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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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data-raw/antibiograms.html
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@ -11,7 +11,7 @@
<meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-08" />
<meta name="date" content="2023-02-18" />
<title>Generating antibiograms with the AMR package</title>
@ -353,7 +353,7 @@ display: none;
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-08</h4>
<h4 class="date">2023-02-18</h4>
</div>
@ -412,7 +412,7 @@ looks like:</p>
<td align="right">22</td>
</tr>
<tr class="even">
<td align="left">E. coli (0-462)</td>
<td align="left"><em>E. coli</em> (0-462)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
@ -421,7 +421,7 @@ looks like:</p>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">E. faecalis (0-39)</td>
<td align="left"><em>E. faecalis</em> (0-39)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
@ -430,7 +430,7 @@ looks like:</p>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">K. pneumoniae (0-58)</td>
<td align="left"><em>K. pneumoniae</em> (0-58)</td>
<td align="right">NA</td>
<td align="right">90</td>
<td align="right">100</td>
@ -439,7 +439,7 @@ looks like:</p>
<td align="right">90</td>
</tr>
<tr class="odd">
<td align="left">P. aeruginosa (17-30)</td>
<td align="left"><em>P. aeruginosa</em> (17-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -448,7 +448,7 @@ looks like:</p>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">P. mirabilis (0-34)</td>
<td align="left"><em>P. mirabilis</em> (0-34)</td>
<td align="right">NA</td>
<td align="right">94</td>
<td align="right">94</td>
@ -457,7 +457,7 @@ looks like:</p>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">S. aureus (2-233)</td>
<td align="left"><em>S. aureus</em> (2-233)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
@ -466,7 +466,7 @@ looks like:</p>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left">S. epidermidis (8-163)</td>
<td align="left"><em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right">NA</td>
@ -475,7 +475,7 @@ looks like:</p>
<td align="right">51</td>
</tr>
<tr class="odd">
<td align="left">S. hominis (3-80)</td>
<td align="left"><em>S. hominis</em> (3-80)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">NA</td>
@ -484,7 +484,7 @@ looks like:</p>
<td align="right">85</td>
</tr>
<tr class="even">
<td align="left">S. pneumoniae (11-117)</td>
<td align="left"><em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -518,49 +518,49 @@ looks like:</p>
<td align="right">NA</td>
</tr>
<tr class="even">
<td align="left">E. coli (416-461)</td>
<td align="left"><em>E. coli</em> (416-461)</td>
<td align="right">94</td>
<td align="right">100</td>
<td align="right">99</td>
</tr>
<tr class="odd">
<td align="left">K. pneumoniae (53-58)</td>
<td align="left"><em>K. pneumoniae</em> (53-58)</td>
<td align="right">89</td>
<td align="right">93</td>
<td align="right">93</td>
</tr>
<tr class="even">
<td align="left">P. aeruginosa (27-30)</td>
<td align="left"><em>P. aeruginosa</em> (27-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">P. mirabilis (27-34)</td>
<td align="left"><em>P. mirabilis</em> (27-34)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. aureus (7-231)</td>
<td align="left"><em>S. aureus</em> (7-231)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. epidermidis (5-128)</td>
<td align="left"><em>S. epidermidis</em> (5-128)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. hominis (0-74)</td>
<td align="left"><em>S. hominis</em> (0-74)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. pneumoniae (112-112)</td>
<td align="left"><em>S. pneumoniae</em> (112-112)</td>
<td align="right">100</td>
<td align="right">100</td>
<td align="right">100</td>
@ -576,6 +576,16 @@ looks like:</p>
syndromic_group = &quot;ward&quot;)
)</code></pre>
<table>
<colgroup>
<col width="29%" />
<col width="33%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
@ -621,7 +631,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">E. coli (0-299)</td>
<td align="left">E. <em>coli</em> (0-299)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
@ -631,7 +641,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">E. coli (0-137)</td>
<td align="left">E. <em>coli</em> (0-137)</td>
<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
@ -641,7 +651,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. pneumoniae (0-51)</td>
<td align="left">K. <em>pneumoniae</em> (0-51)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">100</td>
@ -651,7 +661,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. mirabilis (0-30)</td>
<td align="left">P. <em>mirabilis</em> (0-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -661,7 +671,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. aureus (2-150)</td>
<td align="left">S. <em>aureus</em> (2-150)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
@ -671,7 +681,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. aureus (0-66)</td>
<td align="left">S. <em>aureus</em> (0-66)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
@ -681,7 +691,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. epidermidis (4-79)</td>
<td align="left">S. <em>epidermidis</em> (4-79)</td>
<td align="right">NA</td>
<td align="right">82</td>
<td align="right">NA</td>
@ -691,7 +701,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. epidermidis (4-75)</td>
<td align="left">S. <em>epidermidis</em> (4-75)</td>
<td align="right">NA</td>
<td align="right">72</td>
<td align="right">NA</td>
@ -701,7 +711,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. hominis (1-45)</td>
<td align="left">S. <em>hominis</em> (1-45)</td>
<td align="right">NA</td>
<td align="right">96</td>
<td align="right">NA</td>
@ -711,7 +721,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">S. pneumoniae (5-78)</td>
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -721,7 +731,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">S. pneumoniae (5-30)</td>
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
@ -745,8 +755,8 @@ looks like:</p>
)</code></pre>
<table>
<colgroup>
<col width="23%" />
<col width="35%" />
<col width="24%" />
<col width="34%" />
<col width="5%" />
<col width="14%" />
<col width="5%" />