P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-04-27 18:43:47 +02:00
Code Releases Activity

Built site for AMR@2.1.1.9147: d94efb0

Browse Source
This commit is contained in:
github-actions 2025-02-14 13:23:46 +00:00
parent 97df961c58
commit 6d225ab56e
104 changed files with 489 additions and 503 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
404.html
View File

@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/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">

2
LICENSE-text.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="">2.1.1.9146</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">

269
articles/AMR.html
View File

@ -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
View File

@ -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">

6
articles/AMR_with_tidymodels.html
View File

@ -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
View File

@ -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">

2
articles/MDR.html
View File

@ -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">

2
articles/PCA.html
View File

@ -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">

5
articles/WHONET.html
View File

@ -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
View File

@ -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">
@ -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
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="">2.1.1.9146</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">

2
articles/resistance_predict.html
View File

@ -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">

2
articles/welcome_to_AMR.html
View File

@ -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">

2
authors.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="">2.1.1.9146</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">

2
index.html
View File

@ -34,7 +34,7 @@
<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">

17
news/index.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="">2.1.1.9146</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">
@ -48,18 +48,18 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9146" id="amr-2119146">AMR 2.1.1.9146<a class="anchor" aria-label="anchor" href="#amr-2119146"></a></h2>
<h2 class="pkg-version" data-toc-text="2.1.1.9147" id="amr-2119147">AMR 2.1.1.9147<a class="anchor" aria-label="anchor" href="#amr-2119147"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9146">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9146"></a></h5>
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9147">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9147"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div>
<div class="section level3">
<h3 id="breaking-2-1-1-9146">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9146"></a></h3>
<h3 id="breaking-2-1-1-9147">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9147"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents two years ago</li>
</ul></div>
<div class="section level3">
<h3 id="new-2-1-1-9146">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9146"></a></h3>
<h3 id="new-2-1-1-9147">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9147"></a></h3>
<ul><li>
<strong>One Health implementation</strong>
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -110,11 +110,12 @@
</ul></li>
</ul></div>
<div class="section level3">
<h3 id="changed-2-1-1-9146">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9146"></a></h3>
<h3 id="changed-2-1-1-9147">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9147"></a></h3>
<ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
<li>To get quantitative values, <code><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
<li>Fix for <code>conserve_capped_values</code>, which now again works as expected: in MIC values, <code>&lt;x</code> will always be S, <code>&gt;x</code> will always be R</li>
</ul></li>
<li>
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> function
@ -178,7 +179,7 @@
<li>Added console colours support of <code>sir</code> class for Positron</li>
</ul></div>
<div class="section level3">
<h3 id="other-2-1-1-9146">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9146"></a></h3>
<h3 id="other-2-1-1-9147">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9147"></a></h3>
<ul><li>Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way</li>
<li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
<li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
@ -186,7 +187,7 @@
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
</ul></div>
<div class="section level3">
<h3 id="older-versions-2-1-1-9146">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9146"></a></h3>
<h3 id="older-versions-2-1-1-9147">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9147"></a></h3>
<p>This changelog only contains changes from AMR v3.0 (February 2025) and later.</p>
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>

2
pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
last_built: 2025-02-13T18:53Z
last_built: 2025-02-14T13:20Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
reference/AMR-deprecated.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="">2.1.1.9146</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">

2
reference/AMR-options.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="">2.1.1.9146</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">

2
reference/AMR.html
View File

@ -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="">2.1.1.9146</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">

2
reference/WHOCC.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="">2.1.1.9146</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">

2
reference/WHONET.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="">2.1.1.9146</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">

2
reference/ab_from_text.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="">2.1.1.9146</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">

2
reference/ab_property.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="">2.1.1.9146</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">

2
reference/add_custom_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="">2.1.1.9146</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">

2
reference/add_custom_microorganisms.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="">2.1.1.9146</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">

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="">2.1.1.9146</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">
@ -111,16 +111,16 @@
<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 1965-12-05 59 59.19178 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.95616 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.28493 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.99726 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.98356 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.09315 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.46575 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.04932 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.66027 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.51233 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.19452 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.95890 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.28767 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.00000 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.98630 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.09589 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.46849 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.05205 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.66301 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.51507 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

5
reference/age_groups.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="">2.1.1.9146</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">
@ -146,9 +146,6 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<span class="r-in"><span> <span class="op">)</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 package: ggplot2</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>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 class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">scale_fill_sir()</span>, please use that instead. This warning will be shown</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> once per session.</span>
<span class="r-plt img"><img src="age_groups-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

BIN
reference/antibiogram-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 34 KiB

BIN
reference/antibiogram-3.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 31 KiB

