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(v1.8.0.9010) as.mo improvement
This commit is contained in:
@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9010</span>
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</span>
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</div>
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@ -157,14 +157,16 @@
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</div>
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<div class="section level2">
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<h2 class="page-header" data-toc-text="1.8.1" id="amr-181">
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<code>AMR</code> 1.8.1<a class="anchor" aria-label="anchor" href="#amr-181"></a></h2>
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<h2 class="page-header" data-toc-text="1.8.0.9010" id="amr-1809010">
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<code>AMR</code> 1.8.0.9010<a class="anchor" aria-label="anchor" href="#amr-1809010"></a></h2>
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<div class="section level3">
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<h3 id="last-updated-march-1-8-0-9010"><small>Last updated: 15 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9010"></a></h3>
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<p>All functions in this package are considered to be stable. Updates to
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the AMR interpretation rules (such as by EUCAST and CLSI), the microbial
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taxonomy, and the antibiotic dosages will all be updated every 6 to 12
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months.</p>
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<div class="section level4">
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<h4 id="changed-1-8-1">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1"></a></h4>
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<h4 id="changed-1-8-0-9010">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9010"></a></h4>
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<ul><li><p>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on values containing capped
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values (such as <code>>=</code>), sometimes leading to
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<code>NA</code></p></li>
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@ -182,12 +184,14 @@ ignoring non-taxonomic text, such as:</p>
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<li><p>More informative warning messages</p></li>
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<li><p>Added 192 as valid MIC</p></li>
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<li><p>Updated MIC printing in tibbles</p></li>
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<li><p>Increased speed for loading the package</p></li>
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</ul></div>
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<div class="section level4">
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<h4 id="other-1-8-1">Other<a class="anchor" aria-label="anchor" href="#other-1-8-1"></a></h4>
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<h4 id="other-1-8-0-9010">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9010"></a></h4>
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<ul><li>Fix for unit testing on R 3.3</li>
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<li>Fix for size of some image elements, as requested by CRAN</li>
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</ul></div>
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</div>
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</div>
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<div class="section level2">
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<h2 class="page-header" data-toc-text="1.8.0" id="amr-180">
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@ -368,7 +372,7 @@ guideline</li>
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<li>Improved plot legends for MICs and disk diffusion values</li>
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<li>Improved speed of <code><a href="../reference/as.ab.html">as.ab()</a></code> and all <code>ab_*()</code>
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functions</li>
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<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify()</a></code> extensions for plotting methods</li>
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<li>Added <code>fortify()</code> extensions for plotting methods</li>
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<li>
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<code>NA</code> values of the classes <code><mic></code>,
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<code><disk></code> and <code><rsi></code> are now exported
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@ -484,7 +488,7 @@ rewritten.</li>
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selector and function <code>filter_betalactams()</code> as additional
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antbiotic column filter. The group of betalactams consists of all
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carbapenems, cephalosporins and penicillins.</li>
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<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> method for
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<li>A <code>ggplot()</code> method for
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<code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
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</li>
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</ul></div>
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@ -628,7 +632,7 @@ function) to select/filter on e.g. linezolid and tedizolid</p>
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<li><p>Support for custom MDRO guidelines, using the new
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<code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see
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<code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
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<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> generics for classes
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<li><p><code>ggplot()</code> generics for classes
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<code><mic></code> and <code><disk></code></p></li>
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<li>
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<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a
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@ -697,7 +701,7 @@ printing)</li>
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translated if the system language is German, Dutch or Spanish (see
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<code>translate</code>)</li>
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<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and
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with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot()</a></code> on any vector of MIC and disk
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with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk
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diffusion values</li>
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</ul></li>
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<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September
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@ -740,7 +744,7 @@ per hour)</li>
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<li>Argument <code>ampc_cephalosporin_resistance</code> in
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<code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only
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“S”)</li>
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<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a
