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404.html
@ -36,7 +36,7 @@
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<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -402,18 +402,18 @@ names or codes, this would have worked exactly the same way:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
|
||||
<span><span class="co">#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
|
||||
<span><span class="co">#> 1 S R R I I R</span></span>
|
||||
<span><span class="co">#> 2 I R R I S I</span></span>
|
||||
<span><span class="co">#> 3 I S I R R I</span></span>
|
||||
<span><span class="co">#> 4 R R I R I S</span></span>
|
||||
<span><span class="co">#> 5 R S I I I S</span></span>
|
||||
<span><span class="co">#> 6 I S I S I R</span></span>
|
||||
<span><span class="co">#> 1 R S S S I I</span></span>
|
||||
<span><span class="co">#> 2 R I S R S I</span></span>
|
||||
<span><span class="co">#> 3 R I I R S R</span></span>
|
||||
<span><span class="co">#> 4 S I I S R R</span></span>
|
||||
<span><span class="co">#> 5 S R I R S S</span></span>
|
||||
<span><span class="co">#> 6 I R I R R I</span></span>
|
||||
<span><span class="co">#> kanamycin</span></span>
|
||||
<span><span class="co">#> 1 S</span></span>
|
||||
<span><span class="co">#> 2 I</span></span>
|
||||
<span><span class="co">#> 3 R</span></span>
|
||||
<span><span class="co">#> 4 R</span></span>
|
||||
<span><span class="co">#> 5 I</span></span>
|
||||
<span><span class="co">#> 1 I</span></span>
|
||||
<span><span class="co">#> 2 S</span></span>
|
||||
<span><span class="co">#> 3 S</span></span>
|
||||
<span><span class="co">#> 4 S</span></span>
|
||||
<span><span class="co">#> 5 S</span></span>
|
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<span><span class="co">#> 6 I</span></span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can
|
||||
use:</p>
|
||||
@ -455,40 +455,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3187</td>
|
||||
<td align="right">63.74%</td>
|
||||
<td align="right">3187</td>
|
||||
<td align="right">63.74%</td>
|
||||
<td align="right">3200</td>
|
||||
<td align="right">64.00%</td>
|
||||
<td align="right">3200</td>
|
||||
<td align="right">64.00%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">1017</td>
|
||||
<td align="right">20.34%</td>
|
||||
<td align="right">4204</td>
|
||||
<td align="right">84.08%</td>
|
||||
<td align="right">1002</td>
|
||||
<td align="right">20.04%</td>
|
||||
<td align="right">4202</td>
|
||||
<td align="right">84.04%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">456</td>
|
||||
<td align="right">9.12%</td>
|
||||
<td align="right">4660</td>
|
||||
<td align="right">93.20%</td>
|
||||
<td align="right">479</td>
|
||||
<td align="right">9.58%</td>
|
||||
<td align="right">4681</td>
|
||||
<td align="right">93.62%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">230</td>
|
||||
<td align="right">4.60%</td>
|
||||
<td align="right">4890</td>
|
||||
<td align="right">97.80%</td>
|
||||
<td align="right">210</td>
|
||||
<td align="right">4.20%</td>
|
||||
<td align="right">4891</td>
|
||||
<td align="right">97.82%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">110</td>
|
||||
<td align="right">2.20%</td>
|
||||
<td align="right">109</td>
|
||||
<td align="right">2.18%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
@ -904,14 +904,14 @@ inhibitors</td>
|
||||
<code>clinical_breakpoints</code>: Interpretation from MIC values
|
||||
& disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
|
||||
</h2>
|
||||
<p>A data set with 28 885 rows and 12 columns, containing the following
|
||||
<p>A data set with 29 747 rows and 12 columns, containing the following
|
||||
column names:<br><em>guideline</em>, <em>type</em>, <em>method</em>, <em>site</em>,
|
||||
<em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>,
|
||||
<em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em>, and
|
||||
<em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>clinical_breakpoints</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 12 July 2023 10:41:25 UTC. Find more info
|
||||
<p>It was last updated on 12 July 2023 14:20:04 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@ -919,7 +919,7 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
|
||||
R Data Structure (RDS) file</a> (59 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
|
||||
text file</a> (2.2 MB)<br>
|
||||
text file</a> (2.3 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (1.3 MB)<br>
|
||||
@ -928,16 +928,16 @@ Excel workbook</a> (1.3 MB)<br>
|
||||
Feather file</a> (1.2 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
|
||||
Parquet file</a> (87 kB)<br>
|
||||
Parquet file</a> (96 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
|
||||
transport (XPT) file</a> (7.7 MB)<br>
|
||||
transport (XPT) file</a> (7.9 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (4.4 MB)<br>
|
||||
SPSS Statistics data file</a> (4.6 MB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
|
||||
DTA file</a> (7.6 MB)</li>
|
||||
DTA file</a> (7.8 MB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
|
||||
@ -959,7 +959,7 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<col width="14%">
|
||||
<col width="6%">
|
||||
<col width="2%">
|
||||
<col width="15%">
|
||||
<col width="16%">
|
||||
<col width="8%">
|
||||
<col width="8%">
|
||||
<col width="7%">