After

Width:  |  Height:  |  Size: 29 KiB

216
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="">2.1.1.9146</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">
@ -60,18 +60,19 @@ Adhering to previously described approaches (see Source) and especially the Baye
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">x</span>, antibiotics <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>, mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>, syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">wisca</span>, <span class="fl">14</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> simulations <span class="op">=</span> <span class="fl">1000</span>, conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, wisca <span class="op">=</span> <span class="cn">FALSE</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antibiotics <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>, mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>, syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>, digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span><span class="fu">wisca</span><span class="op">(</span><span class="va">x</span>, antibiotics <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>, ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="cn">NULL</span>, add_total_n <span class="op">=</span> <span class="cn">FALSE</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> digits <span class="op">=</span> <span class="fl">1</span>,</span>
<span> formatting_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_antibiogram_formatting_type"</span>, <span class="fl">14</span><span class="op">)</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</span>, sep <span class="op">=</span> <span class="st">" + "</span>, simulations <span class="op">=</span> <span class="fl">1000</span>,</span>
<span> conf_interval <span class="op">=</span> <span class="fl">0.95</span>, interval_side <span class="op">=</span> <span class="st">"two-tailed"</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">retrieve_wisca_parameters</span><span class="op">(</span><span class="va">wisca_model</span>, <span class="va">...</span><span class="op">)</span></span>
@ -121,7 +122,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-add-total-n">add_total_n<a class="anchor" aria-label="anchor" href="#arg-add-total-n"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (default is <code>TRUE</code>). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether <code>n_tested</code> available numbers per pathogen should be added to the table (default is <code>TRUE</code>). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when <code>wisca = TRUE</code>; in that case, use <code>retrieve_wisca_parameters()</code> to get the parameters used for WISCA.</p></dd>
<dt id="arg-only-all-tested">only_all_tested<a class="anchor" aria-label="anchor" href="#arg-only-all-tested"></a></dt>
@ -157,7 +158,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<dt id="arg-wisca">wisca<a class="anchor" aria-label="anchor" href="#arg-wisca"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is <code>FALSE</code>). This will use a Bayesian decision model to estimate regimen coverage probabilities using <a href="https://en.wikipedia.org/wiki/Monte_Carlo_method" class="external-link">Monte Carlo simulations</a>. Set <code>simulations</code> to adjust.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is <code>FALSE</code>). This will use a Bayesian decision model to estimate regimen coverage probabilities using <a href="https://en.wikipedia.org/wiki/Monte_Carlo_method" class="external-link">Monte Carlo simulations</a>. Set <code>simulations</code>, <code>conf_interval</code>, and <code>interval_side</code> to adjust.</p></dd>
<dt id="arg-simulations">simulations<a class="anchor" aria-label="anchor" href="#arg-simulations"></a></dt>
@ -205,7 +206,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<h3 id="formatting-type">Formatting Type<a class="anchor" aria-label="anchor" href="#formatting-type"></a></h3>
<p>The formatting of the 'cells' of the table can be set with the argument <code>formatting_type</code>. In these examples, <code>5</code> is the antimicrobial coverage (for WISCA: <code>4-6</code> indicates the confidence level), <code>15</code> the numerator, and <code>300</code> the denominator:</p><ol><li><p>5</p></li>
<p>The formatting of the 'cells' of the table can be set with the argument <code>formatting_type</code>. In these examples, <code>5</code> is the antimicrobial coverage (<code>4-6</code> indicates the confidence level), <code>15</code> the number of susceptible isolates, and <code>300</code> the number of tested (i.e., available) isolates:</p><ol><li><p>5</p></li>
<li><p>15</p></li>
<li><p>300</p></li>
<li><p>15/300</p></li>
@ -214,12 +215,11 @@ Adhering to previously described approaches (see Source) and especially the Baye
<li><p>5 (N=300)</p></li>
<li><p>5% (N=300)</p></li>
<li><p>5 (15/300)</p></li>
<li><p>5% (15/300) - <strong>default for non-WISCA</strong></p></li>
<li><p>5% (15/300)</p></li>
<li><p>5 (N=15/300)</p></li>
<li><p>5% (N=15/300)</p>
<p>Additional options for WISCA (using <code>antibiogram(..., wisca = TRUE)</code> or <code>wisca()</code>):</p></li>
<li><p>5% (N=15/300)</p></li>
<li><p>5 (4-6)</p></li>
<li><p>5% (4-6%) - <strong>default for WISCA</strong></p></li>
<li><p>5% (4-6%) - <strong>default</strong></p></li>
<li><p>5 (4-6,300)</p></li>
<li><p>5% (4-6%,300)</p></li>
<li><p>5 (4-6,N=300)</p></li>
@ -228,7 +228,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<li><p>5% (4-6%,15/300)</p></li>
<li><p>5 (4-6,N=15/300)</p></li>
<li><p>5% (4-6%,N=15/300)</p></li>
</ol><p>The default is <code>14</code> for WISCA and <code>10</code> for non-WISCA, which can be set globally with the package option <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>. Do note that for WISCA, the numerator and denominator are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.</p>
</ol><p>The default is <code>14</code>, which can be set globally with the package option <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>. Do note that for WISCA, the total numbers of tested and susceptible isolates are less useful to report, since these are included in the Bayesian model and apparent from the susceptibility and its confidence level.</p>
<p>Set <code>digits</code> (defaults to <code>0</code>) to alter the rounding of the susceptibility percentages.</p>
</div>
@ -238,8 +238,8 @@ Adhering to previously described approaches (see Source) and especially the Baye
<p>There are various antibiogram types, as summarised by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
), and they are all supported by <code>antibiogram()</code>.</p>
<p><strong>Use WISCA whenever possible</strong>, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki <em>et al.</em> (2020, <a href="https://doi.org/10.1001.jamanetworkopen.2019.21124" class="external-link">doi:10.1001.jamanetworkopen.2019.21124</a>
). See the section <em>Explaining WISCA</em> on this page.</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
<p>For clinical coverage estimations, <strong>use WISCA whenever possible</strong>, since it provides more precise coverage estimates by accounting for pathogen incidence and antimicrobial susceptibility, as has been shown by Bielicki <em>et al.</em> (2020, <a href="https://doi.org/10.1001.jamanetworkopen.2019.21124" class="external-link">doi:10.1001.jamanetworkopen.2019.21124</a>
). See the section <em>Explaining WISCA</em> on this page. Do note that WISCA is pathogen-agnostic, meaning that the outcome is not stratied by pathogen, but rather by syndrome.</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
<p>Code example:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
@ -285,19 +285,21 @@ Adhering to previously described approaches (see Source) and especially the Baye
<p>In clinical practice, antimicrobial coverage decisions evolve as more microbiological data becomes available. This theoretical stepped approach ensures empirical coverage can continuously assessed to improve patient outcomes:</p><ol><li><p><strong>Initial Empirical Therapy (Admission / Pre-Culture Data)</strong></p>
<p>At admission, no pathogen information is available.</p><ul><li><p>Action: broad-spectrum coverage is based on local resistance patterns and syndromic antibiograms.</p></li>
<p>At admission, no pathogen information is available.</p><ul><li><p>Action: broad-spectrum coverage is based on local resistance patterns and syndromic antibiograms. Using the pathogen-agnostic yet incidence-weighted WISCA is preferred.</p></li>
<li><p>Code example:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="va">selected_regimens</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="co"># all pathogens set to `NA`</span></span></code></pre><p></p></div></li>
<span> mo_transform <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="co"># all pathogens set to `NA`</span></span>
<span></span>
<span><span class="co"># preferred: use WISCA</span></span>
<span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="va">selected_regimens</span><span class="op">)</span></span></code></pre><p></p></div></li>
</ul></li>
