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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</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">
@ -90,7 +90,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 13 February 2025.</p>
generated on 14 February 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -146,21 +146,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-02-13</td>
<td align="center">2025-02-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-02-13</td>
<td align="center">2025-02-14</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-02-13</td>
<td align="center">2025-02-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -697,15 +697,15 @@ previously mentioned antibiotic class selectors:</p>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="16%">
<col width="14%">
<col width="13%">
<col width="14%">
<col width="14%">
<col width="10%">
<col width="14%">
<col width="13%">
<col width="14%">
</colgroup>
<thead><tr class="header">
<th align="left">Pathogen</th>
@ -719,93 +719,93 @@ previously mentioned antibiotic class selectors:</p>
<tbody>
<tr class="odd">
<td align="left">CoNS</td>
<td align="left">0% (0/43)</td>
<td align="left">86% (267/309)</td>
<td align="left">52% (25/48)</td>
<td align="left">0% (0/43)</td>
<td align="left">52% (25/48)</td>
<td align="left">22% (12/55)</td>
<td align="left">0% (0-8%)</td>
<td align="left">86% (82-90%)</td>
<td align="left">52% (37-67%)</td>
<td align="left">0% (0-8%)</td>
<td align="left">52% (37-67%)</td>
<td align="left">22% (12-35%)</td>
</tr>
<tr class="even">
<td align="left"><em>E. coli</em></td>
<td align="left">100% (171/171)</td>
<td align="left">98% (451/460)</td>
<td align="left">100% (422/422)</td>
<td align="left">100% (98-100%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">100% (99-100%)</td>
<td align="left"></td>
<td align="left">100% (418/418)</td>
<td align="left">97% (450/462)</td>
<td align="left">100% (99-100%)</td>
<td align="left">97% (96-99%)</td>
</tr>
<tr class="odd">
<td align="left"><em>E. faecalis</em></td>
<td align="left">0% (0/39)</td>
<td align="left">0% (0/39)</td>
<td align="left">100% (38/38)</td>
<td align="left">0% (0/39)</td>
<td align="left">0% (0-9%)</td>
<td align="left">0% (0-9%)</td>
<td align="left">100% (91-100%)</td>
<td align="left">0% (0-9%)</td>
<td align="left"></td>
<td align="left">0% (0/39)</td>
<td align="left">0% (0-9%)</td>
</tr>
<tr class="even">
<td align="left"><em>K. pneumoniae</em></td>
<td align="left"></td>
<td align="left">90% (52/58)</td>
<td align="left">100% (51/51)</td>
<td align="left">90% (79-96%)</td>
<td align="left">100% (93-100%)</td>
<td align="left"></td>
<td align="left">100% (53/53)</td>
<td align="left">90% (52/58)</td>
<td align="left">100% (93-100%)</td>
<td align="left">90% (79-96%)</td>
</tr>
<tr class="odd">
<td align="left"><em>P. aeruginosa</em></td>
<td align="left"></td>
<td align="left">100% (30/30)</td>
<td align="left">100% (88-100%)</td>
<td align="left"></td>
<td align="left">0% (0/30)</td>
<td align="left">0% (0-12%)</td>
<td align="left"></td>
<td align="left">100% (30/30)</td>
<td align="left">100% (88-100%)</td>
</tr>
<tr class="even">
<td align="left"><em>P. mirabilis</em></td>
<td align="left"></td>
<td align="left">94% (32/34)</td>
<td align="left">94% (30/32)</td>
<td align="left">94% (80-99%)</td>
<td align="left">94% (79-99%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left">94% (32/34)</td>
<td align="left">94% (80-99%)</td>
</tr>
<tr class="odd">
<td align="left"><em>S. aureus</em></td>
<td align="left"></td>
<td align="left">99% (231/233)</td>
<td align="left">99% (97-100%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">98% (84/86)</td>
<td align="left">98% (92-100%)</td>
</tr>
<tr class="even">
<td align="left"><em>S. epidermidis</em></td>
<td align="left">0% (0/44)</td>
<td align="left">79% (128/163)</td>
<td align="left">0% (0-8%)</td>
<td align="left">79% (71-85%)</td>
<td align="left"></td>
<td align="left">0% (0/44)</td>
<td align="left">0% (0-8%)</td>
<td align="left"></td>
<td align="left">51% (45/89)</td>
<td align="left">51% (40-61%)</td>
</tr>
<tr class="odd">
<td align="left"><em>S. hominis</em></td>
<td align="left"></td>
<td align="left">92% (74/80)</td>
<td align="left">92% (84-97%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">85% (53/62)</td>
<td align="left">85% (74-93%)</td>
</tr>
<tr class="even">
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">0% (0/117)</td>
<td align="left">0% (0/117)</td>
<td align="left">0% (0-3%)</td>
<td align="left">0% (0-3%)</td>
<td align="left"></td>
<td align="left">0% (0/117)</td>
<td align="left">0% (0-3%)</td>
