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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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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: .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>
<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: <code>"mo"</code>, <code>"fullname"</code>, <code>"status"</code>, <code>"kingdom"</code>, <code>"phylum"</code>, <code>"class"</code>, <code>"order"</code>, <code>"family"</code>, <code>"genus"</code>, <code>"species"</code>, <code>"subspecies"</code>, <code>"rank"</code>, <code>"ref"</code>, <code>"oxygen_tolerance"</code>, <code>"source"</code>, <code>"lpsn"</code>, <code>"lpsn_parent"</code>, <code>"lpsn_renamed_to"</code>, <code>"mycobank"</code>, <code>"mycobank_parent"</code>, <code>"mycobank_renamed_to"</code>, <code>"gbif"</code>, <code>"gbif_parent"</code>, <code>"gbif_renamed_to"</code>, <code>"prevalence"</code>, or <code>"snomed"</code>. 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>): .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>
<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>): <code>"ab"</code>, <code>"cid"</code>, <code>"name"</code>, <code>"group"</code>, <code>"atc"</code>, <code>"atc_group1"</code>, <code>"atc_group2"</code>, <code>"abbreviations"</code>, <code>"synonyms"</code>, <code>"oral_ddd"</code>, <code>"oral_units"</code>, <code>"iv_ddd"</code>, <code>"iv_units"</code>, or <code>"loinc"</code>. 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>