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(v2.1.1.9237) clean-up

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dr. M.S. (Matthijs) Berends 2025-04-13 09:59:40 +02:00
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14 changed files with 39 additions and 26 deletions
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2
.github/ISSUE_TEMPLATE/config.yml vendored
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@ -1,7 +1,7 @@
blank_issues_enabled: false
contact_links:
- name: I Have a Question - Ask Our AMR for R Assistant
url: https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant
url: https://chat.amr-for-r.org
about: Ask questions or code suggestions to our AMR for R Assistant, a ChatGPT manually-trained model able to answer any question about the AMR package.
- name: I Have a Question - AMR Community Support
url: https://github.com/msberends/AMR/discussions

2
.github/prehooks/pre-commit vendored
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@ -111,7 +111,7 @@ echo ""
# Save the version number for use in the commit-msg hook
echo "${currentversion}" > .git/commit_version.tmp
# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
# Generate GPT knowledge info for our Assistant (https://chat.amr-for-r.org)
bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
git add data-raw/*
git add -u

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9236
Date: 2025-04-12
Version: 2.1.1.9237
Date: 2025-04-13
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

6
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9236
# AMR 2.1.1.9237
*(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://amr-for-r.org/#get-this-package).)*
@ -8,7 +8,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
## Breaking
* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
* Function `resistance_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
* Functions `resistance_predict()` and `sir_predict()` is now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
## New
* **One Health implementation**
@ -49,6 +49,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* It is now possible to use column names for argument `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
* Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
* To get quantitative values, `as.double()` on a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain NI and SDD.
* Following CLSI interpretation rules, values outside the log2-dilution range will be rounded upwards to the nearest log2-level before interpretation. Only if using a CLSI guideline.
* Combined MIC values (e.g., from CLSI) are now supported
* The argument `conserve_capped_values` in `as.sir()` has been replaced with `capped_mic_handling`, which allows greater flexibility in handling capped MIC values (`<`, `<=`, `>`, `>=`). The four available options (`"standard"`, `"strict"`, `"relaxed"`, `"inverse"`) provide full control over whether these values should be interpreted conservatively or ignored. Using `conserve_capped_values` is now deprecated and returns a warning.
* Added argument `info` so silence all console messages
@ -105,6 +106,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Added console colours support of `sir` class for Positron
## Other
* New website domain: <https://amr-for-r.org>! The old links (all based on <http://amr-for-r.org>) will remain to work.
* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
* Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes

4
R/resistance_predict.R
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@ -29,7 +29,9 @@
#' Predict Antimicrobial Resistance
#'
#' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#' @description Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#'
#' **NOTE:** These functions are [deprecated][AMR-deprecated] and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a [basic and short introduction on our website](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
#' @param object Model data to be plotted.
#' @param col_ab Column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`).
#' @param col_date Column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class.

8
R/zz_deprecated.R
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@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Deprecated Functions
#' Deprecated Functions, Arguments, or Datasets
#'
#' These objects are so-called '[Deprecated]'. **They will be removed in a future version of this package.** Using these will give a warning with the name of the alternative object it has been replaced by (if there is one).
#' @keywords internal
@ -40,8 +40,10 @@ NULL
#' @export
"antibiotics"
# REMEMBER to also remove the deprecated `antibiotics` argument in `antibiogram()`
# REMEMBER to also remove the deprecated `converse_capped_values` argument in `as.sir()`
# REMEMBER to search for `deprecation_warning` in the package code to find all instances.
# currently deprecated arguments at least:
# - `antibiotics` in `antibiogram()`
# - `converse_capped_values` in `as.sir()`
#' @rdname AMR-deprecated
#' @export

9
_pkgdown.yml
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@ -38,12 +38,11 @@ template:
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script>
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
bootswatch: "flatly"
assets: "pkgdown/logos" # use logos in this folder
bslib:
base_font: {google: "Lato"}
heading_font: {google: "Lato"}
code_font: {google: "Fira Code"}
# body-text-align: "justify"
# body-text-align: "justify" # this is now only in `p {}` in extra.css
line-height-base: 1.75
# make top bar a bit wider
navbar-padding-y: "0.5rem"
@ -58,7 +57,7 @@ footer:
right: [logo]
components:
devtext: '<code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a> in The Netherlands.'
logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style="max-width: 150px;"></a>'
logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a>'
home:
sidebar:
@ -268,9 +267,9 @@ reference:
- "`kurtosis`"
- "`skewness`"
- title: "Other: deprecated functions"
- title: "Other: deprecated functions/arguments/datasets"
desc: >
These functions are deprecated, meaning that they will still
These objects are deprecated, meaning that they will still
work but show a warning that they will be removed
in a future version.
contents:

