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2
reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">

2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/WHOCC.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/WHONET.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">

22
reference/age.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.68767 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.10411 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.25479 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.01918 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.34795 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.06027 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.04658 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.15616 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.52877 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.11233 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 26 26.69041 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.10685 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.25753 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.02192 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.35068 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.06301 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.04932 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.15890 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.53151 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.11507 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1999-06-30 26 26.68767 0
#> 2 1968-01-29 58 58.10411 31
#> 3 1965-12-05 60 60.25479 34
#> 4 1980-03-01 46 46.01918 19
#> 5 1949-11-01 76 76.34795 50
#> 6 1947-02-14 79 79.06027 52
#> 7 1940-02-19 86 86.04658 59
#> 8 1988-01-10 38 38.15616 11
#> 9 1997-08-27 28 28.52877 2
#> 10 1978-01-26 48 48.11233 21
#> 1 1999-06-30 26 26.69041 0
#> 2 1968-01-29 58 58.10685 31
#> 3 1965-12-05 60 60.25753 34
#> 4 1980-03-01 46 46.02192 19
#> 5 1949-11-01 76 76.35068 50
#> 6 1947-02-14 79 79.06301 52
#> 7 1940-02-19 86 86.04932 59
#> 8 1988-01-10 38 38.15890 11
#> 9 1997-08-27 28 28.53151 2
#> 10 1978-01-26 48 48.11507 21
```

2
reference/age_groups.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">

2
reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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2
reference/antibiogram.html
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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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</small>
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5
reference/antimicrobial_selectors.html
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@@ -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="">3.0.1.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9033</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">
@@ -106,6 +106,8 @@ my_data_with_all_these_columns %&amp;gt;%
<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>
@@ -234,6 +236,7 @@ my_data_with_all_these_columns %&amp;gt;%
<li><p><code>cephalosporins_5th()</code> can select: <br> ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)</p></li>
<li><p><code>fluoroquinolones()</code> can select: <br> besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)</p></li>
<li><p><code>glycopeptides()</code> can select: <br> avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)</p></li>
<li><p><code>ionophores()</code> can select: <br> lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)</p></li>
<li><p><code>isoxazolylpenicillins()</code> can select: <br> cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)</p></li>
<li><p><code>lincosamides()</code> can select: <br> clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)</p></li>
<li><p><code>lipoglycopeptides()</code> can select: <br> dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)</p></li>

6
reference/antimicrobial_selectors.md
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@@ -55,6 +55,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@@ -459,6 +461,10 @@ quite slow in terms of performance.
teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN),
vancomycin-macromethod (VAM), and zorbamycin (ZOR)
- `ionophores()` can select:
lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS),
and salinomycin (SAL)
- `isoxazolylpenicillins()` can select:
cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC),
meticillin (MET), oxacillin (OXA), and oxacillin screening test

16
reference/antimicrobials.html
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@@ -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>Data Sets with 624 Antimicrobial Drugs — antimicrobials • 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="Data Sets with 624 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
<!-- 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>Data Sets with 625 Antimicrobial Drugs — antimicrobials • 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="Data Sets with 625 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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@@ -46,7 +46,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 624 Antimicrobial Drugs</h1>
<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 625 Antimicrobial Drugs</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
<div class="d-none name"><code>antimicrobials.Rd</code></div>
</div>
@@ -69,7 +69,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<div class="section">
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 504 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 505 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
<ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
@@ -103,7 +103,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
</ul></div>
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 504 rows and 14 columns.</p>
<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 505 rows and 14 columns.</p>
<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
</div>
<div class="section level2">
@@ -145,9 +145,9 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 504 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 505 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> <span style="color: #949494; font-style: italic;">&lt;list&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-ami… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acety… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acety… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
@@ -158,7 +158,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [4]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [6]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxi… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #949494;">&lt;chr [1]&gt;</span> <span style="color: #949494;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 494 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 495 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
<span class="r-in"><span><span class="va">antivirals</span></span></span>

12
reference/antimicrobials.md
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@@ -1,4 +1,4 @@
# Data Sets with 624 Antimicrobial Drugs
# Data Sets with 625 Antimicrobial Drugs
Two data sets containing all antimicrobials and antivirals. Use
[`as.ab()`](https://amr-for-r.org/reference/as.ab.md) or one of the
@@ -25,7 +25,7 @@ antivirals
## Format
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 504 observations and 14 variables:
### For the antimicrobials data set: a [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 505 observations and 14 variables:
- `ab`
antimicrobial ID as used in this package (such as `AMC`), using the
@@ -138,7 +138,7 @@ LOINC:
[`av_property()`](https://amr-for-r.org/reference/av_property.md).
An object of class `deprecated_amr_dataset` (inherits from `tbl_df`,
`tbl`, `data.frame`) with 504 rows and 14 columns.
`tbl`, `data.frame`) with 505 rows and 14 columns.
An object of class `tbl_df` (inherits from `tbl`, `data.frame`) with 120
rows and 11 columns.
@@ -219,9 +219,9 @@ unlike any other info from this package.** See
``` r
antimicrobials
#> # A tibble: 504 × 14
#> # A tibble: 505 × 14
#> ab cid name group atc atc_group1 atc_group2 abbreviations synonyms
#> <ab> <dbl> <chr> <lis> <lis> <chr> <chr> <list> <named >
#> <ab> <dbl> <chr> <lis> <lis> <chr> <chr> <list> <list>
#> 1 AMA 4649 4-ami… <chr> <chr> Drugs for… Aminosali… <chr [1]> <chr>
#> 2 ACM 6450012 Acety… <chr> <chr> NA NA <chr [1]> <chr>
#> 3 ASP 49787020 Acety… <chr> <chr> NA NA <chr [1]> <chr>
@@ -232,7 +232,7 @@ antimicrobials
#> 8 AMX 33613 Amoxi… <chr> <chr> Beta-lact… Penicilli… <chr [4]> <chr>
#> 9 AMC 23665637 Amoxi… <chr> <chr> Beta-lact… Combinati… <chr [6]> <chr>
#> 10 AXS 465441 Amoxi… <chr> <chr> NA NA <chr [1]> <chr>
#> # ℹ 494 more rows
#> # ℹ 495 more rows
#> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>,
#> # iv_units <chr>, loinc <list>
antivirals