<li><p><strong>Refinement with Gram Stain Results</strong></p>
<p>When a blood culture becomes positive, the Gram stain provides an initial and crucial first stratification (Gram-positive vs. Gram-negative).</p><ul><li><p>Action: narrow coverage based on Gram stain-specific resistance patterns.</p></li>
<li><p>Code example:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="va">selected_regimens</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span> <span class="co"># all pathogens set to Gram-pos/Gram-neg</span></span></code></pre><p></p></div></li>
</ul></li>
<li><p><strong>Definitive Therapy Based on Species Identification</strong></p>
@ -305,7 +307,6 @@ Adhering to previously described approaches (see Source) and especially the Baye
<li><p>Code example:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
<span> antibiotics <span class="op">=</span> <span class="va">selected_regimens</span>,</span>
<span> wisca <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"shortname"</span><span class="op">)</span> <span class="co"># all pathogens set to 'G. species', e.g., E. coli</span></span></code></pre><p></p></div></li>
</ul></li>
</ol><p>By structuring antibiograms around this stepped approach, clinicians can make data-driven adjustments at each stage, ensuring optimal empirical and targeted therapy while reducing unnecessary broad-spectrum antimicrobial use.</p>
@ -350,7 +351,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<p>WISCA, as outlined by Bielicki <em>et al.</em> (<a href="https://doi.org/10.1093/jac/dkv397" class="external-link">doi:10.1093/jac/dkv397</a>
), stands for Weighted-Incidence Syndromic Combination Antibiogram, which estimates the probability of adequate empirical antimicrobial regimen coverage for specific infection syndromes. This method leverages a Bayesian hierarchical logistic regression framework with random effects for pathogens and regimens, enabling robust estimates in the presence of sparse data.</p>
), stands for Weighted-Incidence Syndromic Combination Antibiogram, which estimates the probability of adequate empirical antimicrobial regimen coverage for specific infection syndromes. This method leverages a Bayesian decision model with random effects for pathogen incidence and susceptibility, enabling robust estimates in the presence of sparse data.</p>
<p>The Bayesian model assumes conjugate priors for parameter estimation. For example, the coverage probability \(\theta\) for a given antimicrobial regimen is modelled using a Beta distribution as a prior:</p>
<p>$$\theta \sim \text{Beta}(\alpha_0, \beta_0)$$</p>
<p>where \(\alpha_0\) and \(\beta_0\) represent prior successes and failures, respectively, informed by expert knowledge or weakly informative priors (e.g., \(\alpha_0 = 1, \beta_0 = 1\)). The likelihood function is constructed based on observed data, where the number of covered cases for a regimen follows a binomial distribution:</p>
@ -368,6 +369,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<p>Stratified results can be provided based on covariates such as age, sex, and clinical complexity (e.g., prior antimicrobial treatments or renal/urological comorbidities) using <code>dplyr</code>'s <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> as a pre-processing step before running <code>wisca()</code>. Posterior odds ratios (ORs) are derived to quantify the effect of these covariates on coverage probabilities:</p>
<p>$$\text{OR}_{\text{covariate}} = \frac{\exp(\beta_{\text{covariate}})}{\exp(\beta_0)}$$</p>
<p>By combining empirical data with prior knowledge, WISCA overcomes the limitations of traditional combination antibiograms, offering disease-specific, patient-stratified estimates with robust uncertainty quantification. This tool is invaluable for antimicrobial stewardship programs and empirical treatment guideline refinement.</p>
<p><strong>Note:</strong> WISCA never gives an output on the pathogen/species level, as all incidences and susceptibilities are already weighted for all species.</p>
</div>
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
@ -409,51 +411,49 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> CoNS 0% (0/43) 86% (267/… 52% (25… 0% (0/43) 52% (25/… 22% (12/5…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli 100% (171/… 98% (451/… 100% (4… <span style="color: #BB0000;">NA</span> 100% (41… 97% (450/…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis 0% (0/39) 0% (0/39) 100% (3… 0% (0/39) <span style="color: #BB0000;">NA</span> 0% (0/39) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae <span style="color: #BB0000;">NA</span> 90% (52/5… 100% (5… <span style="color: #BB0000;">NA</span> 100% (53… 90% (52/5…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa <span style="color: #BB0000;">NA</span> 100% (30/… <span style="color: #BB0000;">NA</span> 0% (0/30) <span style="color: #BB0000;">NA</span> 100% (30/…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis <span style="color: #BB0000;">NA</span> 94% (32/3… 94% (30… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94% (32/3…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus <span style="color: #BB0000;">NA</span> 99% (231/… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98% (84/8…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis 0% (0/44) 79% (128/… <span style="color: #BB0000;">NA</span> 0% (0/44) <span style="color: #BB0000;">NA</span> 51% (45/8…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis <span style="color: #BB0000;">NA</span> 92% (74/8… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85% (53/6…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae 0% (0/117) 0% (0/117) <span style="color: #BB0000;">NA</span> 0% (0/11… <span style="color: #BB0000;">NA</span> 0% (0/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS 0% (0-8%) 86% (82-9… 52% (37… 0% (0-8%) 52% (37-… 22% (12-3…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli 100% (98-1… 98% (96-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (99… 97% (96-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis 0% (0-9%) 0% (0-9%) 100% (9… 0% (0-9%) <span style="color: #BB0000;">NA</span> 0% (0-9%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae <span style="color: #BB0000;">NA</span> 90% (79-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (93… 90% (79-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa <span style="color: #BB0000;">NA</span> 100% (88-… <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> 100% (88-…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis <span style="color: #BB0000;">NA</span> 94% (80-9… 94% (79… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94% (80-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus <span style="color: #BB0000;">NA</span> 99% (97-1… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98% (92-1…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis 0% (0-8%) 79% (71-8… <span style="color: #BB0000;">NA</span> 0% (0-8%) <span style="color: #BB0000;">NA</span> 51% (40-6…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis <span style="color: #BB0000;">NA</span> 92% (84-9… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85% (74-9…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae 0% (0-3%) 0% (0-3%) <span style="color: #BB0000;">NA</span> 0% (0-3%) <span style="color: #BB0000;">NA</span> 0% (0-3%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Gram-negative 96% (658/686) 96% (659/684) 0% (0/35) 98% (251/256)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 34% (228/665) 63% (740/1170) 0% (0/436) 0% (0/436) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Gram-negative 96% (94-97%) 96% (95-98%) 0% (0-10%) 98% (96-99%)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 34% (31-38%) 63% (60-66%) 0% (0-1%) 0% (0-1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Imipenem Meropenem </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Coagulase-negative Staphylococcus (CoNS) 52% (25/48) 52% (25/48) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis 100% (38/38) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli 100% (422/422) 100% (418/418)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 100% (51/51) 100% (53/53) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis 94% (30/32) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) 52% (37-67%) 52% (37-67%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis 100% (91-100%) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli 100% (99-100%) 100% (99-100%)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 100% (93-100%) 100% (93-100%)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis 94% (79-99%) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
@ -463,13 +463,12 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span><span class="co"># combined antibiotics yield higher empiric coverage</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 2 × 4</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Gram-neg… 88% (565/641) 99% (681/691) 98% (679/693) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 86% (296/345) 98% (1018/1044) 95% (524/550) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-neg… 88% (85-91%) 99% (97-99%) 98% (97-99%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 86% (82-89%) 98% (96-98%) 95% (93-97%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Piperacillin/tazobactam`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Piperacillin/tazobactam + Gentamicin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`Piperacillin/tazobactam + Tobramycin`</span></span>