12
data-raw/gpt_training_text_v2.1.1.9236.txt → data-raw/gpt_training_text_v2.1.1.9237.txt
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@ -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 2.1.1.9236. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9237. 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.
----------------------------------------------------------------------------------------------------
@ -559,7 +559,7 @@ ggplot(data.frame(mic = some_mic_values,
```
<a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis">
<img src="./plot_readme.png" style="width: 600px; max-width: 100%;">
<img src="./plot_readme.png" style="width: 1400px; max-width: 100%;">
</a>
#### Calculating resistance per group
@ -736,7 +736,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/AMR-deprecated.Rd':
\alias{antibiotics}
\alias{ab_class}
\alias{ab_selector}
\title{Deprecated Functions}
\title{Deprecated Functions, Arguments, or Datasets}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
}
@ -8317,7 +8317,9 @@ A \link{data.frame} with extra class \code{\link{resistance_predict}} with colum
Furthermore, the model itself is available as an attribute: \code{attributes(x)$model}, see \emph{Examples}.
}
\description{
Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See \emph{Examples} for a real live example.
Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See \emph{Examples} for a real live example.
\strong{NOTE:} These functions are \link[=AMR-deprecated]{deprecated} and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{basic and short introduction on our website}.
}
\details{
Valid options for the statistical model (argument \code{model}) are:
@ -9222,7 +9224,7 @@ knitr::opts_chunk$set(
)
```
> This page was entirely written by our [AMR for R Assistant](https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant), a ChatGPT manually-trained model able to answer any question about the AMR package.
> This page was entirely written by our [AMR for R Assistant](https://chat.amr-for-r.org), a ChatGPT manually-trained model able to answer any question about the AMR package.
Antimicrobial resistance (AMR) is a global health crisis, and understanding resistance patterns is crucial for managing effective treatments. The `AMR` R package provides robust tools for analysing AMR data, including convenient antimicrobial selector functions like `aminoglycosides()` and `betalactams()`.

2
index.md
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@ -162,7 +162,7 @@ ggplot(data.frame(mic = some_mic_values,
```
<a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis">
<img src="./plot_readme.png" style="width: 600px; max-width: 100%;">
<img src="./plot_readme.png" style="width: 1400px; max-width: 100%;">
</a>
#### Calculating resistance per group

2
man/AMR-deprecated.Rd
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@ -6,7 +6,7 @@
\alias{antibiotics}
\alias{ab_class}
\alias{ab_selector}
\title{Deprecated Functions}
\title{Deprecated Functions, Arguments, or Datasets}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
}

4
man/resistance_predict.Rd
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@ -71,7 +71,9 @@ A \link{data.frame} with extra class \code{\link{resistance_predict}} with colum
Furthermore, the model itself is available as an attribute: \code{attributes(x)$model}, see \emph{Examples}.
}
\description{
Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See \emph{Examples} for a real live example.
Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns \code{se_min} and \code{se_max}. See \emph{Examples} for a real live example.
\strong{NOTE:} These functions are \link[=AMR-deprecated]{deprecated} and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{basic and short introduction on our website}.
}
\details{
Valid options for the statistical model (argument \code{model}) are:

4
pkgdown/extra.css
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@ -131,9 +131,13 @@ input[type="search"] {
width: 150px;
}
blockquote {
font-style: italic;
padding: 1.25rem 1.25rem;
border-left: 1rem solid var(--amr-green-dark);
}
p {
text-align: justify;
}
/*
this shows on top of every sidebar to the right

4
pkgdown/extra.js
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@ -31,7 +31,7 @@
$(document).ready(function() {
// add GPT assistant info
$('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"></a></div>');
$('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chat.amr-for-r.org"><img src="https://amr-for-r.org/AMRforRGPT.svg"></a></div>');
// replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
$(".developers h2").text("Maintainers");
@ -62,7 +62,7 @@ $(document).ready(function() {
if (window.location.href.includes('AMR_for_Python')) {
$('body').addClass('amr-for-python'); /* to set colours in CSS */
$('img[src="../logo.svg"]').attr('src', '../logo_python.svg'); /* replace base logo */
$('img[src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"]').attr('src', 'https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT_python.svg'); /* replace GPT logo */
$('img[src="https://amr-for-r.org/AMRforRGPT.svg"]').attr('src', 'https://amr-for-r.org/AMRforRGPT_python.svg'); /* replace GPT logo */
}
// add country flags

2
vignettes/AMR_with_tidymodels.Rmd
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@ -22,7 +22,7 @@ knitr::opts_chunk$set(
)
```
> This page was entirely written by our [AMR for R Assistant](https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant), a ChatGPT manually-trained model able to answer any question about the AMR package.
> This page was entirely written by our [AMR for R Assistant](https://chat.amr-for-r.org), a ChatGPT manually-trained model able to answer any question about the AMR package.
Antimicrobial resistance (AMR) is a global health crisis, and understanding resistance patterns is crucial for managing effective treatments. The `AMR` R package provides robust tools for analysing AMR data, including convenient antimicrobial selector functions like `aminoglycosides()` and `betalactams()`.