* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@ -118,6 +118,7 @@
@@ -118,6 +118,7 @@
* Fix for determining the system's language
* Fix for `key_antibiotics()` on foreign systems
* Added 80 new LIS codes for microorganisms
* Relabeled the factor levels of `mdr_tb()`
#### Other
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
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<p>As an example, I will make a data set to determine multi-drug resistant TB:</p>
<divclass="sourceCode"id="cb1"><preclass="sourceCode r"><codeclass="sourceCode r"><aclass="sourceLine"id="cb1-1"data-line-number="1"><spanclass="co"># a helper function to get a random vector with values S, I and R</span></a>
<aclass="sourceLine"id="cb1-2"data-line-number="2"><spanclass="co"># with the probabilities 50%-10%-40%</span></a>
<aclass="sourceLine"id="cb1-2"data-line-number="2"><spanclass="co"># with the probabilities 50%-10%-40%</span></a>
<aclass="sourceLine"id="cb4-2"data-line-number="2"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
<aclass="sourceLine"id="cb4-8"data-line-number="8"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<p>We also created a package dedicated to data cleaning and checking, called the <code>clean</code> package. It gets automatically installed with the <code>AMR</code> package, so we only have to load it:</p>
<p>It contains the <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function, to create a frequency table:</p>
<p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <ahref="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <ahref="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <ahref="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
<p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <ahref="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <ahref="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <ahref="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <ahref="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <ahref="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -367,6 +367,8 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
@@ -367,6 +367,8 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>Fix for determining the system’s language</li>
<li>Fix for <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> on foreign systems</li>
<li>Added 80 new LIS codes for microorganisms</li>
<li>Relabeled the factor levels of <code><ahref="../reference/mdro.html">mdr_tb()</a></code>
</li>
</ul>
<divid="other"class="section level4">
<h4class="hasAnchor">
@ -1286,7 +1288,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
@@ -1286,7 +1288,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
@ -31,7 +31,7 @@ As an example, I will make a data set to determine multi-drug resistant TB:
@@ -31,7 +31,7 @@ As an example, I will make a data set to determine multi-drug resistant TB:
```{r}
# a helper function to get a random vector with values S, I and R
