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(v1.4.0.9044) mo tibble printing, mo_shortname() fix

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dr. M.S. (Matthijs) Berends
2020-12-24 23:29:10 +01:00
parent 128ebcfd62
commit df37584189
96 changed files with 1039 additions and 2847 deletions
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@@ -6,22 +6,6 @@
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@@ -111,7 +81,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@@ -235,7 +205,6 @@
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@@ -286,7 +255,7 @@ Content not found. Please use links in the navbar.
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@@ -111,7 +81,7 @@
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<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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -235,7 +205,6 @@
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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@@ -534,7 +503,7 @@ END OF TERMS AND CONDITIONS
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</script><title>How to apply EUCAST rules • AMR (for R)</title>
<title>How to apply EUCAST rules • AMR (for R)</title>
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@@ -56,7 +39,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -419,7 +402,7 @@
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<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

126
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document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script><title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
<title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
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@@ -56,7 +39,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -268,7 +251,7 @@
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
<span class="co"># Warning in warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", : NA introduced for isolates where the available percentage of antimicrobial</span>
<span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
@@ -306,48 +289,41 @@ Unique: 2</p>
</table>
<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># a helper function to get a random vector with values S, I and R</span>
<span class="co"># with the probabilities 50% - 10% - 40%</span>
<span class="va">sample_rsi</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span>
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</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">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span><span class="op">)</span>,
size <span class="op">=</span> <span class="fl">5000</span>,
prob <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="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span><span class="op">)</span>,
replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
<span class="op">}</span>
<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
isoniazid <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
gatifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
ethambutol <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
pyrazinamide <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
moxifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
kanamycin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
<span class="co"># a random vector with values S, I and R</span>
<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
INH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
GAT <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
ETH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
PZA <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
MFX <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
KAN <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S R S R R S</span>
<span class="co"># 2 S R S S S S</span>
<span class="co"># 3 S S S S R S</span>
<span class="co"># 4 S R S R S S</span>
<span class="co"># 5 R S R S R S</span>
<span class="co"># 6 S R R R S S</span>
<span class="co"># 1 S S R I R S</span>
<span class="co"># 2 I S R I I R</span>
<span class="co"># 3 R R R S I R</span>
<span class="co"># 4 I I R R S S</span>
<span class="co"># 5 I R I S S R</span>
<span class="co"># 6 I R I I S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></code></pre></div>
<span class="co"># 3 I</span>
<span class="co"># 4 I</span>
<span class="co"># 5 I</span>
<span class="co"># 6 R</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@@ -378,40 +354,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3314</td>
<td align="right">66.28%</td>
<td align="right">3314</td>
<td align="right">66.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">637</td>
<td align="right">12.74%</td>
<td align="right">3951</td>
<td align="right">79.02%</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4211</td>
<td align="right">84.22%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">565</td>
<td align="right">11.30%</td>
<td align="right">4516</td>
<td align="right">90.32%</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4653</td>