@ -481,13 +480,12 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span> antibiotics <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">"Cipro"</span>, <span class="st">"cipro + genta"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" &amp; "</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 2 × 3</span></span>
<span class="r-in"><span> sep <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> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Ciprofloxacin `Ciprofloxacin &amp; Gentamicin`</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Gram-negative 91% (621/684) 99% (684/694) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 77% (560/724) 93% (784/847) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative 91% (88-93%) 99% (97-99%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive 77% (74-80%) 93% (91-94%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
@ -497,28 +495,27 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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="fu"><a href="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Clinical CoNS <span style="color: #BB0000;">NA</span> 89% (183/… 57% (20… <span style="color: #BB0000;">NA</span> 57% (20/…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS <span style="color: #BB0000;">NA</span> 79% (58/7… <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;"> 3</span> Outpatient CoNS <span style="color: #BB0000;">NA</span> 84% (26/3… <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> Clinical E. coli 100% (1… 98% (291/… 100% (2… <span style="color: #BB0000;">NA</span> 100% (27…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli 100% (5… 99% (135/… 100% (1… <span style="color: #BB0000;">NA</span> 100% (11…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumo… <span style="color: #BB0000;">NA</span> 92% (47/5… 100% (4… <span style="color: #BB0000;">NA</span> 100% (46…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabi… <span style="color: #BB0000;">NA</span> 100% (30/… <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;"> 8</span> Clinical S. aureus <span style="color: #BB0000;">NA</span> 99% (148/… <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;"> 9</span> ICU S. aureus <span style="color: #BB0000;">NA</span> 100% (66/… <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;">10</span> Clinical S. epider… <span style="color: #BB0000;">NA</span> 82% (65/7… <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;">11</span> ICU S. epider… <span style="color: #BB0000;">NA</span> 72% (54/7… <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;">12</span> Clinical S. hominis <span style="color: #BB0000;">NA</span> 96% (43/4… <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;">13</span> Clinical S. pneumo… 0% (0/7… 0% (0/78) <span style="color: #BB0000;">NA</span> 0% (0/78) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumo… 0% (0/3… 0% (0/30) <span style="color: #BB0000;">NA</span> 0% (0/30) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS <span style="color: #BB0000;">NA</span> 89% (84-9… 57% (39… <span style="color: #BB0000;">NA</span> 57% (39-…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS <span style="color: #BB0000;">NA</span> 79% (68-8… <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;"> 3</span> Outpatient CoNS <span style="color: #BB0000;">NA</span> 84% (66-9… <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> Clinical E. coli 100% (9… 98% (96-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (99…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli 100% (9… 99% (95-1… 100% (9… <span style="color: #BB0000;">NA</span> 100% (97…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumo… <span style="color: #BB0000;">NA</span> 92% (81-9… 100% (9… <span style="color: #BB0000;">NA</span> 100% (92…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabi… <span style="color: #BB0000;">NA</span> 100% (88-… <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;"> 8</span> Clinical S. aureus <span style="color: #BB0000;">NA</span> 99% (95-1… <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;"> 9</span> ICU S. aureus <span style="color: #BB0000;">NA</span> 100% (95-… <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;">10</span> Clinical S. epider… <span style="color: #BB0000;">NA</span> 82% (72-9… <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;">11</span> ICU S. epider… <span style="color: #BB0000;">NA</span> 72% (60-8… <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;">12</span> Clinical S. hominis <span style="color: #BB0000;">NA</span> 96% (85-9… <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;">13</span> Clinical S. pneumo… 0% (0-5… 0% (0-5%) <span style="color: #BB0000;">NA</span> 0% (0-5%) <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU S. pneumo… 0% (0-1… 0% (0-12%) <span style="color: #BB0000;">NA</span> 0% (0-12… <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: Tobramycin &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
@ -535,35 +532,33 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">ex1</span><span class="op">$</span><span class="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span>,</span></span>
<span class="r-in"><span> <span class="st">"UCI"</span>, <span class="st">"No UCI"</span></span></span>
<span class="r-in"><span> <span class="op">)</span>,</span></span>
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> No UCI E. coli 100% (119/119) 98% (316/323) 98% (318/325)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli 100% (52/52) 99% (135/137) 96% (132/137)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> No UCI E. coli 100% (97-100%) 98% (96-99%) 98% (96-99%)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI E. coli 100% (93-100%) 99% (95-100%) 96% (92-99%)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># WISCA antibiogram ----------------------------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># can be used for any of the above types - just add `wisca = TRUE`</span></span></span>
<span class="r-in"><span><span class="co"># WISCA are not stratified by species, but rather on syndromes</span></span></span>
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 2 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Gram-neg… 88% (85.2-90.5%) 98.4% (97.3-99.2%) 97.9% (96.6-98.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-pos… 85.6% (81.9-89.1%) 97.4% (96.4-98.3%) 95.1% (93.2-96.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Piperacillin/tazobactam`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Piperacillin/tazobactam + Gentamicin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`Piperacillin/tazobactam + Tobramycin`</span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
<span class="r-in"><span> wisca <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> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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> Clinical 78% (70-85.4%) 98.3% (94.9-99.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 90.6% (84.4-94.9%) 97.6% (92.7-99.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 92.2% (79.7-99%) 94.7% (82.7-99.5%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
<span class="r-in"><span></span></span>
@ -572,9 +567,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ureido</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
@ -584,36 +578,20 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Pathogen |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*B. fragilis* |4.4% (0.1-15.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |CoNS |31.4% (17.4-47.1%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*E. cloacae* |73.1% (52.1-88.2%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*E. coli* |94.3% (91.9-96.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*E. faecalis* |94.8% (81.5-99.9%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*E. faecium* |9.7% (1.4-25.6%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |GBS |94.9% (82.5-99.9%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*K. pneumoniae* |87% (77.8-94.3%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*P. aeruginosa* |96.4% (86.8-99.9%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*P. mirabilis* |96.6% (86.9-100%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*S. anginosus* |94.1% (79.6-99.8%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*S. marcescens* |49.9% (30.8-67.8%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*S. pneumoniae* |99.1% (96.9-100%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |*S. pyogenes* |94.2% (81.1-99.8%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |name |73.6% (66-81%) |</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ab1</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">ab2</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>

