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(v0.7.1.9088) bug_drug improvement
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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="Latest development version">0.7.1.9087</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9088</span>
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<div id="amr-0-7-1-9087" class="section level1">
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<div id="amr-0-7-1-9088" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-7-1-9087" class="anchor"></a>AMR 0.7.1.9087<small> Unreleased </small>
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<a href="#amr-0-7-1-9088" class="anchor"></a>AMR 0.7.1.9088<small> Unreleased </small>
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</h1>
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<p><small>Last updated: 23-Sep-2019</small></p>
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<p><small>Last updated: 25-Sep-2019</small></p>
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<div id="breaking" class="section level3">
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<h3 class="hasAnchor">
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<a href="#breaking" class="anchor"></a>Breaking</h3>
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@ -241,7 +247,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
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<li>
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<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
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<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co"># how it works in base R:</span></a>
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<a class="sourceLine" id="cb2-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/factor">factor</a></span>(<span class="st">"A"</span>)</a>
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<a class="sourceLine" id="cb2-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
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<a class="sourceLine" id="cb2-3" data-line-number="3">x[<span class="dv">1</span>] <-<span class="st"> "B"</span></a>
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<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#> Warning message:</span></a>
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<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#> invalid factor level, NA generated</span></a>
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@ -252,7 +258,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
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<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
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<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
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This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
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<li><p>Function <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
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<li><p>Function <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
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</ul>
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</div>
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<div id="new" class="section level3">
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@ -280,8 +286,8 @@ This is important, because a value like <code>"testvalue"</code> could never be
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<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#> 2 AMC Gram-positive 873 2 272 1147</span></a>
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<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#> 3 AMK Gram-negative 251 0 2 253</span></a>
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<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#> 4 AMK Gram-positive 0 0 100 100</span></a></code></pre></div>
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<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://www.rdocumentation.org/packages/base/topics/format">format()</a></code> function:</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/format">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
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<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
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<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
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</li>
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<li>
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<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
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@ -305,7 +311,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
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<li>
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<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
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<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
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<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
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<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
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<a class="sourceLine" id="cb6-3" data-line-number="3">example_isolates <span class="op">%>%</span></a>
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<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
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@ -439,7 +445,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
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<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
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</li>
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<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
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<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
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<li>Small improvements to <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
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<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
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</li>
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</ul>
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@ -503,7 +509,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
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<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
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<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
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</li>
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<li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>):
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<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>):
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<ul>
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<li>speed improvement for microbial IDs</li>
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<li>fixed factor level names for R Markdown</li>
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@ -511,13 +517,13 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
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<li>
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<p>support for boxplots:</p>
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<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
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<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
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<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
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<a class="sourceLine" id="cb9-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
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<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%>%</span></a>
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<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
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<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
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<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
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</li>
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</ul>
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</li>
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@ -527,7 +533,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
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<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
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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 groups of fives and tens end with 100+ instead of 120+</li>
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<li>Fix for <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> for when all values are <code>NA</code>
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<li>Fix for <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
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</li>
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<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
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<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
