mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 20:41:58 +02:00
(v1.4.0.9000) more extensive unit tests
This commit is contained in:
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,6 +236,23 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1409000" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9000">
|
||||
<a href="#amr-1409000" class="anchor"></a>AMR 1.4.0.9000<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-15-october-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-15-october-2020" class="anchor"></a><small>Last updated: 15 October 2020</small>
|
||||
</h2>
|
||||
<div id="other" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>More extensive unit tests</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="amr-140" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0">
|
||||
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
|
||||
@ -251,13 +268,12 @@
|
||||
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
|
||||
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://msberends.github.io/AMR">AMR</a></span>)
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">intrinsic_resistant</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="kw">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span>(<span class="kw">microorganism</span>)
|
||||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span>
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">intrinsic_resistant</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span></pre></div>
|
||||
</li>
|
||||
<li><p>Support for veterinary ATC codes</p></li>
|
||||
<li><p>Support for skimming classes <code><rsi></code>, <code><mic></code>, <code><disk></code> and <code><mo></code> with the <code>skimr</code> package</p></li>
|
||||
@ -275,13 +291,12 @@
|
||||
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit">
|
||||
<span class="co"># until dplyr 1.0.0</span>
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.mic</span>, <span class="kw">as.rsi</span>)
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span>(<span class="kw">is.disk</span>, <span class="kw">as.rsi</span>)
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># since dplyr 1.0.0</span>
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.mic</span>), <span class="kw">as.rsi</span>))
|
||||
<span class="kw">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span>(<span class="fu">where</span>(<span class="kw">is.disk</span>), <span class="kw">as.rsi</span>))
|
||||
</pre></div>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g. <code><a href="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></li>
|
||||
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
|
||||
@ -292,10 +307,9 @@
|
||||
<li>
|
||||
<p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span>))
|
||||
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Class <disk></span>
|
||||
<span class="co">#> [1] 24 24</span>
|
||||
</pre></div>
|
||||
<span class="co">#> [1] 24 24</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</p>
|
||||
@ -330,9 +344,9 @@
|
||||
<li><p>Added parameter <code>excess</code> to the <code><a href="../reference/kurtosis.html">kurtosis()</a></code> function (defaults to <code>FALSE</code>), to return the <em>excess kurtosis</em>, defined as the kurtosis minus three.</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
<div id="other-1" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h3>
|
||||
<a href="#other-1" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Removed functions <code>portion_R()</code>, <code>portion_S()</code> and <code>portion_I()</code> that were deprecated since version 0.9.0 (November 2019) and were replaced with <code><a href="../reference/proportion.html">proportion_R()</a></code>, <code><a href="../reference/proportion.html">proportion_S()</a></code> and <code><a href="../reference/proportion.html">proportion_I()</a></code>
|
||||
</li>
|
||||
@ -353,13 +367,12 @@
|
||||
<li>
|
||||
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span>())
|
||||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span>
|
||||
</pre></div>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
|
||||
<li><p>Added function <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code> to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup <em>Beta-lactam antibacterials, penicillins</em>)</p></li>
|
||||
@ -416,9 +429,9 @@
|
||||
<li><p>Fixed a bug where <code><a href="../reference/as.mic.html">as.mic()</a></code> could not handle dots without a leading zero (like <code>"<=.25</code>)</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-1" class="section level3">
|
||||
<div id="other-2" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-1" class="anchor"></a>Other</h3>
|
||||
<a href="#other-2" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
|
||||
</ul>
|
||||
@ -478,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-2" class="section level3">
|
||||
<div id="other-3" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-2" class="anchor"></a>Other</h3>
|
||||
<a href="#other-3" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/p_symbol.html">p_symbol()</a></code>
|
||||
</li>
|
||||
@ -520,9 +533,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-3" class="section level3">
|
||||
<div id="other-4" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-3" class="anchor"></a>Other</h3>
|
||||
<a href="#other-4" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
|
||||
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
|
||||
@ -542,12 +555,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit">
|
||||
<span class="kw">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="st">"E. coli"</span>)
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
|
||||
|
||||
<span class="kw">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(<span class="kw">antibiotic1</span><span class="op">:</span><span class="kw">antibiotic25</span>), <span class="kw">as.rsi</span>, mo = <span class="kw">.</span><span class="op">$</span><span class="kw">mybacteria</span>)
|
||||
</pre></div>
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">mybacteria</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
|
||||
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as parameter to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
|
||||
@ -571,24 +583,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span>(<span class="st">"ampicillin"</span>)
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Ampicillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="st">"21066-6"</span>)
|
||||