2
reference/antibiotics.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="">2.1.1.9146</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">

2
reference/antimicrobial_class_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="">2.1.1.9146</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">

2
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="">2.1.1.9146</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">

2
reference/as.av.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="">2.1.1.9146</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">

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="">2.1.1.9146</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">

BIN
reference/as.mic-4.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 49 KiB

After

Width:  |  Height:  |  Size: 50 KiB

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="">2.1.1.9146</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">

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="">2.1.1.9146</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">

24
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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">
@ -782,18 +782,18 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-13 <span style="color: #949494;">18:54:33</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-13 <span style="color: #949494;">18:54:40</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-13 <span style="color: #949494;">18:54:40</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-13 <span style="color: #949494;">18:54:41</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-13 <span style="color: #949494;">18:54:41</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-13 <span style="color: #949494;">18:54:33</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-13 <span style="color: #949494;">18:54:40</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-13 <span style="color: #949494;">18:54:40</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-13 <span style="color: #949494;">18:54:41</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-13 <span style="color: #949494;">18:54:41</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-14 <span style="color: #949494;">13:21:00</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-14 <span style="color: #949494;">13:21:07</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-14 <span style="color: #949494;">13:21:07</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-14 <span style="color: #949494;">13:21:08</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-14 <span style="color: #949494;">13:21:08</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-14 <span style="color: #949494;">13:21:00</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-14 <span style="color: #949494;">13:21:07</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-14 <span style="color: #949494;">13:21:07</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-14 <span style="color: #949494;">13:21:08</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-14 <span style="color: #949494;">13:21:08</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># 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;</span></span>
<span class="r-in"><span></span></span>

2
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="">2.1.1.9146</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">

2
reference/av_from_text.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="">2.1.1.9146</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">

2
reference/av_property.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="">2.1.1.9146</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">

2
reference/availability.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="">2.1.1.9146</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">

2
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="">2.1.1.9146</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">

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>
<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">

2
reference/count.html
View File

@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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">

2
reference/custom_eucast_rules.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="">2.1.1.9146</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">

2
reference/dosage.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="">2.1.1.9146</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">

2
reference/eucast_rules.html
View File

@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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">

2
reference/example_isolates.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="">2.1.1.9146</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">

2
reference/example_isolates_unclean.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="">2.1.1.9146</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">

2
reference/export_ncbi_biosample.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="">2.1.1.9146</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">

2
reference/first_isolate.html
View File

@ -9,7 +9,7 @@
<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">

2
reference/g.test.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="">2.1.1.9146</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">