|
||||
@ -988,8 +988,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">DISK</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">MEM</td>
|
||||
<td align="center">Meropenem</td>
|
||||
@ -1004,8 +1004,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">MEM</td>
|
||||
<td align="center">Meropenem</td>
|
||||
@ -1020,8 +1020,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">DISK</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">SXT</td>
|
||||
<td align="center">Trimethoprim/sulfamethoxazole</td>
|
||||
@ -1036,8 +1036,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">SXT</td>
|
||||
<td align="center">Trimethoprim/sulfamethoxazole</td>
|
||||
@ -1052,8 +1052,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">DISK</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">TZP</td>
|
||||
<td align="center">Piperacillin/tazobactam</td>
|
||||
@ -1068,8 +1068,8 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
|
||||
<td align="center">human</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">B_ACHRMB_DNTR</td>
|
||||
<td align="center">Achromobacter denitrificans</td>
|
||||
<td align="center">B_ACHRMB_XYLS</td>
|
||||
<td align="center">Achromobacter xylosoxidans</td>
|
||||
<td align="center">2</td>
|
||||
<td align="center">TZP</td>
|
||||
<td align="center">Piperacillin/tazobactam</td>
|
||||
@ -2046,13 +2046,13 @@ reality and can be used to practise AMR data analysis.</p>
|
||||
<code>microorganisms.groups</code>: Species Groups and
|
||||
Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
|
||||
</h2>
|
||||
<p>A data set with 448 rows and 4 columns, containing the following
|
||||
<p>A data set with 507 rows and 4 columns, containing the following
|
||||
column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
|
||||
<em>mo_name</em>.</p>
|
||||
<p>This data set is in R available as
|
||||
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
|
||||
package.</p>
|
||||
<p>It was last updated on 12 July 2023 10:41:25 UTC. Find more info
|
||||
<p>It was last updated on 12 July 2023 14:04:48 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
@ -2060,25 +2060,25 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
|
||||
R Data Structure (RDS) file</a> (5 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
|
||||
text file</a> (42 kB)<br>
|
||||
text file</a> (48 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
|
||||
Excel workbook</a> (18 kB)<br>
|
||||
Excel workbook</a> (20 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
|
||||
Feather file</a> (17 kB)<br>
|
||||
Feather file</a> (18 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
|
||||
Parquet file</a> (12 kB)<br>
|
||||
Parquet file</a> (13 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
|
||||
transport (XPT) file</a> (0 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
|
||||
SPSS Statistics data file</a> (54 kB)<br>
|
||||
SPSS Statistics data file</a> (62 kB)<br>
|
||||
</li>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
|
||||
DTA file</a> (68 kB)</li>
|
||||
DTA file</a> (79 kB)</li>
|
||||
</ul>
|
||||
<div class="section level3">
|
||||
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -38,7 +38,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -42,7 +42,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
@ -159,9 +159,9 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0.9035" id="amr-2009035">AMR 2.0.0.9035<a class="anchor" aria-label="anchor" href="#amr-2009035"></a></h2>
|
||||
<h2 class="pkg-version" data-toc-text="2.0.0.9039" id="amr-2009039">AMR 2.0.0.9039<a class="anchor" aria-label="anchor" href="#amr-2009039"></a></h2>
|
||||
<div class="section level3">
|
||||
<h3 id="new-2-0-0-9035">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9035"></a></h3>
|
||||
<h3 id="new-2-0-0-9039">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9039"></a></h3>
|
||||
<ul><li>Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations</li>
|
||||
<li>The EUCAST dosage guideline of v13.0 has been added to the <code>dosage</code> data set</li>
|
||||
<li>ECOFF: the <code>clinical_breakpoints</code> data set now contains epidemiological cut-off (ECOFF) values. These ECOFFs can be used for MIC/disk interpretation using <code>as.sir(..., breakpoint_type = "ECOFF")</code>, which is an important new addition for veterinary microbiology.</li>
|
||||
@ -176,7 +176,7 @@
|
||||
<li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
|
||||
</ul></div>
|
||||
<div class="section level3">
|
||||
<h3 id="changed-2-0-0-9035">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9035"></a></h3>
|
||||
<h3 id="changed-2-0-0-9039">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9039"></a></h3>
|
||||
<ul><li>Updated algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> by giving more weight to fungi</li>
|
||||
<li>
|
||||
<code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
|
||||
|
||||
@ -11,7 +11,7 @@ articles:
|
||||
other_pkg: other_pkg.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2023-07-12T10:46Z
|
||||
last_built: 2023-07-12T14:24Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR/reference
|
||||
article: https://msberends.github.io/AMR/articles
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
|
||||
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
||||
and doi:10.33612/diss.192486375
|
||||
).