<span class="co">#> [1] "J01CA01"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "J01CA01"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span>(<span class="st">"S. aureus"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] 115329001 3092008 113961008</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="fl">115329001</span>)
|
||||
<span class="co">#> [1] "Gram-positive"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="fl">115329001</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Gram-positive"</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -624,9 +634,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-4" class="section level3">
|
||||
<div id="other-5" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-4" class="anchor"></a>Other</h3>
|
||||
<a href="#other-5" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Add a <code>CITATION</code> file</li>
|
||||
<li>Full support for the upcoming R 4.0</li>
|
||||
@ -647,12 +657,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit">
|
||||
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span>) <span class="kw">...</span>
|
||||
</pre></div>
|
||||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></pre></div>
|
||||
<p>then please adjust this to:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="downlit">
|
||||
<span class="co">if</span> (<span class="fu"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="kw">somebugs</span>) <span class="op">==</span> <span class="st">"Enterobacterales"</span>) <span class="kw">...</span>
|
||||
</pre></div>
|
||||
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -665,13 +673,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(bug = <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="kw">mo</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(amoxicillin = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>),
|
||||
amox_clav = <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMC</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amoxicillin</span>) <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(<span class="kw">amox_clav</span>))
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>bug <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
|
||||
amox_clav <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">)</span> <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
|
||||
@ -694,17 +701,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Stafylococcus aureus"</span>,
|
||||
<span class="st">"staphylokok aureuz"</span>))
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
|
||||
<span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Warning: </span>
|
||||
<span class="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
|
||||
<span class="co">#> Class 'mo'</span>
|
||||
<span class="co">#> [1] B_STPHY_AURS B_STPHY_AURS</span>
|
||||
|
||||
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span>()
|
||||
<span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co">#> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%)</span>
|
||||
<span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span>
|
||||
</pre></div>
|
||||
<span class="co">#> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -732,9 +738,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-5" class="section level3">
|
||||
<div id="other-6" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#other-5" class="anchor"></a>Other</h3>
|
||||
<a href="#other-6" class="anchor"></a>Other</h3>
|
||||
<ul>
|
||||
<li>Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html">Roxygen2</a>, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.</li>
|
||||
<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
|
||||
@ -753,25 +759,23 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">...</span>, include_unknown = <span class="fl">TRUE</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></pre></div>
|
||||
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
|
||||
</li>
|
||||
<li>
|
||||
<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>
|
||||
<div class="sourceCode" id="cb13"><pre class="downlit">
|
||||
<span class="co"># how it works in base R:</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)
|
||||
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op"><-</span> <span class="st">"B"</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"B"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid factor level, NA generated</span>
|
||||
|
||||
<span class="co"># how it now works similarly for classes 'mo' and 'ab':</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="kw">x</span>[<span class="fl">1</span>] <span class="op"><-</span> <span class="st">"testvalue"</span>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"testvalue"</span>
|
||||
<span class="co">#> Warning message:</span>
|
||||
<span class="co">#> invalid microorganism code, NA generated</span>
|
||||
</pre></div>
|
||||
<span class="co">#> invalid microorganism code, NA generated</span></pre></div>
|
||||
<p>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.</p>
|
||||
</li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/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/cleaner/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>
|
||||
@ -785,9 +789,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="downlit">
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>)
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 A. baumannii AMC 0 0 3 3</span>
|
||||
<span class="co">#> 2 A. baumannii AMK 0 0 0 0</span>
|
||||
@ -796,20 +800,18 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
|
||||
|
||||
<span class="co"># change the transformation with the FUN argument to anything you like:</span>
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(<span class="kw">example_isolates</span>, FUN = <span class="kw">mo_gramstain</span>)
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span>, FUN <span class="op">=</span> <span class="va">mo_gramstain</span><span class="op">)</span>
|
||||
<span class="co">#> NOTE: Using column `mo` as input for `col_mo`.</span>
|
||||
<span class="kw">x</span>[<span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, ]
|
||||
<span class="va">x</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span>, <span class="op">]</span>
|
||||
<span class="co">#> mo ab S I R total</span>
|
||||
<span class="co">#> 1 Gram-negative AMC 469 89 174 732</span>
|
||||
<span class="co">#> 2 Gram-negative AMK 251 0 2 253</span>
|
||||
<span class="co">#> 3 Gram-negative AMP 227 0 405 632</span>
|
||||
<span class="co">#> 4 Gram-negative AMX 227 0 405 632</span>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span>
|
||||
</pre></div>
|
||||