109
reference/get_episode.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="">2.1.1.9146</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">
@ -153,27 +153,28 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 46 4 39 28 8 29 19 40 34 38 7 7 10 28 7 38 41 10 20 5 18 1 22 5 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 35 17 25 27 27 1 32 28 32 41 46 46 45 28 45 43 22 31 5 6 16 45 26 8 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 45 12 4 19 24 42 16 35 44 9 26 11 1 2 32 45 32 39 21 36 19 37 14 29 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 12 41 32 22 19 19 33 15 27 10 30 16 10 45 5 40 13 37 45 28 1 31 20 23 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 52 15 15 49 19 19 1 42 13 30 34 28 41 4 48 39 37 7 11 40 47 50 45 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 13 45 35 23 51 20 16 5 36 39 44 2 7 3 33 45 14 27 44 6 1 17 29 8 39</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 22 52 43 11 38 9 33 8 41 24 11 21 43 40 30 8 19 3 16 46 30 17 37 13 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 51 32 46 7 12 15 25 18 24 26 31 50 21 5 52 13 18 42 34 29 37 36 10 20 42</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</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: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </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 style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-23 F35553 51 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </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 style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-12-13 285137 78 F ICU <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-04 304347 62 M Clinical <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@ -207,19 +208,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [96]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [100]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 022060 2004-05-04 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 036063 2010-01-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927 2002-02-14 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 069276 2015-06-18 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0C0688 2014-09-05 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0E2483 2007-04-06 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 114570 2003-04-08 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 122506 2007-08-10 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 122506 2007-08-11 B FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 13DF24 2011-08-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 006827 2009-07-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 023456 2012-11-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 078381 2014-06-28 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 0C0688 2014-09-05 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0DBF93 2015-12-03 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 118928 2004-02-01 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 125492 2016-05-13 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 136315 2004-02-02 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 2003-01-31 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 179451 2007-09-15 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -233,19 +234,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [90]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</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;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU 2004-05-04 022060 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2010-01-28 036063 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-02-14 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2015-06-18 069276 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-04-06 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-04-08 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2007-08-10 122506 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-08-11 122506 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2011-08-14 13DF24 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-07-24 006827 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-11-24 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2014-06-28 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2015-12-03 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2004-02-01 118928 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2016-05-13 125492 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2004-02-02 136315 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2003-01-31 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU 2007-09-15 179451 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -261,9 +262,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 52 13 30 37</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 30 10 24 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 8 5 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 62 13 40 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 31 11 24 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 4 6 6</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -292,19 +293,19 @@
<span class="r-in"><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="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</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;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CFCF65 <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> CF9318 <span style="color: #949494;">B_</span>CMPYL<span style="color: #949494;">_</span>JEJN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D28985 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 907215 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2FC253 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 582258 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 179451 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 534816 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B12887 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D43214 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 563131 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>EQNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> BF4515 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 262220 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 218912 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 671620 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D22254 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 180928 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>AGLC Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 496896 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 4F9406 <span style="color: #949494;">B_</span>CTRBC<span style="color: #949494;">_</span>FRND Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 690B42 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

4
reference/ggplot_pca.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="">2.1.1.9146</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">
@ -220,7 +220,7 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` and `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">minimum</span> = 30).</span>

2
reference/ggplot_sir.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="">2.1.1.9146</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">

2
reference/guess_ab_col.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="">2.1.1.9146</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">

4
reference/index.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="">2.1.1.9146</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">
@ -282,7 +282,7 @@
<dl><dt>
<code><a href="plot.html">scale_x_mic()</a></code> <code><a href="plot.html">scale_y_mic()</a></code> <code><a href="plot.html">scale_colour_mic()</a></code> <code><a href="plot.html">scale_color_mic()</a></code> <code><a href="plot.html">scale_fill_mic()</a></code> <code><a href="plot.html">scale_x_sir()</a></code> <code><a href="plot.html">scale_colour_sir()</a></code> <code><a href="plot.html">scale_fill_sir()</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">facet_sir()</a></code> <code><a href="plot.html">scale_y_percent()</a></code> <code><a href="plot.html">scale_sir_colours()</a></code> <code><a href="plot.html">theme_sir()</a></code> <code><a href="plot.html">labels_sir_count()</a></code>
<code><a href="plot.html">scale_x_mic()</a></code> <code><a href="plot.html">scale_y_mic()</a></code> <code><a href="plot.html">scale_colour_mic()</a></code> <code><a href="plot.html">scale_fill_mic()</a></code> <code><a href="plot.html">scale_x_sir()</a></code> <code><a href="plot.html">scale_colour_sir()</a></code> <code><a href="plot.html">scale_fill_sir()</a></code> <code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;sir&gt;</i>)</a></code> <code><a href="plot.html">facet_sir()</a></code> <code><a href="plot.html">scale_y_percent()</a></code> <code><a href="plot.html">scale_sir_colours()</a></code> <code><a href="plot.html">theme_sir()</a></code> <code><a href="plot.html">labels_sir_count()</a></code>
</dt>
<dd>Plotting Helpers for AMR Data Analysis</dd>

2
reference/intrinsic_resistant.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="">2.1.1.9146</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">

2
reference/italicise_taxonomy.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="">2.1.1.9146</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">

2
reference/join.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="">2.1.1.9146</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">

2
reference/key_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="">2.1.1.9146</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">

6
reference/kurtosis.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="">2.1.1.9146</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">
@ -90,9 +90,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.018229</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.955944</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <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> [1] 0.05238325</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.03216728</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/like.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="">2.1.1.9146</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">

2
reference/mdro.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="">2.1.1.9146</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">