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<li>Functions <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> on a
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Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print
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additional group info if the original data was grouped using
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<code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">dplyr::group_by()</a></code>
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@ -1266,10 +1270,10 @@ versions of R since R-3.0.0 (April 2013). Our package is being used in
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settings where the resources are very limited. Fewer dependencies on
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newer software is helpful for such settings.</p>
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<p>Negative effects of this change are:</p>
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<ul><li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> that was borrowed from the
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<ul><li>Function <code>freq()</code> that was borrowed from the
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<code>cleaner</code> package was removed. Use
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<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner" class="external-link">library("cleaner")</a></code>
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before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>.</li>
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before you use <code>freq()</code>.</li>
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<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in
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a tibble will no longer be in colour and printing <code>rsi</code> in a
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tibble will show the class <code><ord></code>, not
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@ -1698,9 +1702,9 @@ data integrity, this means that invalid assignments will now result in
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could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the
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class would suggest a valid microbial code.</p>
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</li>
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<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since
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<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean" class="external-link"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean" class="external-link">CRAN link</a>), since
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creating frequency tables actually does not fit the scope of this
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package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function still works, since it is
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package. The <code>freq()</code> function still works, since it is
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re-exported from the <code>clean</code> package (which will be installed
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automatically upon updating this <code>AMR</code> package).</p></li>
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<li><p>Renamed data set <code>septic_patients</code> to
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@ -2072,7 +2076,7 @@ since it uses <code><a href="../reference/count.html">count_df()</a></code> inte
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<code>guess_atc()</code>, <code>EUCAST_rules()</code>,
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<code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
||||
</li>
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>):
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<li>Frequency tables (<code>freq()</code>):
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<ul><li><p>speed improvement for microbial IDs</p></li>
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<li><p>fixed factor level names for R Markdown</p></li>
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<li><p>when all values are unique it now shows a message instead of a
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@ -2082,12 +2086,12 @@ warning</p></li>
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<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
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<code class="sourceCode R">
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<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
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<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
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<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
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<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span>
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<span class="co"># grouped boxplots:</span>
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<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html" class="external-link">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
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||||
</li>
|
||||
</ul></li>
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||||
@ -2099,7 +2103,7 @@ be viewed here</a>
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||||
</li>
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||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let
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groups of fives and tens end with 100+ instead of 120+</li>
|
||||
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> for when all values are
|
||||
<li>Fix for <code>freq()</code> for when all values are
|
||||
<code>NA</code>
|
||||
</li>
|
||||
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
||||
@ -2435,7 +2439,7 @@ unique count, e.g. using <code>summary(mo)</code>
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||||
return <code>S</code>
|
||||
</li>
|
||||
</ul></li>
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code> function):
|
||||
<li>Frequency tables (<code>freq()</code> function):
|
||||
<ul><li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create
|
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frequency tables of function outcomes:</p>
|
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@ -2445,15 +2449,15 @@ frequency tables of function outcomes:</p>
|
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<span class="co"># OLD WAY</span>
|
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<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
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<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the
|
||||
<code>header</code> function</p></li>
|
||||
@ -2580,21 +2584,21 @@ total available isolate is below argument <code>minimum</code></p></li>
|
||||
<code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not
|
||||
set package name as attribute anymore</p></li>
|
||||
<li>
|
||||
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq()</a></code>:</p>
|
||||
<p>Frequency tables - <code>freq()</code>:</p>
|
||||
<ul><li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="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
|
||||
become ceftazidime R in EUCAST rule 4.5</p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for
|
||||
<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">top_freq()</a></code></p></li>
|
||||
<code>top_freq()</code></p></li>
|
||||
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have
|
||||
<code>breaks</code> argument</p></li>
|
||||
<li>
|
||||
@ -2848,13 +2852,13 @@ tables</p></li>
|
||||
<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html" class="external-link">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul></div>
|
||||
<div class="section level5">
|
||||
|
||||
Reference in New Issue
Block a user