(v1.4.0.9032) auto-data guessing for functions

2025-07-25 01:25:51 +02:00 · 2020-12-07 16:06:42 +01:00
parent fdf29e6c5b
commit 1bdb136b3a
38 changed files with 455 additions and 353 deletions
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@ -39,7 +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">1.4.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
      </span>
    </div>

@ -228,8 +228,17 @@
 <span class="co">#            mo ampicillin</span>
 <span class="co"># 1  Klebsiella          R</span>
 <span class="co"># 2 Escherichia          S</span></pre></div>
-<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
+<p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit">
+<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</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">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
+                          <span class="st">"ampicillin"</span><span class="op">)</span>
+<span class="co"># [1]  TRUE FALSE</span>
+
+<span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
+                          <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
+<span class="co"># [1]  TRUE FALSE</span></pre></div>
+<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
+<div class="sourceCode" id="cb3"><pre class="downlit">
 <span class="va">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>mo <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">"Staphylococcus aureus"</span>,
                          <span class="st">"Enterococcus faecalis"</span>,
                          <span class="st">"Escherichia coli"</span>,
@ -243,7 +252,7 @@
                   PEN <span class="op">=</span> <span class="st">"S"</span>,       <span class="co"># Benzylenicillin</span>
                   FOX <span class="op">=</span> <span class="st">"S"</span>,       <span class="co"># Cefoxitin</span>
                   stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></pre></div>
-<div class="sourceCode" id="cb3"><pre class="downlit">
+<div class="sourceCode" id="cb4"><pre class="downlit">
 <span class="va">data</span></pre></div>
 <table class="table">
 <thead><tr class="header">
@ -309,7 +318,7 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb4"><pre class="downlit">
+<div class="sourceCode" id="cb5"><pre class="downlit">
 <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span></pre></div>
 <table class="table">
 <thead><tr class="header">
--- a/docs/articles/MDR.html
+++ b/docs/articles/MDR.html
@ -39,7 +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">1.4.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
      </span>
    </div>

@ -217,7 +217,11 @@
 <p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</p>
 </li>
 <li>
-<p><code>guideline = "EUCAST"</code></p>
+<p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
+<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf">link</a>)</p>
+</li>
+<li>
+<p><code>guideline = "EUCAST3.1"</code></p>
 <p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
 </li>
 <li>
@ -226,13 +230,14 @@
 </li>
 <li>
 <p><code>guideline = "MRGN"</code></p>
-<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. (<a href="https://doi.org/10.1186/s13756-015-0047-6">link</a>)</p>
+<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
 </li>
 <li>
 <p><code>guideline = "BRMO"</code></p>
-<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]” (<a href="https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH">link</a>)</p>
+<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh">link</a>)</p>
 </li>
 </ul>
+<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="uri">https://github.com/msberends/AMR/issues/new</a>.</p>
 </div>
 <div id="examples" class="section level4">
 <h4 class="hasAnchor">
@ -246,8 +251,8 @@
 <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 mdro(.): NA introduced for isolates where the available percentage of</span>
-<span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></pre></div>
+<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"># classes was below 50% (set with `pct_required_classes`)</span></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
@ -313,26 +318,27 @@ Unique: 2</p>
 <div class="sourceCode" id="cb5"><pre class="downlit">
 <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          R         S            S          R            R            S</span>
-<span class="co"># 2          I         R            S          R            S            I</span>
-<span class="co"># 3          R         R            S          S            S            S</span>
-<span class="co"># 4          R         R            S          I            S            S</span>
-<span class="co"># 5          S         I            R          S            R            S</span>
-<span class="co"># 6          S         S            S          R            S            S</span>
+<span class="co"># 1          S         I            R          S            R            R</span>
+<span class="co"># 2          R         S            S          R            I            S</span>
+<span class="co"># 3          I         R            I          S            R            S</span>
+<span class="co"># 4          I         S            S          R            S            R</span>
+<span class="co"># 5          R         R            S          S            R            R</span>
+<span class="co"># 6          S         R            I          S            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         S</span>
-<span class="co"># 6         R</span></pre></div>
+<span class="co"># 4         R</span>
+<span class="co"># 5         R</span>
+<span class="co"># 6         S</span></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">
 <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></pre></div>
 <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit">
 <span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
-<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></pre></div>
+<span class="co"># NOTE: No column found as input for `col_mo`, assuming all records contain</span>
+<span class="co">#       Mycobacterium tuberculosis.</span></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit">
 <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></pre></div>
@ -355,40 +361,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3262</td>
-<td align="right">65.24%</td>
-<td align="right">3262</td>
-<td align="right">65.24%</td>
+<td align="right">3313</td>
+<td align="right">66.26%</td>
+<td align="right">3313</td>
+<td align="right">66.26%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">664</td>
-<td align="right">13.28%</td>
-<td align="right">3926</td>
-<td align="right">78.52%</td>
+<td align="right">631</td>
+<td align="right">12.62%</td>
+<td align="right">3944</td>
+<td align="right">78.88%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">609</td>
-<td align="right">12.18%</td>
-<td align="right">4535</td>
-<td align="right">90.70%</td>
+<td align="right">575</td>
+<td align="right">11.50%</td>
+<td align="right">4519</td>
+<td align="right">90.38%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">283</td>
-<td align="right">5.66%</td>
-<td align="right">4818</td>
-<td align="right">96.36%</td>
+<td align="right">275</td>
+<td align="right">5.50%</td>
+<td align="right">4794</td>
+<td align="right">95.88%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">182</td>
-<td align="right">3.64%</td>
+<td align="right">206</td>
+<td align="right">4.12%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@ -81,7 +81,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
      </span>
    </div>