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(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening

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dr. M.S. (Matthijs) Berends
2020-10-19 17:09:19 +02:00
parent 833a1be36d
commit 4e9ccb4435
76 changed files with 969 additions and 491 deletions
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16
docs/reference/key_antibiotics.html
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@ -82,7 +82,7 @@
</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">1.4.0.9001</span>
</span>
</div>
@ -281,7 +281,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>table with antibiotics coloms, like <code>AMX</code> or <code>amox</code></p></td>
<td><p>a data.frame with antibiotics columns, like <code>AMX</code> or <code>amox</code></p></td>
</tr>
<tr>
<th>col_mo</th>
@ -289,27 +289,27 @@
</tr>
<tr>
<th>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>.</p></td>
<td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
</tr>
<tr>
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
<td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>.</p></td>
<td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
</tr>
<tr>
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
<td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>.</p></td>
<td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. See details for which antibiotics will be used at default (which are guessed with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code>).</p></td>
</tr>
<tr>
<th>warnings</th>
<td><p>give warning about missing antibiotic columns, they will anyway be ignored</p></td>
<td><p>give a warning about missing antibiotic columns (they will be ignored)</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to function</p></td>
<td><p>other parameters passed on to functions</p></td>
</tr>
<tr>
<th>y, z</th>
<td><p>characters to compare</p></td>
<td><p>character vectors to compare</p></td>
</tr>
<tr>
<th>type</th>