|
||||
After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
|
||||
The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
|
||||
This work was published in the Journal of Statistical Software (Volume 104(3); doi:jss.v104.i03
|
||||
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
|
||||
and doi:10.33612/diss.192486375
|
||||
).
|
||||
After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
|
||||
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@ -24,7 +24,7 @@ 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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -180,7 +180,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
||||
) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
|
||||
and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
|
||||
).</p>
|
||||
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated December 2022) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||
<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated december 2022) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||||
<p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
|
||||
</div>
|
||||
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
@ -222,16 +222,16 @@
|
||||
<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">#></span> birth_date age age_exact age_at_y2k</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1966-03-31 57 57.28219 33</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1978-05-07 45 45.18082 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1938-05-09 85 85.17534 61</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1944-10-01 78 78.77808 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1933-10-17 89 89.73425 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1994-05-11 29 29.16986 5</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1950-03-26 73 73.29589 49</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1999-12-14 23 23.57534 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1952-02-05 71 71.43014 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1991-03-26 32 32.29589 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 1946-01-13 77 77.49315 53</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 1954-06-11 69 69.08493 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 1966-03-23 57 57.30411 33</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 1943-02-24 80 80.37808 56</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 1991-04-09 32 32.25753 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 1933-09-03 89 89.85479 66</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 1931-12-10 91 91.58630 68</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 1954-07-04 69 69.02192 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 1983-03-03 40 40.35890 16</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 1949-12-31 73 73.52877 50</span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
@ -626,11 +626,11 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> kefzol</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> R </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>
|
||||
<span class="r-in"><span> <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -14,7 +14,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
@ -353,7 +353,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
|
||||
<h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
|
||||
|
||||
|
||||
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 28 885 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
|
||||
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 29 747 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
|
||||
</div>
|
||||
|
||||
<div class="section">
|
||||
@ -567,19 +567,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 13 × 13</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_user mo_user ab mo input</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-07-12 <span style="color: #949494;">10:47:46</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-07-12 <span style="color: #949494;">10:47:46</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-07-12 <span style="color: #949494;">10:47:45</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-07-12 <span style="color: #949494;">10:47:45</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-07-12 <span style="color: #949494;">10:47:35</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2023-07-12 <span style="color: #949494;">10:47:34</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2023-07-12 <span style="color: #949494;">10:47:34</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2023-07-12 <span style="color: #949494;">10:47:34</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2023-07-12 <span style="color: #949494;">14:25:35</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2023-07-12 <span style="color: #949494;">14:25:35</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2023-07-12 <span style="color: #949494;">14:25:35</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2023-07-12 <span style="color: #949494;">14:25:35</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2023-07-12 <span style="color: #949494;">14:25:25</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2023-07-12 <span style="color: #949494;">14:25:25</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2023-07-12 <span style="color: #949494;">14:25:25</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2023-07-12 <span style="color: #949494;">14:25:25</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2023-07-12 <span style="color: #949494;">14:25:25</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2023-07-12 <span style="color: #949494;">14:25:24</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2023-07-12 <span style="color: #949494;">14:25:24</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2023-07-12 <span style="color: #949494;">14:25:24</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2023-07-12 <span style="color: #949494;">14:25:24</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 6 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># guideline <chr>, ref_table <chr>, uti <lgl></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
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||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
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|
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
@ -170,7 +170,7 @@
|
||||
|
||||
<div class="section level2">
|
||||
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 28 885 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 29 747 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
|
||||
<li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
|
||||
<li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
|
||||
<li><p><code>site</code><br> Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"</p></li>
|
||||
@ -225,20 +225,20 @@
|
||||
<div class="section level2">
|