<td align="right">93.06%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">298</td>
<td align="right">5.96%</td>
<td align="right">4814</td>
<td align="right">96.28%</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">186</td>
<td align="right">3.72%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@@ -433,7 +409,7 @@ Unique: 5</p>
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<title>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
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@@ -56,7 +39,7 @@
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<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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -353,7 +336,7 @@
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<title>How to import data from SPSS / SAS / Stata • AMR (for R)</title>
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@@ -56,7 +39,7 @@
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<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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -210,7 +193,7 @@
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">21 December 2020</h4>
<h4 class="date">24 December 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -431,7 +414,7 @@
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@@ -430,7 +413,7 @@ Drug group: Beta-lactams/penicillins<br>
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@@ -56,7 +39,7 @@
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<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">1.4.0.9042</span>
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@@ -244,20 +227,20 @@
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 10.0 11.0 20.0 13.0 38.0 41.0</span>
<span class="co"># as.mo("stau") 100.0 110.0 120.0 110.0 140.0 140.0</span>
<span class="co"># as.mo("STAU") 100.0 110.0 130.0 140.0 140.0 160.0</span>
<span class="co"># as.mo("staaur") 10.0 12.0 23.0 14.0 38.0 58.0</span>
<span class="co"># as.mo("STAAUR") 10.0 11.0 18.0 13.0 14.0 42.0</span>
<span class="co"># as.mo("S. aureus") 26.0 30.0 46.0 44.0 58.0 78.0</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 32.0 31.0 31.0 56.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.0 2.4 2.6 2.7 2.8 3.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910.0 920.0 920.0 930.0 960.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 380.0 390.0 400.0 390.0 400.0 430.0</span>
<span class="co"># as.mo("MRSA") 9.9 11.0 16.0 14.0 14.0 41.0</span>
<span class="co"># as.mo("VISA") 17.0 19.0 28.0 21.0 45.0 52.0</span>
<span class="co"># as.mo("VRSA") 17.0 19.0 26.0 21.0 22.0 53.0</span>
<span class="co"># expr min lq mean median uq max</span>
<span class="co"># as.mo("sau") 9.9 12.0 15.0 13.0 13.0 42.0</span>
<span class="co"># as.mo("stau") 100.0 100.0 130.0 120.0 140.0 190.0</span>
<span class="co"># as.mo("STAU") 110.0 110.0 130.0 130.0 140.0 150.0</span>
<span class="co"># as.mo("staaur") 9.8 12.0 26.0 13.0 41.0 60.0</span>
<span class="co"># as.mo("STAAUR") 11.0 11.0 15.0 13.0 13.0 41.0</span>
<span class="co"># as.mo("S. aureus") 26.0 28.0 50.0 58.0 63.0 75.0</span>
<span class="co"># as.mo("S aureus") 26.0 27.0 46.0 51.0 60.0 67.0</span>
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2.2 2.5 2.5 2.8 3.1</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0 910.0 1000.0 2400.0</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 400.0 380.0 420.0 540.0</span>
<span class="co"># as.mo("MRSA") 9.7 11.0 17.0 12.0 13.0 66.0</span>
<span class="co"># as.mo("VISA") 19.0 19.0 36.0 35.0 53.0 56.0</span>
<span class="co"># as.mo("VRSA") 17.0 20.0 20.0 21.0 21.0 23.0</span>
<span class="co"># neval</span>
<span class="co"># 10</span>
<span class="co"># 10</span>
@@ -301,8 +284,8 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 128 167 205 195 232 298 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.195 seconds. You only lose time on your unique input values.</p>
<span class="co"># mo_name(x) 134 167 201 179 207 310 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@@ -316,10 +299,10 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.35 7.70 8.15 8.11 8.68 8.96 10</span>
<span class="co"># B 22.50 22.80 28.10 24.30 25.70 62.60 10</span>
<span class="co"># C 1.84 1.98 2.13 2.13 2.17 2.43 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0021 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<span class="co"># A 7.59 7.93 8.24 8.09 8.66 9.06 10</span>
<span class="co"># B 23.60 23.70 29.20 24.30 27.10 66.10 10</span>
<span class="co"># C 1.84 2.13 2.22 2.19 2.35 2.62 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
@@ -333,14 +316,14 @@
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.60 1.63 1.74 1.70 1.83 2.02 10</span>
<span class="co"># B 1.37 1.40 1.62 1.54 1.74 2.07 10</span>
<span class="co"># C 1.39 1.45 1.63 1.65 1.77 1.86 10</span>
<span class="co"># D 1.37 1.40 1.58 1.51 1.62 2.27 10</span>
<span class="co"># E 1.44 1.64 1.70 1.66 1.81 2.13 10</span>
<span class="co"># F 1.38 1.42 1.57 1.58 1.67 1.81 10</span>
<span class="co"># G 1.38 1.62 1.64 1.63 1.70 1.82 10</span>
