mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 11:51:59 +02:00
(v0.8.0.9030) depend on tidyr >= 1.0.0
This commit is contained in:
@ -84,7 +84,7 @@
|
||||
</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">0.8.0.9029</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9030</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -231,16 +231,24 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0-8-0-9029" class="section level1">
|
||||
<div id="amr-0-8-0-9030" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0-8-0-9029" class="anchor"></a>AMR 0.8.0.9029<small> Unreleased </small>
|
||||
<a href="#amr-0-8-0-9030" class="anchor"></a>AMR 0.8.0.9030<small> Unreleased </small>
|
||||
</h1>
|
||||
<p><small>Last updated: 10-Nov-2019</small></p>
|
||||
<p><small>Last updated: 11-Nov-2019</small></p>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>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.</li>
|
||||
<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="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb1-2" data-line-number="2">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(<span class="dt">bug =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo)) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">amoxicillin =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX),</a>
|
||||
<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dt">amox_clav =</span> <span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMC)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amoxicillin) <span class="op">|</span><span class="st"> </span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span>(amox_clav))</a></code></pre></div>
|
||||
</li>
|
||||
<li>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).
|
||||
<ul>
|
||||
<li>This is now the new default guideline for the <code><a href="../reference/mdro.html">mdro()</a></code> function</li>
|
||||
@ -287,21 +295,21 @@
|
||||
<ul>
|
||||
<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="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(..., <span class="dt">include_unknown =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
|
||||
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.</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="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co"># how it works in base R:</span></a>
|
||||
<a class="sourceLine" id="cb2-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-3" data-line-number="3">x[<span class="dv">1</span>] <-<span class="st"> "B"</span></a>
|
||||
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#> invalid factor level, NA generated</span></a>
|
||||
<a class="sourceLine" id="cb2-6" data-line-number="6"></a>
|
||||
<a class="sourceLine" id="cb2-7" data-line-number="7"><span class="co"># how it now works similarly for classes 'mo' and 'ab':</span></a>
|
||||
<a class="sourceLine" id="cb2-8" data-line-number="8">x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb2-9" data-line-number="9">x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></a>
|
||||
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co"># how it works in base R:</span></a>
|
||||
<a class="sourceLine" id="cb3-2" data-line-number="2">x <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-3" data-line-number="3">x[<span class="dv">1</span>] <-<span class="st"> "B"</span></a>
|
||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#> invalid factor level, NA generated</span></a>
|
||||
<a class="sourceLine" id="cb3-6" data-line-number="6"></a>
|
||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># how it now works similarly for classes 'mo' and 'ab':</span></a>
|
||||
<a class="sourceLine" id="cb3-8" data-line-number="8">x <-<span class="st"> </span><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-9" data-line-number="9">x[<span class="dv">1</span>] <-<span class="st"> "testvalue"</span></a>
|
||||
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co">#> Warning message:</span></a>
|
||||
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
|
||||
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
|
||||
<li>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).</li>
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
@ -313,55 +321,55 @@ This is important, because a value like <code>"testvalue"</code> could never be
|
||||
<ul>
|
||||
<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="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
|
||||
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb3-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co">#> 1 A. baumannii AMC 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co">#> 2 A. baumannii AMK 0 0 0 0</span></a>
|
||||
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co">#> 3 A. baumannii AMP 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#> 4 A. baumannii AMX 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a>
|
||||
<a class="sourceLine" id="cb3-10" data-line-number="10"></a>
|
||||
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># change the transformation with the FUN argument to anything you like:</span></a>
|
||||
<a class="sourceLine" id="cb3-12" data-line-number="12">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</a>
|
||||
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb3-14" data-line-number="14">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#> 1 Gram-negative AMC 469 89 174 732</span></a>
|
||||
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#> 2 Gram-negative AMK 251 0 2 253</span></a>
|
||||
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#> 3 Gram-negative AMP 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#> 4 Gram-negative AMX 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates)</a>
|
||||
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb4-3" data-line-number="3">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co">#> 1 A. baumannii AMC 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co">#> 2 A. baumannii AMK 0 0 0 0</span></a>
|
||||
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co">#> 3 A. baumannii AMP 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co">#> 4 A. baumannii AMX 0 0 3 3</span></a>
|
||||
<a class="sourceLine" id="cb4-9" data-line-number="9"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a>
|
||||
<a class="sourceLine" id="cb4-10" data-line-number="10"></a>
|
||||
<a class="sourceLine" id="cb4-11" data-line-number="11"><span class="co"># change the transformation with the FUN argument to anything you like:</span></a>
|
||||
<a class="sourceLine" id="cb4-12" data-line-number="12">x <-<span class="st"> </span><span class="kw"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span>(example_isolates, <span class="dt">FUN =</span> mo_gramstain)</a>
|
||||
<a class="sourceLine" id="cb4-13" data-line-number="13"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `mo` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb4-14" data-line-number="14">x[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, ]</a>
|
||||
<a class="sourceLine" id="cb4-15" data-line-number="15"><span class="co">#> mo ab S I R total</span></a>
|
||||
<a class="sourceLine" id="cb4-16" data-line-number="16"><span class="co">#> 1 Gram-negative AMC 469 89 174 732</span></a>
|
||||
<a class="sourceLine" id="cb4-17" data-line-number="17"><span class="co">#> 2 Gram-negative AMK 251 0 2 253</span></a>
|
||||
<a class="sourceLine" id="cb4-18" data-line-number="18"><span class="co">#> 3 Gram-negative AMP 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb4-19" data-line-number="19"><span class="co">#> 4 Gram-negative AMX 227 0 405 632</span></a>
|
||||
<a class="sourceLine" id="cb4-20" data-line-number="20"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Use 'format()' on this result to get a publicable/printable format.</span></a></code></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="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
|
||||
</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>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># --------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
|
||||
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># ----------------------- -----------------------</span></a>
|
||||
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># Drug A Drug B include as include as include as include as</span></a>
|
||||
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a>
|
||||