<td align="left"></td>
<td align="left">0% (0/117)</td>
<td align="left">0% (0-3%)</td>
</tr>
</tbody>
</table>
@ -827,13 +827,6 @@ language to be Spanish using the <code>language</code> argument:</p>
<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="20%">
<col width="20%">
<col width="22%">
<col width="16%">
<col width="20%">
</colgroup>
<thead><tr class="header">
<th align="left">Patógeno</th>
<th align="left">Amikacina</th>
@ -844,17 +837,17 @@ language to be Spanish using the <code>language</code> argument:</p>
<tbody>
<tr class="odd">
<td align="left">Gram negativo</td>
<td align="left">98% (251/256)</td>
<td align="left">96% (659/684)</td>
<td align="left">0% (0/35)</td>
<td align="left">96% (658/686)</td>
<td align="left">98% (96-99%)</td>
<td align="left">96% (95-98%)</td>
<td align="left">0% (0-10%)</td>
<td align="left">96% (94-97%)</td>
</tr>
<tr class="even">
<td align="left">Gram positivo</td>
<td align="left">0% (0/436)</td>
<td align="left">63% (740/1170)</td>
<td align="left">0% (0/436)</td>
<td align="left">34% (228/665)</td>
<td align="left">0% (0-1%)</td>
<td align="left">63% (60-66%)</td>
<td align="left">0% (0-1%)</td>
<td align="left">34% (31-38%)</td>
</tr>
</tbody>
</table>
@ -883,57 +876,57 @@ a plus <code>+</code> character like this:</p>
<tbody>
<tr class="odd">
<td align="left">CoNS</td>
<td align="left">30% (10/33)</td>
<td align="left">97% (267/274)</td>
<td align="left">30% (16-49%)</td>
<td align="left">97% (95-99%)</td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left"><em>E. coli</em></td>
<td align="left">94% (393/416)</td>
<td align="left">100% (457/459)</td>
<td align="left">99% (455/461)</td>
<td align="left">94% (92-96%)</td>
<td align="left">100% (98-100%)</td>
<td align="left">99% (97-100%)</td>
</tr>
<tr class="odd">
<td align="left"><em>K. pneumoniae</em></td>
<td align="left">89% (47/53)</td>
<td align="left">93% (54/58)</td>
<td align="left">93% (54/58)</td>
<td align="left">89% (77-96%)</td>
<td align="left">93% (83-98%)</td>
<td align="left">93% (83-98%)</td>
</tr>
<tr class="even">
<td align="left"><em>P. aeruginosa</em></td>
<td align="left"></td>
<td align="left">100% (30/30)</td>
<td align="left">100% (30/30)</td>
<td align="left">100% (88-100%)</td>
<td align="left">100% (88-100%)</td>
</tr>
<tr class="odd">
<td align="left"><em>P. mirabilis</em></td>
<td align="left"></td>
<td align="left">100% (34/34)</td>
<td align="left">100% (34/34)</td>
<td align="left">100% (90-100%)</td>
<td align="left">100% (90-100%)</td>
</tr>
<tr class="even">
<td align="left"><em>S. aureus</em></td>
<td align="left"></td>
<td align="left">100% (231/231)</td>
<td align="left">100% (91/91)</td>
<td align="left">100% (98-100%)</td>
<td align="left">100% (96-100%)</td>
</tr>
<tr class="odd">
<td align="left"><em>S. epidermidis</em></td>
<td align="left"></td>
<td align="left">100% (128/128)</td>
<td align="left">100% (46/46)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (92-100%)</td>
</tr>
<tr class="even">
<td align="left"><em>S. hominis</em></td>
<td align="left"></td>
<td align="left">100% (74/74)</td>
<td align="left">100% (53/53)</td>
<td align="left">100% (95-100%)</td>
<td align="left">100% (93-100%)</td>
</tr>
<tr class="odd">
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">100% (112/112)</td>
<td align="left">100% (112/112)</td>
<td align="left">100% (112/112)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (97-100%)</td>
<td align="left">100% (97-100%)</td>
</tr>
</tbody>
</table>
@ -958,7 +951,7 @@ argument must be used. This can be any column in the data, or e.g. an
<col width="12%">
<col width="12%">
<col width="12%">
<col width="8%">
<col width="9%">
<col width="12%">
<col width="12%">
</colgroup>
@ -977,17 +970,17 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Clinical</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">89% (183/205)</td>
<td align="left">57% (20/35)</td>
<td align="left">89% (84-93%)</td>
<td align="left">57% (39-74%)</td>
<td align="left"></td>
<td align="left">57% (20/35)</td>
<td align="left">26% (8/31)</td>
<td align="left">57% (39-74%)</td>
<td align="left">26% (12-45%)</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">79% (58/73)</td>
<td align="left">79% (68-88%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -997,7 +990,7 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Outpatient</td>
<td align="left">CoNS</td>
<td align="left"></td>
<td align="left">84% (26/31)</td>
<td align="left">84% (66-95%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -1006,58 +999,58 @@ argument must be used. This can be any column in the data, or e.g. an
<tr class="even">