<span class="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
|
||||
<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>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit">
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span>(<span class="kw">x</span>, combine_IR = <span class="fl">FALSE</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<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 susceptibility 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>
|
||||
@ -829,19 +831,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># S or I <NA> X X - -</span>
|
||||
<span class="co"># R <NA> - - - -</span>
|
||||
<span class="co"># <NA> <NA> - - - -</span>
|
||||
<span class="co"># --------------------------------------------------------------------</span>
|
||||
</pre></div>
|
||||
<span class="co"># --------------------------------------------------------------------</span></pre></div>
|
||||
<p>Since this is a major change, usage of the old <code>also_single_tested</code> will throw an informative error that it has been replaced by <code>only_all_tested</code>.</p>
|
||||
</li>
|
||||
<li>
|
||||
<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>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit">
|
||||
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org">dplyr</a></span>)
|
||||
<span class="kw">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">mo</span><span class="op">:</span><span class="kw">AMC</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span>()
|
||||
</pre></div>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span><span class="op">:</span><span class="va">AMC</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -898,9 +898,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
|
||||
</ul>
|
||||
<div id="other-6" class="section level4">
|
||||
<div id="other-7" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-6" class="anchor"></a>Other</h4>
|
||||
<a href="#other-7" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
|
||||
<li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
|
||||
@ -919,15 +919,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">AMX</span>, <span class="kw">CIP</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># antibiotic interpretation value isolates</span>
|
||||
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
|
||||
<span class="co"># 2 Amoxicillin R 0.5557364 683</span>
|
||||
<span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span>
|
||||
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span>
|
||||
</pre></div>
|
||||
<span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
|
||||
@ -946,13 +945,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</ul>
|
||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
|
||||
<span class="co"># B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
|
||||
<span class="co"># "Escherichia coli"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)
|
||||
<span class="co"># "Gram-negative"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span>
|
||||
<span class="co"># "Gram-negative"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
|
||||
@ -985,9 +983,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-7" class="section level4">
|
||||
<div id="other-8" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-7" class="anchor"></a>Other</h4>
|
||||
<a href="#other-8" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Fixed a note thrown by CRAN tests</li>
|
||||
</ul>
|
||||
@ -1051,15 +1049,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -1081,9 +1078,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-8" class="section level4">
|
||||
<div id="other-9" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-8" class="anchor"></a>Other</h4>
|
||||
<a href="#other-9" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
|
||||
</li>
|
||||
@ -1146,37 +1143,34 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(result = <span class="st">"R"</span>, scope = <span class="st">"all"</span>)
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span>
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span>, scope <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span>
|
||||
<span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="downlit">
|
||||
<span class="kw">ab_property</span> <span class="op">-></span> <span class="fu">atc_property</span>()
|
||||
<span class="kw">ab_name</span> <span class="op">-></span> <span class="fu">atc_name</span>()
|
||||
<span class="kw">ab_official</span> <span class="op">-></span> <span class="fu">atc_official</span>()
|
||||
<span class="kw">ab_trivial_nl</span> <span class="op">-></span> <span class="fu">atc_trivial_nl</span>()
|
||||
<span class="kw">ab_certe</span> <span class="op">-></span> <span class="fu">atc_certe</span>()
|
||||
<span class="kw">ab_umcg</span> <span class="op">-></span> <span class="fu">atc_umcg</span>()
|
||||
<span class="kw">ab_tradenames</span> <span class="op">-></span> <span class="fu">atc_tradenames</span>()
|
||||
</pre></div>
|
||||
<span class="va">ab_property</span> <span class="op">-></span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_name</span> <span class="op">-></span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_official</span> <span class="op">-></span> <span class="fu">atc_official</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_trivial_nl</span> <span class="op">-></span> <span class="fu">atc_trivial_nl</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_certe</span> <span class="op">-></span> <span class="fu">atc_certe</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_umcg</span> <span class="op">-></span> <span class="fu">atc_umcg</span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">ab_tradenames</span> <span class="op">-></span> <span class="fu">atc_tradenames</span><span class="op">(</span><span class="op">)</span></pre></div>
|
||||
<p>These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online_property.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</p>
|
||||
</li>
|
||||
<li><p>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</p></li>
|
||||
@ -1190,25 +1184,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/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>
|
||||
<div class="sourceCode" id="cb24"><pre class="downlit">
|
||||
<span class="kw">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="kw">septic_patients</span>, col_ab = <span class="st">"amox"</span>)
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span>(<span class="kw">x</span>)
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(<span class="kw">x</span>)
