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20
news/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9007</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,9 +49,19 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9004" id="amr-3019004">AMR 3.0.1.9004<a class="anchor" aria-label="anchor" href="#amr-3019004"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9007" id="amr-3019007">AMR 3.0.1.9007<a class="anchor" aria-label="anchor" href="#amr-3019007"></a></h2>
<div class="section level4">
<h4 id="changed-3-0-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9004"></a></h4>
<h4 id="new-3-0-1-9007">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9007"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
<li>New <code>tidyselect</code> helpers: <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk_predictors()</a></code>
</li>
</ul></li>
<li>Data set <code>esbl_isolates</code> to practise with AMR modelling</li>
</ul></div>
<div class="section level4">
<h4 id="changed-3-0-1-9007">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-1-9007"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Added taniborbactam (<code>TAN</code>) and cefepime/taniborbactam (<code>FTA</code>) to the <code>antimicrobials</code> data set</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where for numeric input the arguments <code>S</code>, <code>i</code>, and <code>R</code> would not be considered (<a href="https://github.com/msberends/AMR/issues/244" class="external-link">#244</a>)</li>
@@ -104,7 +114,7 @@
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
<div class="section level4">
<h4 id="breaking-3-0-0">Breaking<a class="anchor" aria-label="anchor" href="#breaking-3-0-0"></a></h4>
<ul><li>Dataset <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<ul><li>Data set <code>antibiotics</code> has been renamed to <code>antimicrobials</code> as the data set contains more than just antibiotics. Using <code>antibiotics</code> will still work, but now returns a warning.</li>
<li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over two years ago.</li>
<li>Functions <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> and <code><a href="../reference/resistance_predict.html">sir_predict()</a></code> are now deprecated and will be removed in a future version. Use the <code>tidymodels</code> framework instead, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a basic introduction</a>.</li>
</ul></div>
@@ -122,7 +132,7 @@
</ul></li>
<li>
<strong>Support for WISCA antibiograms</strong>
<ul><li>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated <code><a href="../reference/antibiogram.html">wisca()</a></code> function is also available for easy usage.</li>
<ul><li>The <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in data sets with sparse data. A dedicated <code><a href="../reference/antibiogram.html">wisca()</a></code> function is also available for easy usage.</li>
</ul></li>
<li>
<strong>More global coverage of languages</strong>

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news/index.md
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@@ -1,6 +1,23 @@
# Changelog
## AMR 3.0.1.9004
## AMR 3.0.1.9007
#### New
- Integration with the **tidymodels** framework to allow seamless use of
SIR, MIC and disk data in modelling pipelines via `recipes`
- [`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md)
to transform `<mic>` columns with log2, and
[`step_sir_numeric()`](https://amr-for-r.org/reference/amr-tidymodels.md)
to convert `<sir>` columns to numeric
- New `tidyselect` helpers:
[`all_sir()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_sir_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_mic()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_mic_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_disk()`](https://amr-for-r.org/reference/amr-tidymodels.md),
[`all_disk_predictors()`](https://amr-for-r.org/reference/amr-tidymodels.md)
- Data set `esbl_isolates` to practise with AMR modelling
#### Changed
@@ -119,8 +136,8 @@ this change.
#### Breaking
- Dataset `antibiotics` has been renamed to `antimicrobials` as the data
set contains more than just antibiotics. Using `antibiotics` will
- Data set `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
@@ -158,7 +175,7 @@ this change.
Combination Antibiograms (WISCA), a powerful Bayesian method for
estimating regimen coverage probabilities using pathogen incidence
and antimicrobial susceptibility data. WISCA offers improved
precision for syndrome-specific treatment, even in datasets with
precision for syndrome-specific treatment, even in data sets with
sparse data. A dedicated
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) function
is also available for easy usage.