Built site for AMR@3.0.1.9061: 0c1709c

2026-06-24 07:36:21 +02:00 · 2026-06-23 18:00:14 +00:00
parent 9447e0f2c2
commit 2a7bfb9ffb
328 changed files with 5357 additions and 3687 deletions
--- a/reference/antimicrobial_selectors.html
+++ b/reference/antimicrobial_selectors.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.
 Simply puy, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class, code or name: column names "cefazolin", "kefzol", "CZO" and "J01DB04" would all be included in the following selection:
 library(dplyr)
 my_data_with_all_these_columns %&amp;gt;%
@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%

    <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="">3.0.1.9057</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</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">
@@ -69,8 +69,12 @@ my_data_with_all_these_columns %&amp;gt;%

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aminoglycosides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aminoglycosides</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">aminopenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -78,41 +82,68 @@ my_data_with_all_these_columns %&amp;gt;%
 <span></span>
 <span><span class="fu">antimycobacterials</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">betalactams</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">betalactams</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">betalactams_with_inhibitor</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">betalactams_with_inhibitor</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">carbapenems</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">carbapenems</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">cephalosporins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">cephalosporins</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">cephalosporins_1st</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">cephalosporins_2nd</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">cephalosporins_3rd</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">cephalosporins_3rd</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">cephalosporins_4th</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">cephalosporins_5th</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">fluoroquinolones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">fluoroquinolones</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">glycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">ionophores</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">isoxazolylpenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">isoxazolylpenicillins</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">lincosamides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">lincosamides</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">lipoglycopeptides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -132,11 +163,19 @@ my_data_with_all_these_columns %&amp;gt;%
 <span></span>
 <span><span class="fu">phosphonics</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">polymyxins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">polymyxins</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">quinolones</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">quinolones</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">rifamycins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -146,25 +185,43 @@ my_data_with_all_these_columns %&amp;gt;%
 <span></span>
 <span><span class="fu">sulfonamides</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">tetracyclines</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">tetracyclines</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">trimethoprims</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">ureidopenicillins</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">amr_class</span><span class="op">(</span><span class="va">amr_class</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">amr_class</span><span class="op">(</span></span>
+<span>  <span class="va">amr_class</span>,</span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">amr_selector</span><span class="op">(</span><span class="va">filter</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
-<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">amr_selector</span><span class="op">(</span></span>
+<span>  <span class="va">filter</span>,</span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  only_treatable <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  return_all <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">administrable_per_os</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">administrable_iv</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, return_all <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">not_intrinsic_resistant</span><span class="op">(</span>only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">not_intrinsic_resistant</span><span class="op">(</span></span>
+<span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">