<span class="co"># H 1.44 1.65 1.84 1.82 1.99 2.60 10</span></code></pre></div>
<span class="co"># A 1.69 1.77 1.82 1.83 1.86 1.92 10</span>
<span class="co"># B 1.78 1.79 1.89 1.91 1.95 2.06 10</span>
<span class="co"># C 1.74 1.79 1.88 1.87 1.94 2.06 10</span>
<span class="co"># D 1.75 1.77 1.94 1.95 1.99 2.41 10</span>
<span class="co"># E 1.70 1.75 1.84 1.81 1.87 2.08 10</span>
<span class="co"># F 1.66 1.70 1.76 1.74 1.80 1.89 10</span>
<span class="co"># G 1.68 1.70 1.82 1.75 1.93 2.09 10</span>
<span class="co"># H 1.66 1.69 1.75 1.74 1.80 1.92 10</span></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@@ -367,14 +350,14 @@
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
<span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 15.77 16.36 18.40 16.85 17.50 53.58 100</span>
<span class="co"># de 19.03 19.70 24.60 20.14 21.06 59.83 100</span>
<span class="co"># nl 30.93 32.03 36.58 32.80 33.78 85.59 100</span>
<span class="co"># es 18.78 19.62 24.49 19.98 20.60 58.73 100</span>
<span class="co"># it 18.80 19.50 22.68 19.92 20.89 63.99 100</span>
<span class="co"># fr 18.78 19.59 21.99 19.90 20.75 58.87 100</span>
<span class="co"># pt 18.79 19.65 23.04 20.08 20.82 59.30 100</span></code></pre></div>
<span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 15.91 16.98 21.87 17.54 18.34 168.50 100</span>
<span class="co"># de 18.98 20.14 26.30 20.74 22.64 66.68 100</span>
<span class="co"># nl 31.02 32.71 37.56 33.84 35.81 82.77 100</span>
<span class="co"># es 19.13 20.06 22.96 20.54 21.42 65.26 100</span>
<span class="co"># it 18.90 19.84 24.26 20.59 22.80 60.30 100</span>
<span class="co"># fr 18.89 19.92 23.46 20.49 21.72 62.85 100</span>
<span class="co"># pt 18.90 19.99 23.80 20.70 22.17 61.42 100</span></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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@@ -392,7 +375,7 @@
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@@ -56,7 +39,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
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@@ -1163,7 +1146,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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@@ -111,7 +81,7 @@
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@@ -235,7 +205,6 @@
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@@ -303,7 +272,7 @@
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<title>How to predict antimicrobial resistance • AMR (for R)</title>
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@@ -56,7 +39,7 @@
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<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">1.4.0.9042</span>
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@@ -305,8 +288,7 @@
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></code></pre></div>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
@@ -351,8 +333,7 @@
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</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="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></code></pre></div>
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>This seems more likely, doesn’t it?</p>
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
@@ -387,7 +368,7 @@
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@@ -56,7 +39,7 @@
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<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">1.4.0.9042</span>
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</span>
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@@ -266,7 +249,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@@ -235,7 +205,6 @@
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@@ -356,7 +325,7 @@
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<title>Antimicrobial Resistance Analysis • AMR (for R)</title>
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@@ -60,7 +43,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
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</span>
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@@ -531,7 +514,7 @@ Since you are one of our users, we would like to know how you use the package an
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@@ -6,22 +6,6 @@
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@@ -36,21 +20,10 @@
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@@ -111,7 +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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -235,7 +205,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -267,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409043" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9043">
<a href="#amr-1409043" class="anchor"></a>AMR 1.4.0.9043<small> Unreleased </small>
<div id="amr-1409044" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9044">
<a href="#amr-1409044" class="anchor"></a>AMR 1.4.0.9044<small> Unreleased </small>
</h1>
<div id="last-updated-22-december-2020" class="section level2">
<div id="last-updated-24-december-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-22-december-2020" class="anchor"></a><small>Last updated: 22 December 2020</small>