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@ -638,9 +644,9 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
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<li>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
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<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
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<li>
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<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
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<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
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<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
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<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
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<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</a>
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<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
@ -738,7 +744,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> using the new <code>threshold</code> parameter</li>
|
||||
<li>New colours for <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code>
|
||||
</li>
|
||||
<li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary(mo)</a></code>
|
||||
<li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://rdrr.io/r/base/summary.html">summary(mo)</a></code>
|
||||
</li>
|
||||
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
|
||||
</li>
|
||||
@ -749,7 +755,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function):
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
@ -757,20 +763,20 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb19-3" data-line-number="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb19-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb19-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb19-9" data-line-number="9"></a>
|
||||
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb19-11" data-line-number="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
</li>
|
||||
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
||||
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
||||
<li>Added header info for class <code>mo</code> to show unique count of families, genera and species</li>
|
||||
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://www.rdocumentation.org/packages/base/topics/options">getOption("OutDec")</a></code>
|
||||
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://rdrr.io/r/base/options.html">getOption("OutDec")</a></code>
|
||||
</li>
|
||||
<li>The new <code>big.mark</code> parameter will at default be <code>","</code> when <code>decimal.mark = "."</code> and <code>"."</code> otherwise</li>
|
||||
<li>Fix for header text where all observations are <code>NA</code>
|
||||
@ -785,7 +791,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>Updated examples for resistance prediction (<code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> function)</li>
|
||||
<li>Fix for <code><a href="../reference/as.mic.html">as.mic()</a></code> to support more values ending in (several) zeroes</li>
|
||||
<li>if using different lengths of pattern and x in <code>%like%</code>, it will now return the call</li>
|
||||
<li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-3" class="section level4">
|
||||
@ -852,21 +858,21 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
|
||||
</li>
|
||||
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
|
||||
<li>Frequency tables - <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>:
|
||||
<li>Frequency tables - <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>:
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
|
||||
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
|
||||
<li>Check for <code><a href="https://rdrr.io/pkg/hms/man/Deprecated.html">hms::is.hms</a></code>
|
||||
</li>
|
||||
<li>Now prints in markdown at default in non-interactive sessions</li>
|
||||
<li>No longer adds the factor level column and sorts factors on count again</li>
|
||||
@ -906,7 +912,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>Fix for <code>join</code> functions</li>
|
||||
<li>Speed improvement for <code>is.rsi.eligible</code>, now 15-20 times faster</li>
|
||||
<li>In <code>g.test</code>, when <code><a href="https://www.rdocumentation.org/packages/base/topics/sum">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
|
||||
<li>In <code>g.test</code>, when <code><a href="https://rdrr.io/r/base/sum.html">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
|
||||
<li>
|
||||
<code>ab_name</code> will try to fall back on <code>as.atc</code> when no results are found</li>
|
||||
<li>Removed the addin to view data sets</li>
|
||||
@ -973,8 +979,8 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<a class="sourceLine" id="cb25-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb25-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb26-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb26-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb26-4" data-line-number="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb26-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
@ -1007,9 +1013,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb27-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
||||
@ -1041,12 +1047,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb30-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb30-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -1112,7 +1118,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li><del>For example: <code>ratio(c(10, 500, 10), ratio = "1:2:1")</code> would return <code>130, 260, 130</code></del></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Support for Addins menu in RStudio to quickly insert <code>%in%</code> or <code>%like%</code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li>
|
||||
<li>Support for Addins menu in RStudio to quickly insert <code><a href="https://rdrr.io/r/base/match.html">%in%</a></code> or <code><a href="../reference/like.html">%like%</a></code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li>
|
||||
<li>Function <code>p.symbol</code> to transform p values to their related symbols: <code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code>
|
||||
</li>
|
||||
<li>Functions <code>clipboard_import</code> and <code>clipboard_export</code> as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the <code>clipr</code> package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)</li>
|
||||
@ -1120,17 +1126,17 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<ul>
|
||||
<li>A vignette to explain its usage</li>
|
||||
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
|
||||
<li>Support for <code>table</code> to use as input: <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq(table(x, y))</a></code>
|
||||
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(table(x, y))</a></code>
|
||||
</li>
|
||||
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code>
|
||||
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
|
||||
</li>
|
||||
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
|
||||
</li>
|
||||
<li>Support for quasiquotation: <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
||||
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
||||
</li>
|
||||
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
|
||||
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
|
||||
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
|
||||
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://rdrr.io/r/base/options.html">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
@ -1148,7 +1154,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Column names for the <code>key_antibiotics</code> function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs</li>
|
||||
<li>Speed improvement for the <code>abname</code> function</li>
|
||||
<li>
|
||||
<code>%like%</code> now supports multiple patterns</li>
|
||||
<code><a href="../reference/like.html">%like%</a></code> now supports multiple patterns</li>
|
||||
<li>Frequency tables are now actual <code>data.frame</code>s with altered console printing to make it look like a frequency table. Because of this, the parameter <code>toConsole</code> is not longer needed.</li>
|
||||
<li>Fix for <code>freq</code> where the class of an item would be lost</li>
|
||||
<li>Small translational improvements to the <code>septic_patients</code> dataset and the column <code>bactid</code> now has the new class <code>"bactid"</code>
|
||||
@ -1236,7 +1242,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>Added support for character vector in <code>join</code> functions</li>
|
||||
<li>Added warnings when a join results in more rows after than before the join</li>
|
||||
<li>Altered <code>%like%</code> to make it case insensitive</li>
|
||||
<li>Altered <code><a href="../reference/like.html">%like%</a></code> to make it case insensitive</li>
|
||||
<li>For parameters of functions <code>first_isolate</code> and <code>EUCAST_rules</code> column names are now case-insensitive</li>
|
||||
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
|
||||
</ul>
|
||||
@ -1280,7 +1286,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0-7-1-9087">0.7.1.9087</a></li>
|
||||
<li><a href="#amr-0-7-1-9088">0.7.1.9088</a></li>
|
||||
<li><a href="#amr-0-7-1">0.7.1</a></li>
|
||||
<li><a href="#amr-0-7-0">0.7.0</a></li>
|
||||
<li><a href="#amr-0-6-1">0.6.1</a></li>
|
||||
@ -1297,14 +1303,16 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
@ -1327,6 +1335,8 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user