<td align="left">Clinical</td>
<td align="left"><em>E. coli</em></td>
<td align="left">100% (104/104)</td>
<td align="left">98% (291/297)</td>
<td align="left">100% (266/266)</td>
<td align="left">100% (97-100%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">100% (99-100%)</td>
<td align="left"></td>
<td align="left">100% (276/276)</td>
<td align="left">98% (293/299)</td>
<td align="left">100% (99-100%)</td>
<td align="left">98% (96-99%)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left"><em>E. coli</em></td>
<td align="left">100% (52/52)</td>
<td align="left">99% (135/137)</td>
<td align="left">100% (133/133)</td>
<td align="left">100% (93-100%)</td>
<td align="left">99% (95-100%)</td>
<td align="left">100% (97-100%)</td>
<td align="left"></td>
<td align="left">100% (118/118)</td>
<td align="left">96% (132/137)</td>
<td align="left">100% (97-100%)</td>
<td align="left">96% (92-99%)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left"><em>K. pneumoniae</em></td>
<td align="left"></td>
<td align="left">92% (47/51)</td>
<td align="left">100% (44/44)</td>
<td align="left">92% (81-98%)</td>
<td align="left">100% (92-100%)</td>
<td align="left"></td>
<td align="left">100% (46/46)</td>
<td align="left">92% (47/51)</td>
<td align="left">100% (92-100%)</td>
<td align="left">92% (81-98%)</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left"><em>P. mirabilis</em></td>
<td align="left"></td>
<td align="left">100% (30/30)</td>
<td align="left">100% (88-100%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">100% (30/30)</td>
<td align="left">100% (88-100%)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left"><em>S. aureus</em></td>
<td align="left"></td>
<td align="left">99% (148/150)</td>
<td align="left">99% (95-100%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">97% (61/63)</td>
<td align="left">97% (89-100%)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left"><em>S. aureus</em></td>
<td align="left"></td>
<td align="left">100% (66/66)</td>
<td align="left">100% (95-100%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
@ -1067,51 +1060,51 @@ argument must be used. This can be any column in the data, or e.g. an
<td align="left">Clinical</td>
<td align="left"><em>S. epidermidis</em></td>
<td align="left"></td>
<td align="left">82% (65/79)</td>
<td align="left">82% (72-90%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">55% (24/44)</td>
<td align="left">55% (39-70%)</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left"><em>S. epidermidis</em></td>
<td align="left"></td>
<td align="left">72% (54/75)</td>
<td align="left">72% (60-82%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">41% (17/41)</td>
<td align="left">41% (26-58%)</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left"><em>S. hominis</em></td>
<td align="left"></td>
<td align="left">96% (43/45)</td>
<td align="left">96% (85-99%)</td>
<td align="left"></td>
<td align="left"></td>
<td align="left"></td>
<td align="left">94% (29/31)</td>
<td align="left">94% (79-99%)</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">0% (0/78)</td>
<td align="left">0% (0/78)</td>
<td align="left">0% (0-5%)</td>
<td align="left">0% (0-5%)</td>
<td align="left"></td>
<td align="left">0% (0/78)</td>
<td align="left">0% (0-5%)</td>
<td align="left"></td>
<td align="left">0% (0/78)</td>
<td align="left">0% (0-5%)</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">0% (0/30)</td>
<td align="left">0% (0/30)</td>
<td align="left">0% (0-12%)</td>
<td align="left">0% (0-12%)</td>
<td align="left"></td>
<td align="left">0% (0/30)</td>
<td align="left">0% (0-12%)</td>
<td align="left"></td>
<td align="left">0% (0/30)</td>
<td align="left">0% (0-12%)</td>
</tr>
</tbody>
</table>
@ -1157,34 +1150,34 @@ just gives an idea of how a WISCA can be created:</p>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-negative</td>
<td align="left">76% (216/285)</td>
<td align="left">95% (270/284)</td>
<td align="left">89% (231/261)</td>
<td align="left">99% (270/274)</td>
<td align="left">76% (70-81%)</td>
<td align="left">95% (92-97%)</td>
<td align="left">89% (84-92%)</td>
<td align="left">99% (96-100%)</td>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-negative</td>
<td align="left">76% (336/441)</td>
<td align="left">98% (432/442)</td>
<td align="left">88% (334/380)</td>
<td align="left">98% (409/419)</td>
<td align="left">76% (72-80%)</td>
<td align="left">98% (96-99%)</td>
<td align="left">88% (84-91%)</td>
<td align="left">98% (96-99%)</td>
</tr>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-positive</td>
<td align="left">76% (310/406)</td>
<td align="left">89% (347/392)</td>
