website update

docs/articles/MDR.html

@@ -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="cb3-3" 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            R          S            R            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          R         S            S          I            S            S</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            S          R            S            S</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          R         R            S          I            I            R</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          R         S            S          S            S            S</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="cb3-14" title="14"><span class="co"># 5         R</span></a>
-<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6         I</span></a></code></pre></div>
+<a class="sourceLine" id="cb3-15" 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>
+<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>
-<a class="sourceLine" id="cb5-2" title="2"><span class="co"># </span></a>
+<p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
-<a class="sourceLine" id="cb5-3" title="3"><span class="co"># </span></a>
+<p>Class: <code>factor</code> &gt; <code>ordered</code> (<code>numeric</code>)<br>
-<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>
+Length: 5,000 (of which NA: 0 = 0.00%)<br>
-<a class="sourceLine" id="cb5-5" title="5"><span class="co"># </span></a>
+Levels: 5: <code>Negative</code> &lt; <code>Mono-resistance</code> &lt; <code>Poly-resistance</code> &lt; <code>Multidrug res...</code><br>
-<a class="sourceLine" id="cb5-6" title="6"><span class="co"># Class:   `factor` &gt; `ordered` (`numeric`)  </span></a>
+Unique: 5</p>
-<a class="sourceLine" id="cb5-7" title="7"><span class="co"># Length:  5,000 (of which NA: 0 = 0.00%)  </span></a>
+<table class="table">
-<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>
+<thead><tr class="header">
-<a class="sourceLine" id="cb5-9" title="9"><span class="co"># Unique:  5</span></a>
+<th align="left"></th>
-<a class="sourceLine" id="cb5-10" title="10"><span class="co"># </span></a>
+<th align="left">Item</th>
-<a class="sourceLine" id="cb5-11" title="11"><span class="co"># </span></a>
+<th align="right">Count</th>
-<a class="sourceLine" id="cb5-12" title="12"><span class="co"># |   |Item                      | Count| Percent| Cum. Count| Cum. Percent|</span></a>
+<th align="right">Percent</th>
-<a class="sourceLine" id="cb5-13" title="13"><span class="co"># |:--|:-------------------------|-----:|-------:|----------:|------------:|</span></a>
+<th align="right">Cum. Count</th>
-<a class="sourceLine" id="cb5-14" title="14"><span class="co"># |1  |Mono-resistance           | 3,297|   65.9%|      3,297|        65.9%|</span></a>
+<th align="right">Cum. Percent</th>
-<a class="sourceLine" id="cb5-15" title="15"><span class="co"># |2  |Negative                  |   627|   12.5%|      3,924|        78.5%|</span></a>
+</tr></thead>
-<a class="sourceLine" id="cb5-16" title="16"><span class="co"># |3  |Multidrug resistance      |   612|   12.2%|      4,536|        90.7%|</span></a>
+<tbody>
-<a class="sourceLine" id="cb5-17" title="17"><span class="co"># |4  |Poly-resistance           |   263|    5.3%|      4,799|        96.0%|</span></a>
+<tr class="odd">
-<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>
+<td align="left">1</td>
-  </div>
+<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>

docs/articles/freq.html

@@ -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>
 

docs/index.html

@@ -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>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
-</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>

docs/reference/antibiotics.html

@@ -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>
 

docs/reference/as.rsi.html

@@ -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>
 

docs/reference/count.html

@@ -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>
 

docs/reference/eucast_rules.html

@@ -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>
 

docs/reference/ggplot_rsi.html

@@ -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>
 

index.md

@@ -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:

vignettes/MDR.Rmd

@@ -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)
 ```