<a href="#last-updated-24-december-2020" class="anchor"></a><small>Last updated: 24 December 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@@ -333,6 +302,9 @@
<li><p>Fix for plotting MIC values with <code><a href="../reference/plot.html">plot()</a></code></p></li>
<li><p>Added <code><a href="../reference/plot.html">plot()</a></code> generic to class <code>&lt;disk&gt;</code></p></li>
<li><p>LA-MRSA and CA-MRSA are now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("LA-MRSA")</a></code> will return <code>"Staphylococcus"</code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive("LA-MRSA")</a></code> will return <code>TRUE</code>.</p></li>
<li><p>Fix for printing class <mo> in tibbles when all values are <code>NA</code></mo></p></li>
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> when the input contains <code>NA</code></p></li>
<li><p>If <code><a href="../reference/as.mo.html">as.mo()</a></code> takes more than 30 seconds, some suggestions will be done to improve speed</p></li>
</ul>
</div>
<div id="other" class="section level3">
@@ -343,7 +315,6 @@
<li>More extensive unit tests</li>
<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>mo_env</code>
</li>
<li>Our website now also has a dark theme, that switches on automatically based on system settings (such as Night Mode in macOS)</li>
</ul>
</div>
</div>
@@ -548,7 +519,7 @@
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -885,7 +856,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; invalid microorganism code, NA generated</span></code></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>freq()</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>freq()</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>
<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>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@@ -1154,7 +1125,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
</li>
<li>Frequency tables (<code>freq()</code>):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
<ul>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
@@ -1164,12 +1135,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</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">%&gt;%</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="va">septic_patients</span> <span class="op">%&gt;%</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">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</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">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
</li>
</ul>
@@ -1179,7 +1150,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -1420,7 +1391,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</li>
<li>Frequency tables (<code>freq()</code> function):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -1430,15 +1401,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co"># OLD WAY</span>
<span class="va">septic_patients</span> <span class="op">%&gt;%</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">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</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="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
<span class="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="va">septic_patients</span> <span class="op">%&gt;%</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">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<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></code></pre></div>
</li>
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@@ -1521,7 +1492,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
<li>
<p>Frequency tables - <code>freq()</code>:</p>
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
<ul>
<li>
<p>Support for grouping variables, test with:</p>
@@ -1529,14 +1500,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</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">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
<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></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</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">%&gt;%</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></code></pre></div>
</li>
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@@ -1554,7 +1525,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@@ -1722,13 +1693,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">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">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<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></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">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">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
<span class="va">my_list</span> <span class="op">%&gt;%</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">%&gt;%</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></code></pre></div>
</li>
</ul>
</div>
@@ -1802,13 +1773,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@@ -1973,7 +1944,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