<td align="left">81% (100/123)</td>
<td align="left">95% (184/193)</td>
<td align="left">76% (72-80%)</td>
<td align="left">89% (85-92%)</td>
<td align="left">81% (73-88%)</td>
<td align="left">95% (91-98%)</td>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-positive</td>
<td align="left">76% (556/732)</td>
<td align="left">89% (617/695)</td>
<td align="left">88% (196/222)</td>
<td align="left">95% (340/357)</td>
<td align="left">76% (73-79%)</td>
<td align="left">89% (86-91%)</td>
<td align="left">88% (83-92%)</td>
<td align="left">95% (92-97%)</td>
</tr>
</tbody>
</table>

2
articles/AMR_for_Python.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</small>
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6
articles/AMR_with_tidymodels.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</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">
@ -130,7 +130,7 @@ package.</p>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span> <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span>
<span><span class="co">#&gt; ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.2.0 ──</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.7 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.1.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.3.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dplyr </span> 1.1.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.2.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">ggplot2 </span> 3.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span></span>
<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.7 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.2.1</span></span>
@ -142,7 +142,7 @@ package.</p>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span> masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
<span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span> masks <span style="color: #0000BB;">stats</span>::step()</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Learn how to get started at <span style="color: #00BB00;">https://www.tidymodels.org/start/</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Dig deeper into tidy modeling with R at <span style="color: #00BB00;">https://www.tmwr.org</span></span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span> <span class="co"># For AMR data analysis</span></span>
<span></span>
<span><span class="co"># Load the example_isolates dataset</span></span>

2
articles/EUCAST.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</small>
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2
articles/MDR.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</small>
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2
articles/PCA.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</small>
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5
articles/WHONET.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</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">
@ -310,9 +310,6 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</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="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</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="fu"><a href="../reference/ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Warning: Using <span style="background-color: #EEEEEE;">scale_sir_colours()</span> for the <span style="background-color: #EEEEEE;">fill</span> aesthetic has been superseded by</span></span>
<span><span class="co">#&gt; <span style="background-color: #EEEEEE;">scale_fill_sir()</span>, please use that instead. This warning will be shown</span></span>
<span><span class="co">#&gt; once per session.</span></span></code></pre>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

4
articles/datasets.html
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@ -31,7 +31,7 @@
<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="">2.1.1.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9147</small>
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@ -79,7 +79,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">13 February 2025</h4>
<h4 data-toc-skip class="date">14 February 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

2
articles/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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articles/resistance_predict.html
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@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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articles/welcome_to_AMR.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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