72
reference/mean_amr_distance.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="">2.1.1.9146</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">
@ -109,30 +109,30 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S I I I S S S R R</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R R S R S I R I R S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4743416 -0.4743416 1.8973666 1.8973666</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9486833 -0.9486833 0.9486833 -0.9486833</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 1 0.001 8 0.5 16 64 128 4 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.125 2 0.005 0.5 64 0.002 128 2 2 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1967905 -0.2158758 -2.0527259 0.3370712 -0.4001915 0.5213868</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8900182 1.0743338 0.1527555 0.8900182</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0902697 -0.4972145 0.2860978 -1.4066119 -0.1055584 1.2652381</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6654825 1.4610662 0.2860978 0.2860978</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.1967905 -0.2158758 -2.0527259 0.3370712 -0.4001915 0.5213868</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.8900182 1.0743338 0.1527555 0.8900182</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0902697 -0.4972145 0.2860978 -1.4066119 -0.1055584 1.2652381</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.6654825 1.4610662 0.2860978 0.2860978</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 42 8 24 15 32 45 46 42 49 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 19 18 10 16 48 41 6 26 24</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.67331608 -1.54928069 -0.50335280 -1.09168723 0.01961115 0.86942756</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.93479805 0.67331608 1.13090953 -1.15705773</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.47901421 -0.43578097 -0.50180839 -1.03002776 -0.63386323 1.47901421</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.01682227 -1.29413744 0.02641097 -0.10564387</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</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> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -142,22 +142,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</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="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 27 8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 21 8 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 22 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 22 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 19 8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 30 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G R 20 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 27 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 20 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 17 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A S 22 &lt;=0.25 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 24 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C S 21 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 18 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E R 26 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 22 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 23 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 23 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 27 &lt;=0.25 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 25 4 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.27346725 0.04720942 -0.67302993 0.39497313 -0.68358519 0.01305317</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.64812902 0.49329507 -0.98062442 0.46711247</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3343139 0.1355870 0.1534539 -0.7329889 0.8453491 -0.2831686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.3456668 -0.4126742 -0.4661540 0.7492427</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -173,17 +173,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> and "tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 22 2 1 -0.67302993 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E S 19 8 0.5 -0.68358519 0.01055526</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I S 20 1 1 -0.98062442 0.30759449</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F S 30 2 2 0.01305317 0.68608310</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B I 21 8 4 0.04720942 0.72023935</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 A R 27 8 0.5 0.27346725 0.94649718</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D R 22 4 4 0.39497313 1.06800305</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 17 16 4 0.46711247 1.14014240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H R 27 4 2 0.49329507 1.16632499</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G R 20 16 4 0.64812902 1.32115894</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C S 21 4 4 0.1534539 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B I 24 4 2 0.1355870 0.01786681</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 G I 23 4 4 0.3456668 0.19221294</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F R 22 0.5 1 -0.2831686 0.43662245</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A S 22 &lt;=0.25 4 -0.3343139 0.48776774</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H S 23 2 1 -0.4126742 0.56612805</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 J R 25 4 2 0.7492427 0.59578882</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 I S 27 &lt;=0.25 1 -0.4661540 0.61960784</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E R 26 4 2 0.8453491 0.69189529</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D I 18 1 2 -0.7329889 0.88644273</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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>

2
reference/microorganisms.codes.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="">2.1.1.9146</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">

2
reference/microorganisms.groups.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="">2.1.1.9146</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">

2
reference/microorganisms.html
View File

@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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">

2
reference/mo_matching_score.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="">2.1.1.9146</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">

2
reference/mo_property.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="">2.1.1.9146</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">

2
reference/mo_source.html
View File

@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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">

4
reference/pca.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="">2.1.1.9146</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">
@ -157,7 +157,7 @@
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> only_all_tested = FALSE) ...`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` and `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` `genus = "Enterococcus"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">minimum</span> = 30).</span>

BIN
reference/plot-1.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 27 KiB

After

Width:  |  Height:  |  Size: 26 KiB

BIN
reference/plot-12.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 76 KiB

After

Width:  |  Height:  |  Size: 80 KiB

BIN
reference/plot-13.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 68 KiB

After

Width:  |  Height:  |  Size: 69 KiB

BIN
reference/plot-14.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 25 KiB

After

Width:  |  Height:  |  Size: 28 KiB

BIN
reference/plot-15.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 70 KiB

After

Width:  |  Height:  |  Size: 19 KiB

BIN
reference/plot-16.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 36 KiB

After

Width:  |  Height:  |  Size: 71 KiB

BIN
reference/plot-17.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 53 KiB

After

Width:  |  Height:  |  Size: 90 KiB

BIN
reference/plot-18.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 24 KiB

After

Width:  |  Height:  |  Size: 84 KiB

BIN
reference/plot-19.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 28 KiB

After

Width:  |  Height:  |  Size: 36 KiB

BIN
reference/plot-2.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 26 KiB

After

Width:  |  Height:  |  Size: 26 KiB

BIN
reference/plot-20.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 19 KiB

After

Width:  |  Height:  |  Size: 56 KiB

BIN
reference/plot-21.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 29 KiB

After

Width:  |  Height:  |  Size: 25 KiB

BIN
reference/plot-22.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 28 KiB

BIN
reference/plot-23.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 19 KiB

BIN
reference/plot-24.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 29 KiB

BIN
reference/plot-3.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 27 KiB

After

Width:  |  Height:  |  Size: 27 KiB

BIN
reference/plot-4.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 40 KiB

After

Width:  |  Height:  |  Size: 39 KiB

BIN
reference/plot-5.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 40 KiB

After

Width:  |  Height:  |  Size: 40 KiB

BIN
reference/plot-6.png
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 39 KiB