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># -------- -------- ---------- ----------- ---------- -----------</span></a>
|
||||
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># S or I S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># R S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># <NA> S or I X X - -</span></a>
|
||||
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># S or I R X X X X</span></a>
|
||||
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># R R - X - X</span></a>
|
||||
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># <NA> R - - - -</span></a>
|
||||
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># S or I <NA> X X - -</span></a>
|
||||
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># R <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># <NA> <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb5-16" data-line-number="16"><span class="co"># --------------------------------------------------------------------</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># --------------------------------------------------------------------</span></a>
|
||||
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span></a>
|
||||
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="co"># ----------------------- -----------------------</span></a>
|
||||
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="co"># Drug A Drug B include as include as include as include as</span></a>
|
||||
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="co"># numerator denominator numerator denominator</span></a>
|
||||
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># -------- -------- ---------- ----------- ---------- -----------</span></a>
|
||||
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># S or I S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># R S or I X X X X</span></a>
|
||||
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co"># <NA> S or I X X - -</span></a>
|
||||
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co"># S or I R X X X X</span></a>
|
||||
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># R R - X - X</span></a>
|
||||
<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># <NA> R - - - -</span></a>
|
||||
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># S or I <NA> X X - -</span></a>
|
||||
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># R <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># <NA> <NA> - - - -</span></a>
|
||||
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># --------------------------------------------------------------------</span></a></code></pre></div>
|
||||
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>.</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="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
|
||||
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb6-3" data-line-number="3">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="co"># (run this on your own console, as this page does not support colour printing)</span></a>
|
||||
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
|
||||
<a class="sourceLine" id="cb7-3" data-line-number="3">example_isolates <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -438,14 +446,14 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
||||
<ul>
|
||||
<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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">rsi_df</a></span>()</a>
|
||||
<a class="sourceLine" id="cb7-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
||||
<a class="sourceLine" id="cb7-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
||||
<a class="sourceLine" id="cb7-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
||||
<a class="sourceLine" id="cb7-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
||||
<a class="sourceLine" id="cb7-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(AMX, CIP) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">rsi_df</a></span>()</a>
|
||||
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># antibiotic interpretation value isolates</span></a>
|
||||
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
|
||||
<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
|
||||
<a class="sourceLine" id="cb8-7" data-line-number="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
|
||||
<a class="sourceLine" id="cb8-8" data-line-number="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></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>
|
||||
@ -463,12 +471,12 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
|
||||
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
|
||||
</ul>
|
||||
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
||||
<a class="sourceLine" id="cb8-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># "Escherichia coli"</span></a>
|
||||
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"EHEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="co"># "Gram-negative"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>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</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>
|
||||
@ -567,14 +575,14 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
|
||||
<li>when all values are unique it now shows a message instead of a warning</li>
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
|
||||
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb9-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb10-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb10-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb10-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
@ -659,32 +667,32 @@ This data is updated annually - check the included version with the new function
|
||||
</li>
|
||||
<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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb10-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-7" data-line-number="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-8" data-line-number="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-9" data-line-number="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-10" data-line-number="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb11-11" data-line-number="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb11-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb12-2" data-line-number="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb12-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
||||
<a class="sourceLine" id="cb12-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
||||
<a class="sourceLine" id="cb12-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
||||
<a class="sourceLine" id="cb12-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
||||
<a class="sourceLine" id="cb12-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb12-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb12-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">ab_property -><span class="st"> </span><span class="kw">atc_property</span>()</a>
|
||||
<a class="sourceLine" id="cb13-2" data-line-number="2">ab_name -><span class="st"> </span><span class="kw">atc_name</span>()</a>
|
||||
<a class="sourceLine" id="cb13-3" data-line-number="3">ab_official -><span class="st"> </span><span class="kw">atc_official</span>()</a>
|
||||
<a class="sourceLine" id="cb13-4" data-line-number="4">ab_trivial_nl -><span class="st"> </span><span class="kw">atc_trivial_nl</span>()</a>
|
||||
<a class="sourceLine" id="cb13-5" data-line-number="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb13-6" data-line-number="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb13-7" data-line-number="7">ab_tradenames -><span class="st"> </span><span class="kw">atc_tradenames</span>()</a></code></pre></div>
|
||||
These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.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>.</li>
|
||||
<li>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</li>
|
||||
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
||||
@ -696,20 +704,20 @@ These functions use <code>as.atc()</code> internally. The old <code>atc_property
|
||||
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
||||
<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="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<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="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb15-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb15-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb16-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
