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Built site for AMR: 1.8.2.9138@dad2530

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2023-02-22 13:47:35 +00:00
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reference/first_isolate.html
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@ -12,7 +12,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9137</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9138</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -197,15 +197,15 @@
<dt>col_date</dt>
<dd><p>column name of the result date (or date that is was received on the lab), defaults to the first column with a date class</p></dd>
<dd><p>column name of the result date (or date that is was received on the lab) - the default is the first column with a date class</p></dd>
<dt>col_patient_id</dt>
<dd><p>column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dd><p>column name of the unique IDs of the patients - the default is the first column that starts with 'patient' or 'patid' (case insensitive)</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>col_testcode</dt>
@ -221,7 +221,7 @@
<dt>col_keyantimicrobials</dt>
<dd><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>.</p></dd>
<dd><p>(only useful when <code>method = "phenotype-based"</code>) column name of the key antimicrobials to determine first isolates, see <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>. The default is the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use <code>col_keyantimicrobials = FALSE</code> to prevent this. Can also be the output of <code><a href="key_antimicrobials.html">key_antimicrobials()</a></code>.</p></dd>
<dt>episode_days</dt>
@ -257,7 +257,7 @@
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate info should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
<dt>include_unknown</dt>