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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">3.0.1.9041</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9042</small>
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@@ -123,11 +123,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt>
<dd><p>A character to transform microorganism input - must be <code>"name"</code>, <code>"shortname"</code> (default), <code>"gramstain"</code>, or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input or <code>NA</code> to consider all microorganisms 'unknown'.</p></dd>
<dd><p>A character to transform microorganism input - must be <code>"name"</code>, <code>"shortname"</code> (default), <code>"gramstain"</code>, or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: .val mo, .val fullname, .val status, .val kingdom, .val phylum, .val class, .val order, .val family, .val genus, .val species, .val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif, .val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val snomed. Can also be <code>NULL</code> to not transform the input or <code>NA</code> to consider all microorganisms 'unknown'.</p></dd>
<dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt>
<dd><p>A character to transform antimicrobial input - must be one of the column names of the <a href="antimicrobials.html">antimicrobials</a> data set (defaults to <code>"name"</code>): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dd><p>A character to transform antimicrobial input - must be one of the column names of the <a href="antimicrobials.html">antimicrobials</a> data set (defaults to <code>"name"</code>): .val ab, .val cid, .val name, .val group, .val atc, .val atc_group1, .val atc_group2, .val abbreviations, .val synonyms, .val oral_ddd, .val oral_units, .val iv_ddd, .val iv_units, or .val loinc. Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>