45
docs/pkgdown.css
View File

@@ -264,7 +264,50 @@ table {
/* Syntax highlighting ---------------------------------------------------- */
/* Moved to new files.*/
pre {
word-wrap: normal;
word-break: normal;
border: 1px solid #eee;
}
pre, code {
background-color: #f8f8f8;
color: #333;
}
pre code {
overflow: auto;
word-wrap: normal;
white-space: pre;
}
pre .img {
margin: 5px 0;
}
pre .img img {
background-color: #fff;
display: block;
height: auto;
}
code a, pre a {
color: #375f84;
}
a.sourceLine:hover {
text-decoration: none;
}
.fl {color: #1514b5;}
.fu {color: #000000;} /* function */
.ch,.st {color: #036a07;} /* string */
.kw {color: #264D66;} /* keyword */
.co {color: #888888;} /* comment */
.message { color: black; font-weight: bolder;}
.error { color: orange; font-weight: bolder;}
.warning { color: #6A0366; font-weight: bolder;}
/* Clipboard --------------------------*/

2
docs/pkgdown.yml
View File

@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-21T23:50Z
last_built: 2020-12-24T22:24Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

39
docs/reference/AMR-deprecated.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Deprecated functions — AMR-deprecated • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- Flatly Theme - Light -->
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<!-- Darkly Theme - Dark -->
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
<!-- preferably CSS -->
<link rel="stylesheet" href="../preferably.css">
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -303,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/AMR.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>The AMR Package — AMR • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -341,7 +310,7 @@ The Netherlands
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/WHOCC.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -311,7 +280,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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);
}
</script>
<title>Data set with 500 isolates - WHONET example — WHONET • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -333,7 +302,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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@@ -6,22 +6,6 @@
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// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
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);
}
</script>
<title>Retrieve antimicrobial drug names and doses from clinical text — ab_from_text • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -394,7 +363,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/ab_property.html
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@@ -6,22 +6,6 @@
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<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get properties of an antibiotic — ab_property • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -432,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Age in years of individuals — age • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/age_groups.html
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Split ages into age groups — age_groups • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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);
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</script>
<title>Antibiotic class selectors — antibiotic_class_selectors • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -373,7 +342,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/antibiotics.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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// no media filter so that it will be downloaded with highest priority.
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"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -377,7 +346,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

39
docs/reference/as.ab.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to an antibiotic ID — as.ab • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -394,7 +363,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
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39
docs/reference/as.disk.html
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to disk diffusion diameters — as.disk • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -348,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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</div>
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39
docs/reference/as.mic.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to minimum inhibitory concentrations (MIC) — as.mic • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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</div>
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39
docs/reference/as.mo.html
View File

@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -506,7 +475,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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docs/reference/as.rsi.html
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<meta name="color-scheme" content="dark light">
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// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
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"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Interpret MIC and disk values, or clean raw R/SI data — as.rsi • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -547,7 +516,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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docs/reference/atc_online.html
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<meta name="color-scheme" content="dark light">
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// i.e. In this case, inject the `light` CSS before the others, with
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"beforeend",
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);
}
</script>
<title>Get ATC properties from WHOCC website — atc_online_property • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -383,7 +352,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/availability.html
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@@ -6,22 +6,6 @@
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// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Check availability of columns — availability • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -332,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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docs/reference/bug_drug_combinations.html
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@@ -6,22 +6,6 @@
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// i.e. In this case, inject the `light` CSS before the others, with
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if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Determine bug-drug combinations — bug_drug_combinations • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -403,7 +372,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/catalogue_of_life.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>The Catalogue of Life — catalogue_of_life • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -352,7 +321,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
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<title>Version info of included Catalogue of Life — catalogue_of_life_version • AMR (for R)</title>
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@@ -36,21 +20,10 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
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@@ -313,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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<title>Count available isolates — count • AMR (for R)</title>
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@@ -87,9 +60,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -113,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -237,7 +207,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -317,7 +286,7 @@
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</button>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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@@ -312,7 +281,7 @@
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<title>Filter isolates on result in antimicrobial class — filter_ab_class • AMR (for R)</title>
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<span class="navbar-brand">
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</div>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
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@@ -395,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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</div>
<div class="pkgdown">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<a href="https://github.com/msberends/AMR">
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</div>
<div class="pkgdown">
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</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -462,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
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<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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<a href="https://github.com/msberends/AMR">
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@@ -548,7 +517,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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@@ -355,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
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<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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -708,7 +677,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/intrinsic_resistant.html
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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<title>Data set with bacterial intrinsic resistance — intrinsic_resistant • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -321,7 +290,7 @@
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/is_new_episode.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
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// i.e. In this case, inject the `light` CSS before the others, with
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<title>Determine (new) episodes for patients — is_new_episode • AMR (for R)</title>
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@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/join.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
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document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
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);
}
</script>
<title>Join microorganisms to a data set — join • AMR (for R)</title>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -360,7 +329,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/key_antibiotics.html
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@@ -6,22 +6,6 @@
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
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);
}
</script>
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -471,7 +440,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/kurtosis.html
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@@ -6,22 +6,6 @@
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Kurtosis of the sample — kurtosis • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -332,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/lifecycle.html
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<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<li>
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@@ -326,7 +295,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
</div>
<div class="pkgdown">
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<title>Pattern matching with keyboard shortcut — like • AMR (for R)</title>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<a href="https://github.com/msberends/AMR">
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@@ -366,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
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<title>Data set with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
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<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -319,7 +288,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -362,7 +331,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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<title>Data set with previously accepted taxonomic names — microorganisms.old • AMR (for R)</title>
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@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -325,7 +294,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -338,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>