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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-08 <span style="color: #949494;">19:43:01</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-08 <span style="color: #949494;">19:43:01</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-08 <span style="color: #949494;">19:43:02</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-08 <span style="color: #949494;">19:43:02</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-09 <span style="color: #949494;">11:05:00</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-09 <span style="color: #949494;">11:05:01</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

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@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-03-08 19:43:01 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-08 19:43:01 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-08 19:43:02 1 DISK tobra Escherich… human 16
#> 4 2026-03-08 19:43:02 1 DISK genta Escherich… human 18
#> 1 2026-03-09 11:05:00 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-09 11:05:00 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-09 11:05:00 1 DISK tobra Escherich… human 16
#> 4 2026-03-09 11:05:01 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

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2
reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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2
reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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5
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9032</small>
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@@ -147,7 +147,8 @@
<span><span class="co">#&gt;</span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<p>These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminocoumarins<br>(clorobiocin, novobiocin, and penicillin/novobiocin)</p></li>
<li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)</p></li>
<li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>

5
reference/custom_eucast_rules.md
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@@ -135,9 +135,12 @@ TZP (piperacillin/tazobactam) is "R":
#> 1. If TZP is "R" then set to "R":
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
These 42 antimicrobial groups are allowed in the rules
These 43 antimicrobial groups are allowed in the rules
(case-insensitive) and can be used in any combination:
- aminocoumarins
(clorobiocin, novobiocin, and penicillin/novobiocin)
- aminoglycosides
(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,

5
reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -144,7 +144,7 @@
<span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins_2nd</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #2"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">glycopeptides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span> <span class="op">~</span> <span class="st">"My MDRO #3"</span></span>
<span><span class="op">)</span></span></code></pre><p></p></div>
<p>All 42 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
<p>All 43 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
<li><p><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, and ampicillin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <br> amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole</p></li>
<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
@@ -159,6 +159,7 @@
<li><p><code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> can select: <br> ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam</p></li>
<li><p><code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> can select: <br> besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> can select: <br> avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">ionophores()</a></code> can select: <br> lasalocid, monensin sodium, narasin, nystatin, and salinomycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> can select: <br> cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test</p></li>
<li><p><code><a href="antimicrobial_selectors.html">lincosamides()</a></code> can select: <br> clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin</p></li>
<li><p><code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> can select: <br> dalbavancin, oritavancin, and telavancin</p></li>

6
reference/custom_mdro_guideline.md
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@@ -126,7 +126,7 @@ antimicrobial group:
all(glycopeptides() == "R") ~ "My MDRO #3"
)
All 42 antimicrobial selectors are supported for use in the rules:
All 43 antimicrobial selectors are supported for use in the rules:
- [`aminoglycosides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
@@ -312,6 +312,10 @@ All 42 antimicrobial selectors are supported for use in the rules:
ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
vancomycin, vancomycin-macromethod, and zorbamycin
- [`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
lasalocid, monensin sodium, narasin, nystatin, and salinomycin
- [`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
can select:
cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and

2
reference/dosage.html
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@@ -7,7 +7,7 @@
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reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/first_isolate.html
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@@ -9,7 +9,7 @@
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reference/g.test.html
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
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6
reference/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -263,7 +263,7 @@
<dt>
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">peptides()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
<code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">ionophores()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">peptides()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">phosphonics()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">spiropyrimidinetriones()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">sulfonamides()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>
</dt>
<dd>Antimicrobial Selectors</dd>
@@ -393,7 +393,7 @@
<code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>
</dt>
<dd>Data Sets with 624 Antimicrobial Drugs</dd>
<dd>Data Sets with 625 Antimicrobial Drugs</dd>
<dt>

3
reference/index.md
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@@ -252,6 +252,7 @@ or determine multi-drug resistant microorganisms (MDRO,
[`cephalosporins_5th()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`fluoroquinolones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`glycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`ionophores()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`isoxazolylpenicillins()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`lincosamides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
[`lipoglycopeptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
@@ -393,7 +394,7 @@ information about how to work with functions in this package.
- [`antimicrobials`](https://amr-for-r.org/reference/antimicrobials.md)
[`antibiotics`](https://amr-for-r.org/reference/antimicrobials.md)
[`antivirals`](https://amr-for-r.org/reference/antimicrobials.md) :
Data Sets with 624 Antimicrobial Drugs
Data Sets with 625 Antimicrobial Drugs
- [`clinical_breakpoints`](https://amr-for-r.org/reference/clinical_breakpoints.md)
: Data Set with Clinical Breakpoints for SIR Interpretation
- [`example_isolates`](https://amr-for-r.org/reference/example_isolates.md)

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reference/interpretive_rules.html
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@@ -13,7 +13,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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reference/intrinsic_resistant.html
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reference/join.html
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reference/key_antimicrobials.html
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reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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reference/mo_property.html
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reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/resistance_predict.html
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