|
||||
</pre></div>
|
||||
<span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">...</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
|
||||
<span class="co"># or</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(only_firsts = <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span>(<span class="kw">septic_patients</span>, <span class="kw">...</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">only_firsts</span> <span class="op">==</span> <span class="fl">TRUE</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">only_firsts</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">only_firsts</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">only_firsts</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></p></li>
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
@ -1239,24 +1230,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit">
|
||||
<span class="co"># mo_fullname() uses as.mo() internally</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"Sthafilokockus aaureuz"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus aureus"</span>
|
||||
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)
|
||||
<span class="co">#> [1] "Staphylococcus kloosii"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. klossi"</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Staphylococcus kloosii"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||
<div class="sourceCode" id="cb28"><pre class="downlit">
|
||||
<span class="co"># equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">TRUE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">2</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># also equal:</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">FALSE</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">...</span>, allow_uncertain = <span class="fl">0</span>)
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></pre></div>
|
||||
<p>Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</p>
|
||||
</li>
|
||||
<li><p>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></p></li>
|
||||
@ -1264,11 +1253,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb29"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, language = <span class="st">"es"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"qwerty"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>
|
||||
<span class="co"># Warning: </span>
|
||||
<span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span>
|
||||
<span class="co">#> [1] "(género desconocido)"</span>
|
||||
</pre></div>
|
||||
<span class="co">#> [1] "(género desconocido)"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Fix for vector containing only empty values</p></li>
|
||||
<li><p>Finds better results when input is in other languages</p></li>
|
||||
@ -1316,18 +1304,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb30"><pre class="downlit">
|
||||
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(genus = <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>)) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">genus</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">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">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">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="co"># Even supports grouping variables:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">gender</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="kw">mo</span>))
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">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></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
@ -1348,9 +1335,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<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-9" class="section level4">
|
||||
<div id="other-10" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-9" class="anchor"></a>Other</h4>
|
||||
<a href="#other-10" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
|
||||
</ul>
|
||||
@ -1398,11 +1385,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||
<div class="sourceCode" id="cb31"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span> <span class="co"># B_ESCHR</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span> <span class="co"># "Escherichia species"</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. spp"</span><span class="op">)</span> <span class="co"># B_STPHY</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. species"</span><span class="op">)</span> <span class="co"># "Staphylococcus species"</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></li>
|
||||
<li><p>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</p></li>
|
||||
@ -1415,18 +1401,16 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb32"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb33"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">hospital_id</span>) <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw">count</span>, <span class="op">-</span><span class="kw">cum_count</span>) <span class="co"># only get item, percent, cum_percent</span>
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">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></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
|
||||
@ -1470,9 +1454,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-10" class="section level4">
|
||||
<div id="other-11" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-10" class="anchor"></a>Other</h4>
|
||||
<a href="#other-11" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
|
||||
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
|
||||
@ -1503,21 +1487,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb34"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Gram negative"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"de"</span>) <span class="co"># German</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># German</span>
|
||||
<span class="co"># [1] "Gramnegativ"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, language = <span class="st">"es"</span>) <span class="co"># Spanish</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># Spanish</span>
|
||||
<span class="co"># [1] "Gram negativo"</span>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, language = <span class="st">"pt"</span>) <span class="co"># Portuguese</span>
|
||||
<span class="co"># [1] "Streptococcus grupo A"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
|
||||
<span class="co"># [1] "Streptococcus grupo A"</span></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb35"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)
|
||||
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
