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AMR
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dr. M.S. (Matthijs) Berends 2019-05-23 18:53:18 +02:00
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96
docs/articles/MDR.html
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@ -40,7 +40,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>
@ -242,19 +242,19 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R R R R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S R R S R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S I S S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S S R S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S I I R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S S S S</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R S I S S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S R I R S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S S S S R R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S R S S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 I R R S R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 S S S S S S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</span></a></code></pre></div>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 R</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -267,25 +267,65 @@
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># would be available too: `CAP` (capreomycin), `RIB` (rifabutin), `RFP`</span></a>
<a class="sourceLine" id="cb4-10" title="10"><span class="co"># (rifapentine)</span></a></code></pre></div>
<p>And review the result with a frequency table:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-4" title="4"><span class="co"># **Frequency table of `mdr` from `my_TB_data` (5,000 x 8)** </span></a>
<a class="sourceLine" id="cb5-5" title="5"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-6" title="6"><span class="co"># Class: `factor` &gt; `ordered` (`numeric`) </span></a>
<a class="sourceLine" id="cb5-7" title="7"><span class="co"># Length: 5,000 (of which NA: 0 = 0.00%) </span></a>
<a class="sourceLine" id="cb5-8" title="8"><span class="co"># Levels: 5: `Negative` &lt; `Mono-resistance` &lt; `Poly-resistance` &lt; `Multidrug res...` </span></a>
<a class="sourceLine" id="cb5-9" title="9"><span class="co"># Unique: 5</span></a>
<a class="sourceLine" id="cb5-10" title="10"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-11" title="11"><span class="co"># </span></a>
<a class="sourceLine" id="cb5-12" title="12"><span class="co"># | |Item | Count| Percent| Cum. Count| Cum. Percent|</span></a>
<a class="sourceLine" id="cb5-13" title="13"><span class="co"># |:--|:-------------------------|-----:|-------:|----------:|------------:|</span></a>
<a class="sourceLine" id="cb5-14" title="14"><span class="co"># |1 |Mono-resistance | 3,297| 65.9%| 3,297| 65.9%|</span></a>
<a class="sourceLine" id="cb5-15" title="15"><span class="co"># |2 |Negative | 627| 12.5%| 3,924| 78.5%|</span></a>
<a class="sourceLine" id="cb5-16" title="16"><span class="co"># |3 |Multidrug resistance | 612| 12.2%| 4,536| 90.7%|</span></a>
<a class="sourceLine" id="cb5-17" title="17"><span class="co"># |4 |Poly-resistance | 263| 5.3%| 4,799| 96.0%|</span></a>
<a class="sourceLine" id="cb5-18" title="18"><span class="co"># |5 |Extensive drug resistance | 201| 4.0%| 5,000| 100.0%|</span></a></code></pre></div>
</div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
<p>Class: <code>factor</code> &gt; <code>ordered</code> (<code>numeric</code>)<br>
Length: 5,000 (of which NA: 0 = 0.00%)<br>
Levels: 5: <code>Negative</code> &lt; <code>Mono-resistance</code> &lt; <code>Poly-resistance</code> &lt; <code>Multidrug res...</code><br>
Unique: 5</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,288</td>
<td align="right">65.8%</td>
<td align="right">3,288</td>
<td align="right">65.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">686</td>
<td align="right">13.7%</td>
<td align="right">3,974</td>
<td align="right">79.5%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">560</td>
<td align="right">11.2%</td>
<td align="right">4,534</td>
<td align="right">90.7%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">269</td>
<td align="right">5.4%</td>
<td align="right">4,803</td>
<td align="right">96.1%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">197</td>
<td align="right">3.9%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
</div>

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docs/articles/freq.html
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@ -40,7 +40,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

3
docs/index.html
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@ -219,8 +219,7 @@
<li>Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Determining first isolates to be used for AMR analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>
</li>
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Descriptive statistics: frequency tables, kurtosis and skewness (<a href="./articles/freq.html">tutorial</a>)</li>
</ul>
<p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>

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docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

2
docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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="Released version">0.6.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9037</span>
</span>
</div>

2
index.md
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@ -25,7 +25,7 @@ This package can be used for:
* Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name) ([manual](./reference/ab_property.html))
* Plotting antimicrobial resistance ([tutorial](./articles/AMR.html))
* Determining first isolates to be used for AMR analysis ([manual](./reference/first_isolate.html))
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Descriptive statistics: frequency tables, kurtosis and skewness ([tutorial](./articles/freq.html))
This package is ready-to-use for a professional environment by specialists in the following fields:

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vignettes/MDR.Rmd
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@ -74,6 +74,6 @@ my_TB_data$mdr <- mdr_tb(my_TB_data)
And review the result with a frequency table:
```{r}
```{r, results = 'asis'}
freq(my_TB_data$mdr)
```