43
docs/reference/mo_property.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Get properties of a microorganism — mo_property • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -332,7 +301,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing in <code>mo_is_*()</code> functions when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing the column containing microorganism codes when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
</tr>
<tr>
<th>language</th>
@@ -348,7 +317,7 @@
</tr>
<tr>
<th>open</th>
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>browseURL()</a></code></p></td>
</tr>
<tr>
<th>property</th>
@@ -550,7 +519,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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51
docs/reference/mo_source.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>User-defined reference data set for microorganisms — mo_source • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -76,8 +49,8 @@
<script src="../extra.js"></script>
<meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@@ -87,9 +60,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -113,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -237,7 +207,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -271,8 +240,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</div>
<div class="ref-description">
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>.</p>
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>).</p>
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
</div>
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
@@ -348,7 +317,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
<span class='co'>#&gt; NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
<span class='co'>#&gt; '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
<span class='co'>#&gt; "Organisation XYZ" and "mo"</span>
<span class='co'>#&gt; Class &lt;mo&gt;</span>
<span class='co'>#&gt; [1] B_ESCHR_COLI</span>
@@ -361,7 +330,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<span class='co'>#&gt; Removed mo_source file '/Users/me/mo_source.rds'</span>
</pre>
<p>If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code>.</p>
<p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code> or any <code><a href='mo_property.html'>mo_*</a></code> function.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@@ -390,7 +359,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
docs/reference/pca.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Principal Component Analysis (for AMR) — pca • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9042</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
</div>
@@ -236,7 +206,6 @@
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -388,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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39
docs/reference/plot.html
View File

@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<!-- Inform modern browsers that this page supports both dark and light color schemes,
and the page author prefers light. -->
<meta name="color-scheme" content="dark light">
<script>
// If `prefers-color-scheme` is not supported, fall back to light mode.
// i.e. In this case, inject the `light` CSS before the others, with
// no media filter so that it will be downloaded with highest priority.
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
document.documentElement.style.display = "none";
document.head.insertAdjacentHTML(
"beforeend",
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
);
}
</script>
<title>Plotting for classes rsi, mic and disk — plot • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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<!-- bootstrap-toc -->
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<script src="../bootstrap-toc.js"></script>
@@ -86,9 +59,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -112,7 +82,7 @@
</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">1.4.0.9043</span>
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@@ -236,7 +206,6 @@
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@@ -87,9 +60,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -113,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@@ -237,7 +207,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
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@@ -112,7 +82,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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@@ -236,7 +206,6 @@
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@@ -491,7 +460,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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</span>
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@@ -236,7 +206,6 @@
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@@ -113,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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@@ -237,7 +207,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<title>Translate strings from AMR package — translate • AMR (for R)</title>
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@@ -36,21 +20,10 @@
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@@ -86,9 +59,6 @@
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</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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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39
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@@ -6,22 +6,6 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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);
}
</script>
<title>Survey • AMR (for R)</title>
<!-- favicons -->
@@ -36,21 +20,10 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<script src="bootstrap-toc.js"></script>
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<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">1.4.0.9043</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
</span>
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</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
@@ -286,7 +255,7 @@
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<div class="pkgdown">
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
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