After

Width:  |  Height:  |  Size: 39 KiB

45
reference/plot.html
View File

@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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">
@ -63,8 +63,6 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span></span>
<span><span class="fu">scale_colour_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_color_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_fill_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_x_sir</span><span class="op">(</span>colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
@ -80,7 +78,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language</span>
<span> <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
@ -91,8 +90,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span></span>
<span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span>, title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>,</span>
<span> ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
<span> <span class="va">language</span><span class="op">)</span>, colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
@ -103,7 +103,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
@ -113,8 +113,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="st">"EUCAST"</span>, colours_SIR <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">"#3CAEA3"</span>,</span>
<span> <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> colours_SIR <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">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@ -265,14 +266,14 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<h3 id="the-scale-mic-functions">The <code>scale_*_mic()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-mic-functions"></a></h3>
<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous scale. They allow to rescale the MIC range, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.</p>
<p>The functions <code>scale_x_mic()</code>, <code>scale_y_mic()</code>, <code>scale_colour_mic()</code>, and <code>scale_fill_mic()</code> functions allow to plot the <a href="as.mic.html">mic</a> class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.</p>
</div>
<div class="section">
<h3 id="the-scale-sir-functions">The <code>scale_*_sir()</code> Functions<a class="anchor" aria-label="anchor" href="#the-scale-sir-functions"></a></h3>
<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class (S/I/R values). They can translate the S/I/R values to any of the 20 supported languages, and set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
<p>The functions <code>scale_x_sir()</code>, <code>scale_colour_sir()</code>, and <code>scale_fill_sir()</code> functions allow to plot the <a href="as.sir.html">sir</a> class in the right order (S &lt; SDD &lt; I &lt; R &lt; NI). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the 20 supported languages (use <code>language = NULL</code> to keep S/I/R). Also, except for <code>scale_x_sir()</code>, they set colour-blind friendly colours to the <code>colour</code> and <code>fill</code> aesthetics.</p>
</div>
<div class="section">
@ -285,7 +286,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<li><p><code>theme_sir()</code> is a [ggplot2 theme][<code><a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2::theme()</a></code> with minimal distraction.</p></li>
<li><p><code>labels_sir_count()</code> print datalabels on the bars with percentage and number of isolates, using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
</ul><p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2024", "EUCAST 2023", "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2024", "CLSI 2023", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", and "CLSI 2011". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2024, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
</div>
</div>
@ -396,7 +397,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_sir</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_x_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_y_mic() and scale_colour_sir() ------------------</span></span></span>
@ -420,36 +421,36 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># and now with our MIC and SIR scale functions:</span></span></span>
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_colour_sir</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_colour_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span>language <span class="op">=</span> <span class="st">"el"</span>, eucast_I <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"In Greek!"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> Apply <span style="background-color: #EEEEEE;">scale_colour_sir()</span> to a variable of class 'sir', see <span style="background-color: #EEEEEE;">?as.sir</span>.</span>
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using ggplot2's autoplot() ----------------------------------</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_y_percent() -------------------------------------</span></span></span>
@ -470,9 +471,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> limits <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">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">theme_sir</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-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-22.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-23.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-24.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/proportion.html
View File

@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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">

36
reference/random.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="">2.1.1.9146</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">
@ -99,42 +99,44 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 0.0625 32 4 128 0.0625 0.5 0.025 256 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 16 0.025 0.025 4 256 0.5 8 4 0.005 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.01 0.0625 0.025 64 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 0.005 8 0.25 8 16 256 0.0625 128 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 64 16 0.01 32 8 8 0.25 128 0.5 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 0.001 0.005 8 16 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 35 45 37 36 16 17 25 47 47 40 50 10 6 31 33 37 29 14 33 41 31 7 13 46 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 20 30 25 46 47 38 10 17 47 32 10 12 26 17 42 20 43 46 20 26 43 7 16 29</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R S I S I S S I S I S R S R R R I S S I S S R S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I I R S I I S R S S S R S I I I S R S I S I S S</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.0625 0.25 0.0625 16 4 1 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 8 0.5 &lt;=0.001 8 16 &lt;=0.001 4 0.25 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 16 0.005 0.025 16 0.0625 0.0625 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 4 0.5 64 4 0.125 0.0625 0.005 2 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.5 128 4 16 128 16 0.002 1 1 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 2 4 0.002 0.025 0.0625</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 2 2 32 8 &gt;=64 1 16 16 16 16 1 0.5 4 &gt;=64</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 1 8 &gt;=64 1 0.5 32 4 16 0.5 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 &lt;=0.25 1 2 1 8 2 8 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2 &lt;=0.25 2 &lt;=0.25 4 0.5 4 &lt;=0.25 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1 16 8 8 2 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 0.5 0.5 0.5 0.025 2 1 0.5 0.025 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.125 4 0.25 0.25 0.0625 0.0625 0.0625 0.5 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.025 0.5 2 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.125 &lt;=0.0625 0.5 1 1 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.5 &lt;=0.0625 0.125 0.5 0.25 1 0.25 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 8 0.125 0.125 &lt;=0.0625 0.5 8 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &gt;=16 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 42 21 25 17 47 14 34 35 40 45 18 35 24 40 48 45 19 31 45 9 35 26 30 26 48</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 29 50 11 24 10 19 24 15 15 38 13 45 46 48 40 50 40 44 36 40 26 15 36 45</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 13 13 17 14 11 14 14 14 17 17 17 14 17 15 12 12 12 15 16 17 14 16 14 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 12 12 13 15 11 15 14 12 12 12 11 11 17 13 14 17 15 12 13 16 14 17 16 11 13</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 24 20 26 20 18 27 18 15 18 17 16 20 24 21 25 21 25 18 23 25 17 24 17 16 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 26 16 18 17 26 21 21 21 16 20 21 26 24 23 20 20 18 17 17 18 25 24 22 24</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/resistance_predict.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="">2.1.1.9146</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">

8
reference/scale_color_sir.html Normal file
View File

@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/plot.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://msberends.github.io/AMR/reference/plot.html">
</head>
</html>

8
reference/scale_sir_colors.html Normal file
View File

@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/plot.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://msberends.github.io/AMR/reference/plot.html">
</head>
</html>

Some files were not shown because too many files have changed in this diff Show More