|
||||
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
|
||||
<span class="co"># [1] "Gram negative"</span>
|
||||
</pre></div>
|
||||
<span class="co"># [1] "Gram negative"</span></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</p>
|
||||
@ -1529,21 +1511,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||
<div class="sourceCode" id="cb36"><pre class="downlit">
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_ESCHR_COL</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_STPHY_AUR</span>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)
|
||||
<span class="co"># [1] B_STRPTC_GRA</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
|
||||
<span class="co"># [1] B_STRPTC_GRA</span></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="cb37"><pre class="downlit">
|
||||
<span class="kw">thousands_of_E_colis</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="fl">25000</span>)
|
||||
<span class="kw">microbenchmark</span>::<span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="kw">thousands_of_E_colis</span>), unit = <span class="st">"s"</span>)
|
||||
<span class="va">thousands_of_E_colis</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
|
||||
<span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
|
||||
<span class="co"># Unit: seconds</span>
|
||||
<span class="co"># min median max neval</span>
|
||||
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span>
|
||||
</pre></div>
|
||||
<span class="co"># 0.01817717 0.01843957 0.03878077 100</span></pre></div>
|
||||
</li>
|
||||
<li><p>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</p></li>
|
||||
<li>
|
||||
@ -1572,13 +1552,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<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="cb38"><pre class="downlit">
|
||||
<span class="fu">ab_official</span>(<span class="st">"Bactroban"</span>)
|
||||
<span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Mupirocin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="fu"><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>))
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_name</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="fu"><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>))
|
||||
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span>
|
||||
</pre></div>
|
||||
<span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></pre></div>
|
||||
</li>
|
||||
<li><p>For <code>first_isolate</code>, rows will be ignored when there’s no species available</p></li>
|
||||
<li><p>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</p></li>
|
||||
@ -1589,14 +1568,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb39"><pre class="downlit">
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>) <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>()
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># which is the same as:</span>
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span>(<span class="kw">amox</span>, <span class="kw">cipr</span>)
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span>
|
||||
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>)
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>, <span class="kw">gent</span>)
|
||||
<span class="kw">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span>(<span class="kw">amcl</span>, <span class="kw">gent</span>, <span class="kw">pita</span>)
|
||||
</pre></div>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span><span class="op">)</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span><span class="op">)</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu">portion_S</span><span class="op">(</span><span class="va">amcl</span>, <span class="va">gent</span>, <span class="va">pita</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
<li><p>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</p></li>
|
||||
<li><p>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</p></li>
|
||||
@ -1609,21 +1587,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb40"><pre class="downlit">
|
||||
<span class="kw">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span>(<span class="kw">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">age</span>, <span class="kw">gender</span>), ncol = <span class="fl">2</span>))
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">my_matrix</span>)
|
||||
</pre></div>
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">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">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">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">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb41"><pre class="downlit">
|
||||
<span class="kw">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(age = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">age</span>, gender = <span class="kw">septic_patients</span><span class="op">$</span><span class="kw">gender</span>)
|
||||
<span class="kw">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">age</span>)
|
||||
<span class="kw">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw">gender</span>)
|
||||
</pre></div>
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">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">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">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">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-11" class="section level4">
|
||||
<div id="other-12" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-11" class="anchor"></a>Other</h4>
|
||||
<a href="#other-12" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>More unit tests to ensure better integrity of functions</li>
|
||||
</ul>
|
||||
@ -1750,9 +1726,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Other small fixes</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-12" class="section level4">
|
||||
<div id="other-13" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-12" class="anchor"></a>Other</h4>
|
||||
<a href="#other-13" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
|
||||
<ul>
|
||||
@ -1812,9 +1788,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other-13" class="section level4">
|
||||
<div id="other-14" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
<a href="#other-13" class="anchor"></a>Other</h4>
|
||||
<a href="#other-14" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Expanded <code>README.md</code> with more examples</li>
|
||||
<li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>
|
||||
@ -1862,7 +1838,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Reference in New Issue
Block a user