All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
@ -14,6 +14,7 @@ All functions in this package are considered to be stable. Updates to the AMR in
<h3id="last-updated-march-1-8-0-9010"><small>Last updated: 15 March 2022</small><aclass="anchor"aria-label="anchor"href="#last-updated-march-1-8-0-9010"></a></h3>
<p>All functions in this package are considered to be stable. Updates to
<p>All functions in this package are considered to be stable. Updates to
the AMR interpretation rules (such as by EUCAST and CLSI), the microbial
the AMR interpretation rules (such as by EUCAST and CLSI), the microbial
taxonomy, and the antibiotic dosages will all be updated every 6 to 12
taxonomy, and the antibiotic dosages will all be updated every 6 to 12
@ -628,7 +632,7 @@ function) to select/filter on e.g.linezolid and tedizolid</p>
<li><p>Support for custom MDRO guidelines, using the new
<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">custom_mdro_guideline()</a></code> function, please see
<code><ahref="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<code><ahref="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><ahref="https://ggplot2.tidyverse.org/reference/ggplot.html"class="external-link">ggplot()</a></code> generics for classes
<li><p><code>ggplot()</code> generics for classes
<code><mic></code> and <code><disk></code></p></li>
<code><mic></code> and <code><disk></code></p></li>
<li>
<li>
<p>Function <code><ahref="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a
<p>Function <code><ahref="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a
@ -697,7 +701,7 @@ printing)</li>
translated if the system language is German, Dutch or Spanish (see
translated if the system language is German, Dutch or Spanish (see
<code>translate</code>)</li>
<code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><ahref="../reference/plot.html">plot()</a></code> and
<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"class="external-link">ggplot()</a></code> on any vector of MIC and disk
with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk
diffusion values</li>
diffusion values</li>
</ul></li>
</ul></li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September
@ -740,7 +744,7 @@ per hour)</li>
<li>Argument <code>ampc_cephalosporin_resistance</code> in
<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
<code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only
“S”)</li>
“S”)</li>
<li>Functions <code><ahref="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print()</a></code> and <code><ahref="https://rdrr.io/r/base/summary.html"class="external-link">summary()</a></code> on a
<li>Functions <code><ahref="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> and <code><ahref="https://rdrr.io/r/base/summary.html"class="external-link">summary()</a></code> on a
Principal Components Analysis object (<code><ahref="../reference/pca.html">pca()</a></code>) now print
Principal Components Analysis object (<code><ahref="../reference/pca.html">pca()</a></code>) now print
additional group info if the original data was grouped using
additional group info if the original data was grouped using
@ -1266,10 +1270,10 @@ versions of R since R-3.0.0 (April 2013). Our package is being used in
settings where the resources are very limited. Fewer dependencies on
settings where the resources are very limited. Fewer dependencies on
newer software is helpful for such settings.</p>
newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<p>Negative effects of this change are:</p>
<ul><li>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">freq()</a></code> that was borrowed from the
<ul><li>Function <code>freq()</code> that was borrowed from the
<code>cleaner</code> package was removed. Use
<code>cleaner</code> package was removed. Use
<code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner"class="external-link">library("cleaner")</a></code>
<code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner"class="external-link">library("cleaner")</a></code>
before you use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">freq()</a></code>.</li>
before you use <code>freq()</code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in
a tibble will no longer be in colour and printing <code>rsi</code> in a
a tibble will no longer be in colour and printing <code>rsi</code> in a
tibble will show the class <code><ord></code>, not
tibble will show the class <code><ord></code>, not
@ -1698,9 +1702,9 @@ data integrity, this means that invalid assignments will now result in
could never be understood by e.g.<code><ahref="../reference/mo_property.html">mo_name()</a></code>, although the
could never be understood by e.g.<code><ahref="../reference/mo_property.html">mo_name()</a></code>, although the
class would suggest a valid microbial code.</p>
class would suggest a valid microbial code.</p>
</li>
</li>
<li><p>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">freq()</a></code> has moved to a new package, <ahref="https://github.com/msberends/clean"class="external-link"><code>clean</code></a> (<ahref="https://cran.r-project.org/package=clean"class="external-link">CRAN link</a>), since
<li><p>Function <code>freq()</code> has moved to a new package, <ahref="https://github.com/msberends/clean"class="external-link"><code>clean</code></a> (<ahref="https://cran.r-project.org/package=clean"class="external-link">CRAN link</a>), since
creating frequency tables actually does not fit the scope of this
creating frequency tables actually does not fit the scope of this
package. The <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html"class="external-link">freq()</a></code> function still works, since it is
package. The <code>freq()</code> function still works, since it is
re-exported from the <code>clean</code> package (which will be installed
re-exported from the <code>clean</code> package (which will be installed
automatically upon updating this <code>AMR</code> package).</p></li>
automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Renamed data set <code>septic_patients</code> to
<li><p>Renamed data set <code>septic_patients</code> to
@ -2072,7 +2076,7 @@ since it uses <code><a href="../reference/count.html">count_df()</a></code> inte
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/select.html"class="external-link">select</a></span><spanclass="op">(</span><spanclass="op">-</span><spanclass="va">count</span>, <spanclass="op">-</span><spanclass="va">cum_count</span><spanclass="op">)</span><spanclass="co"># only get item, percent, cum_percent</span></code></pre></div>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/select.html"class="external-link">select</a></span><spanclass="op">(</span><spanclass="op">-</span><spanclass="va">count</span>, <spanclass="op">-</span><spanclass="va">cum_count</span><spanclass="op">)</span><spanclass="co"># only get item, percent, cum_percent</span></code></pre></div>
</li>
</li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html"class="external-link">hms::is.hms</a></code></p></li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html"class="external-link">hms::is.hms</a></code></p></li>
@ -2623,7 +2627,7 @@ to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would
become ceftazidime R in EUCAST rule 4.5</p></li>
become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for
<li><p>Support for named vectors of class <code>mo</code>, useful for
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