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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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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-options.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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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, Chinese, Czech, Danish, Dutch, Finnish,
<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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">

17
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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
@ -172,7 +172,7 @@
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Amoxicillin"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA04" "QG51AA03" "QJ01CA04"</span>
<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 33613</span>
<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span></span></span>
@ -265,7 +265,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $atc</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA04" "QG51AA03" "QJ01CA04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $atc_group1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactam antibacterials, penicillins"</span>
@ -326,7 +326,7 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span></span></span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA01" "S01AA19"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CA01" "QJ01CA01" "QJ51CA01" "QS01AA19" "S01AA19" </span>
<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Beta-lactams/penicillins"</span>
<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span></span></span>
@ -343,13 +343,13 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># use set_ab_names() for renaming columns</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
@ -418,6 +418,7 @@
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">set_ab_names()</span>: no atc found for column(s): "SXT" and "IPM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" "gender" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "ward" "mo" "PEN" "OXA" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] "FLC" "AMX" "AMC" "AMP" </span>

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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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 25 25.83288 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.24932 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.40000 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.16438 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.49315 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.20548 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.19178 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.30137 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.67397 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.25753 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.83562 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.25205 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.40274 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.16712 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.49589 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.20822 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.19452 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.30411 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.67671 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.26027 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>

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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/antibiogram.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</small>
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2
reference/antimicrobial_selectors.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">

10
reference/antimicrobials.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
@ -87,7 +87,7 @@
<ul><li><p><code>av</code><br> Antiviral ID as used in this package (such as <code>ACI</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em> Combinations are codes that contain a <code>+</code> to indicate this, such as <code>ATA+COBI</code> for atazanavir/cobicistat.</p></li>
<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO. <em><strong>This is a unique identifier.</strong></em></p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, see <em>Details</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>
<li><p><code>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
@ -109,8 +109,10 @@
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and consequently only available where a CID is available.</p>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>. Do note that ATC codes are not unique. For example, J01CR02 is officially the ATC code for "amoxicillin and beta-lactamase inhibitor". Consequently, these two items from the antimicrobials data set both return <code>"J01CR02"</code>:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amoxicillin/clavulanic acid"</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amoxicillin/sulbactam"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and are consequently only available where a CID is available.</p>
</div>
<div class="section level2">
<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>

13
reference/as.ab.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
@ -164,13 +164,13 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span> <span class="co"># small spelling error</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span> <span class="co"># or a bit more severe</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span> <span class="co"># and even this works</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01DD04" "QJ01DD04"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># use ab_* functions to get a specific properties (see ?ab_property);</span></span></span>
<span class="r-in"><span><span class="co"># they use as.ab() internally:</span></span></span>
@ -185,6 +185,7 @@
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">set_ab_names()</span>: no atc found for column(s): "SXT" and "IPM"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
@ -202,7 +203,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 37 more variables: J01CA04 &lt;sir&gt;, J01CR02 &lt;sir&gt;, J01CA01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01CR05 &lt;sir&gt;, J01DB04 &lt;sir&gt;, J01DE01 &lt;sir&gt;, J01DC02 &lt;sir&gt;, J01DC01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01DD01 &lt;sir&gt;, J01DD02 &lt;sir&gt;, J01DD04 &lt;sir&gt;, J01GB03 &lt;sir&gt;, J01GB01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01GB06 &lt;sir&gt;, J01GB04 &lt;sir&gt;, J01EA01 &lt;sir&gt;, J01EE01 &lt;sir&gt;, J01XE01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01GB06 &lt;sir&gt;, J01GB04 &lt;sir&gt;, J01EA01 &lt;sir&gt;, SXT &lt;sir&gt;, J01XE01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01XX01 &lt;sir&gt;, J01XX08 &lt;sir&gt;, J01MA02 &lt;sir&gt;, J01MA14 &lt;sir&gt;, J01XA01 &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># J01XA02 &lt;sir&gt;, J01AA07 &lt;sir&gt;, J01AA12 &lt;sir&gt;, J01AA02 &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>

