diff --git a/DESCRIPTION b/DESCRIPTION index 9db4c3eb1..ccaf79ac5 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index 26c46c548..2b8a0379e 100644 --- a/NEWS.md +++ b/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).)* diff --git a/data-raw/gpt_training_text_v2.1.1.9228.txt b/data-raw/gpt_training_text_v2.1.1.9229.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9228.txt rename to data-raw/gpt_training_text_v2.1.1.9229.txt index ee1780dbf..839799ad1 100644 --- a/data-raw/gpt_training_text_v2.1.1.9228.txt +++ b/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 { diff --git a/pkgdown/extra.css b/pkgdown/extra.css index 584f2f7ba..683a800f9 100644 --- a/pkgdown/extra.css +++ b/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 diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index abb165fc8..ab82a59c5 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/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)) diff --git a/vignettes/datasets.Rmd b/vignettes/datasets.Rmd index 142a035e0..c2e077abd 100644 --- a/vignettes/datasets.Rmd +++ b/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 {