* This package has been archived on 22 May 2021 because of errors in the dplyr package, causing the skimr package to fail: <https://github.com/tidyverse/dplyr/issues/5881>. This AMR package contains a fix around this error. Nonetheless, an automated email sent to the maintainer with a warning that the AMR package would be archived would have saved us this archiving. Perhaps an idea for future development of CRAN?
* This package has a tarball size of over 7 MB and an installation size of over 5 MB, which will return a NOTE on R CMD CHECK. The package size is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package. This was written and explained in a manuscript that was accepted for publication in the Journal of Statistical Software 4 weeks ago. We will add the paper as a vignette in the next version. Please allow this exception in package size for CRAN. We already compressed all data sets using `compression = "xz"` to make them as small as possible.
<ahref="#last-updated-24-may-2021"class="anchor"></a><small>Last updated: 24 May 2021</small>
@ -288,7 +288,7 @@
</ul>
</li>
<li>Function <code><ahref="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><ahref="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code>ggplot()</code> method for <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -387,7 +387,7 @@
<spanclass="co">#> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><ahref="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><ahref="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code>ggplot()</code> generics for classes <code><mic></code> and <code><disk></code></p></li>
<li><p><code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code><mic></code> and <code><disk></code></p></li>
<li>
<p>Function <code><ahref="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><ahref="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><ahref="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -461,7 +461,7 @@
<code><ahref="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
<li>Functions <code><ahref="../reference/get_episode.html">get_episode()</a></code> and <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
<li>Functions <code><ahref="https://rdrr.io/r/base/print.html">print()</a></code> and <code><ahref="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><ahref="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><ahref="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
<li>Functions <code><ahref="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><ahref="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><ahref="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><ahref="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
</li>
<li>Improved speed and reliability of <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> and <code><ahref="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
<li>Fix for <code><ahref="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
<preclass="examples"><spanclass='fu'><ahref='https://rdrr.io/r/base/summary.html'>summary</a></span><spanclass='op'>(</span><spanclass='va'>example_isolates</span><spanclass='op'>)</span><spanclass='co'># see all R/SI results at a glance</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9055</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9063</span>
</span>
</div>
@ -327,7 +327,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<spanclass='fu'>atc_online_property</span><spanclass='op'>(</span><spanclass='st'>"J01CA04"</span>, property <spanclass='op'>=</span><spanclass='st'>"groups"</span><spanclass='op'>)</span><spanclass='co'># search hierarchical groups of amoxicillin</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9055</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.6.0.9063</span>
</span>
</div>
@ -429,7 +429,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <ahref='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <ahref='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <ahref='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <ahref='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