2
reference/as.av.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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/as.disk.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/as.mic.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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/as.mo.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">

157
reference/as.sir.html
View File

@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
@ -180,7 +180,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s to <code>"R"</code> only if the R breakpoint is missing. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s in these cases to <code>"R"</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
@ -212,7 +212,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> &lt; 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the most efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> &lt; 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
@ -353,7 +353,8 @@ 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;"># FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
@ -375,94 +376,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMC AMP TZP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CZO FEP CXM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FOX CTX CAZ </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CRO GEN TOB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> AMK KAN TMP </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SXT NIT FOS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> LNZ CIP MFX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> VAN TEC TCY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> TGC DOX ERY </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CLI AZM IPM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> MEM MTR CHL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> COL MUP RIF </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class:sir Class:sir Class:sir </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># example data sets, with combined MIC values and disk zones</span></span></span>
<span class="r-in"><span><span class="co"># create some example data sets, with combined MIC values and disk zones</span></span></span>
<span class="r-in"><span><span class="va">df_wide</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
<span class="r-in"><span> amoxicillin <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
@ -478,6 +393,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> disks <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"EUCAST 2021"</span>, <span class="st">"EUCAST 2022"</span>, <span class="st">"EUCAST 2023"</span>, <span class="st">"EUCAST 2024"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># and clean previous SIR interpretation logs</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># most basic application:</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
@ -486,23 +406,13 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14 × 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> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pn… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escheric… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escheric… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC amoxicillin Escheric… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC cipro Escheric… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK tobra Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK genta Escheric… human 18 </span>
<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> 2025-05-01 <span style="color: #949494;">09:53:45</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> 2025-05-01 <span style="color: #949494;">09:53:45</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> 2025-05-01 <span style="color: #949494;">09:53:45</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> 2025-05-01 <span style="color: #949494;">09:53:45</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>
@ -675,34 +585,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 114 × 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> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_P… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 104 more rows</span></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>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># using parallel computing, which is available in base R</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli S I S S R</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># for single values</span></span></span>
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
@ -741,6 +623,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 3 4 5 NA</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 2 3 NA NA</span>
@ -757,7 +640,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is_sir_eligible</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be:</span></span></span>
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be the more impractical:</span></span></span>
<span class="r-in"><span> <span class="co"># example_isolates %&gt;%</span></span></span>
<span class="r-in"><span> <span class="co"># mutate(across(where(is_sir_eligible), as.sir))</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>

8
reference/atc_online.html
View File

@ -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="">2.1.1.9266</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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">
@ -135,6 +135,12 @@
<span class="r-in"><span> <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required namespace: rvest</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QG51AA03. Please</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> check</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&amp;showdescription=no.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QJ01CA04. Please</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> check</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&amp;showdescription=no.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [2] "ANTIBACTERIALS FOR SYSTEMIC USE" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>

2
reference/av_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="">2.1.1.9266</small>
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reference/av_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/availability.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="">2.1.1.9266</small>
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6
reference/bug_drug_combinations.html
View File

@ -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="">2.1.1.9266</small>
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@ -174,7 +174,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0 0 0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Use 'format()' on this result to get a publishable/printable format.</span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 37 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span>
<span class="r-out co"><span class="r-pr">#&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 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> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
@ -187,7 +187,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Fluc… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 29 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 27 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: `P. mirabilis` &lt;chr&gt;, `S. aureus` &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `S. epidermidis` &lt;chr&gt;, `S. hominis` &lt;chr&gt;, `S. pneumoniae` &lt;chr&gt;</span></span>
<span class="r-in"><span></span></span>

2
reference/clinical_breakpoints.html
View File

@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
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reference/dosage.html
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@ -7,7 +7,7 @@
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reference/eucast_rules.html
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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 @@
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reference/first_isolate.html
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@ -9,7 +9,7 @@
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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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reference/index.html
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@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
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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_property.html
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@ -7,7 +7,7 @@
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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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@ -7,7 +7,7 @@
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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/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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reference/resistance_predict.html
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@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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