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(v2.1.1.9220) unit test

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dr. M.S. (Matthijs) Berends 2025-03-19 16:13:43 +01:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9219
Version: 2.1.1.9220
Date: 2025-03-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 2.1.1.9219
# AMR 2.1.1.9220
*(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).)*

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R/ab.R
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@ -358,7 +358,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
FUN.VALUE = double(1),
ab_df$generalised_synonyms,
function(y) {
ifelse(length(y[nchar(y) >= 5]) == 0,
ifelse(all(is.na(y)) || length(y[nchar(y) >= 5]) == 0,
999,
min(as.double(utils::adist(x[i], y[nchar(y) >= 5],
ignore.case = FALSE,

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R/amr_selectors.R
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@ -955,7 +955,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
`+.amr_selector` <- function(e1, e2) {
# this is useful for `antibiogram()`: antibiogram(example_isolates, carbapenems() + c("", "GEN", "TOB"))
structure(as.character(outer(e1, e2, paste, sep = " + ")),
class = c("amr_selector", "character")
class = c("amr_selector", "character")
)
}

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R/antibiogram.R
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@ -336,7 +336,7 @@
#' antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
#' mo_transform = "gramstain"
#' )
#'
#'
#' # you can use any antimicrobial selector with `+` too:
#' antibiogram(example_isolates,
#' antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"),

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data-raw/gpt_training_text_v2.1.1.9219.txt → data-raw/gpt_training_text_v2.1.1.9220.txt
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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 2.1.1.9219. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9220. 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.
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