }
+blockquote {
+  padding: 1.25rem 1.25rem;
+  border-left: 1rem solid var(--amr-green-dark);
+}
 
 /* 
 this shows on top of every sidebar to the right

tests/testthat/test-eucast_rules.R

@@ -117,7 +117,7 @@ test_that("test-eucast_rules.R", {
             TIC = as.sir("R"),
             PIP = as.sir("S")
           ) %>%
-          eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE, overwrite = TRUE) %>%
+          eucast_rules(col_mo = "mo", version_expertrules = 3.1, rules = "expert", info = FALSE, overwrite = TRUE) %>%
           pull(PIP) %>%
           unique() %>%
           as.character()
@@ -136,6 +136,7 @@ test_that("test-eucast_rules.R", {
       stringsAsFactors = FALSE
     ),
     version_expertrules = 3.1,
+    rules = "expert",
     overwrite = TRUE,
     only_sir_columns = FALSE
   )$CLR))

vignettes/datasets.Rmd

@@ -42,7 +42,7 @@ download_txt <- function(filename) {
     trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
     ". Find more info about the contents, (scientific) source, and structure of this [data set here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
   )
-  github_base <- "https://github.com/msberends/AMR/raw/main/"
+  github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/datasets/"
   local_filename <- paste0("../data-raw/datasets/", filename)
   rds <- paste0(local_filename, ".rds")
   txt <- paste0(local_filename, ".txt")
@@ -54,7 +54,7 @@ download_txt <- function(filename) {
   create_txt <- function(filename, type, software, exists) {
     if (isTRUE(exists)) {
       paste0(
-        "* Download as [", software, "](", github_base, filename, ") (",
+        "* Download as [", software, "](", github_base, basename(filename), ") (",
         AMR:::formatted_filesize(filename), ")  \n"
       )
     } else {