</li>
|
||||
<li>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>
|
||||
</li>
|
||||
@ -738,33 +746,33 @@ These functions use <code>as.atc()</code> internally. The old <code>atc_property
|
||||
<ul>
|
||||
<li>
|
||||
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb16-2" data-line-number="2"></a>
|
||||
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb16-5" data-line-number="5"></a>
|
||||
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-7" data-line-number="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb17-2" data-line-number="2"></a>
|
||||
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb17-5" data-line-number="5"></a>
|
||||
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-7" data-line-number="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb17-4" data-line-number="4"></a>
|
||||
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb17-7" data-line-number="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb18-4" data-line-number="4"></a>
|
||||
<a class="sourceLine" id="cb18-5" data-line-number="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb18-6" data-line-number="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb18-7" data-line-number="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
|
||||
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
|
||||
</li>
|
||||
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
|
||||
<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="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb18-4" data-line-number="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb19-3" data-line-number="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb19-4" data-line-number="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Fix for vector containing only empty values</li>
|
||||
<li>Finds better results when input is in other languages</li>
|
||||
@ -810,19 +818,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb19-3" data-line-number="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb19-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb19-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb19-9" data-line-number="9"></a>
|
||||
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb19-11" data-line-number="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb19-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb20-3" data-line-number="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb20-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb20-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb20-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb20-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb20-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb20-9" data-line-number="9"></a>
|
||||
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb20-11" data-line-number="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb20-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb20-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
</li>
|
||||
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
||||
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
||||
@ -897,10 +905,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
|
||||
<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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb20-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb20-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb21-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>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)</li>
|
||||
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
|
||||
@ -913,15 +921,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb23-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb23-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Check for <code><a href="https://rdrr.io/pkg/hms/man/Deprecated.html">hms::is.hms</a></code>
|
||||
</li>
|
||||
@ -1001,18 +1009,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb23-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb23-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb23-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb23-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb23-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb23-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb23-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb24-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb24-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb24-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb24-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb24-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb24-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb24-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb24-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb25-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>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
|
||||
<ul>
|
||||
@ -1023,18 +1031,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<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="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb25-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb25-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb25-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb25-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb26-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb26-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb26-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb26-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb26-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb26-4" data-line-number="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb26-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb27-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb27-4" data-line-number="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb27-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>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</li>
|
||||
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
|
||||
@ -1062,12 +1070,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
|
||||
<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="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb27-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb27-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb28-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb28-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb28-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb28-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb28-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
||||
<li>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</li>
|
||||
@ -1078,13 +1086,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<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="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb28-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb28-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb28-4" data-line-number="4"></a>
|
||||
<a class="sourceLine" id="cb28-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb28-6" data-line-number="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb28-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb29-3" data-line-number="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb29-4" data-line-number="4"></a>
|
||||
<a class="sourceLine" id="cb29-5" data-line-number="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb29-6" data-line-number="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb29-7" data-line-number="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
</li>
|
||||
<li>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>.</li>
|
||||
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
|
||||
@ -1098,12 +1106,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb30-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb30-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb31-2" data-line-number="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb31-3" data-line-number="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@ -1337,7 +1345,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0-8-0-9029">0.8.0.9029</a></li>
|
||||
<li><a href="#amr-0-8-0-9030">0.8.0.9030</a></li>
|
||||
<li><a href="#amr-0-8-0">0.8.0</a></li>
|
||||
<li><a href="#amr-0-7-1">0.7.1</a></li>
|
||||
<li><a href="#amr-0-7-0">0.7.0</a></li>
|
||||
|
||||
Reference in New Issue
Block a user