||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">clinical_breakpoints</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 28,885 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 29,747 × 12</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> guideline type method site mo rank_index ab ref_tbl disk_dose</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 MEM A. xylo… 10ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 SXT A. xylo… 1.25ug/2…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 TZP A. xylo… 30ug/6ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_DNTR 2 TZP A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… 10ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… 1.25ug/2…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 28,875 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… 10ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 MEM A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… 1.25ug/2…</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 SXT A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo… 30ug/6ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACHRMB_XYLS 2 TZP A. xylo… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2… human DISK <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto… 30ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2… human DISK Unco… B_ACNTB 3 AMK Acineto… 30ug </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2… human MIC <span style="color: #BB0000;">NA</span> B_ACNTB 3 AMK Acineto… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> EUCAST 2… human MIC Unco… B_ACNTB 3 AMK Acineto… <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 29,737 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
@ -12,7 +12,7 @@ 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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
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|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -10,7 +10,7 @@
|
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|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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|
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@ -12,7 +12,7 @@ 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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
||||
|
||||
|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||
|
||||
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
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|
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</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">
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|
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@ -10,7 +10,7 @@
|
||||
|
||||
<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="">2.0.0.9035</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9039</small>
|
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|
||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -263,27 +263,29 @@
|
||||
<span class="r-in"><span><span class="va">df</span> <span class="op"><-</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 42 21 48 39 7 47 25 24 36 9 4 28 35 10 14 1 35 38 46 26 30 1 5 40 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 43 49 16 5 15 30 10 26 8 7 12 50 12 2 20 45 30 14 11 30 42 25 41 23 27</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 2 27 39 18 44 15 50 32 37 31 12 25 40 34 50 44 37 22 32 44 14 43 50 12 44</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 8 29 6 19 33 50 42 8 13 42 44 17 4 42 11 48 3 7 8 28 39 49 38 49 21</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 15 45 31 22 22 23 38 11 5 22 8 18 20 3 23 47 24 15 40 26 21 11 35 42 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [26] 33 2 26 20 8 28 43 40 48 2 32 7 14 34 14 19 46 35 34 12 8 47 37 33 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [51] 24 33 4 21 10 38 11 32 38 13 47 26 3 18 41 37 6 27 37 25 5 9 1 16 45</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [76] 29 6 3 17 39 34 16 1 27 4 31 29 42 41 46 35 30 43 29 19 45 26 5 36 44</span>
|
||||
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE TRUE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE TRUE TRUE</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">#></span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-09-23 F35553 51 M ICU B_STPHY_AURS S NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-21 450741 77 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
|
||||
@ -317,19 +319,19 @@
|
||||
<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">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [96]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [99]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 032343 2003-06-09 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 05C73F 2006-01-12 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 066895 2002-02-27 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 067927 2002-02-14 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 080086 2010-08-08 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 101305 2006-12-13 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 105248 2005-06-16 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 116866 2011-11-07 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 122506 2007-08-10 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 141061 2014-10-22 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 001213 2009-08-03 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 065187 2003-05-26 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 067927 2002-01-07 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 067927 2002-02-14 B FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0C0688 2014-09-05 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0DBF93 2015-10-12 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 136315 2004-02-02 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 146120 2011-09-23 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 146F70 2009-08-14 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 161740 2005-06-21 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
@ -343,19 +345,19 @@
|
||||
<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">#></span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [92]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [98]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2003-06-09 032343 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical 2006-01-12 05C73F 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2002-02-27 066895 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-02-14 067927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2010-08-08 080086 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2006-12-13 101305 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2005-06-16 105248 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-11-07 116866 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-08-10 122506 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2014-10-22 141061 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-08-03 001213 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-05-26 065187 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-01-07 067927 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2002-02-14 067927 1 FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-10-12 0DBF93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2004-02-02 136315 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical 2011-09-23 146120 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2009-08-14 146F70 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2005-06-21 161740 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
@ -371,9 +373,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 60 14 38 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 28 9 22 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 4 4 4 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 66 13 38 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 26 11 22 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 6 6 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>
|
||||
@ -402,19 +404,19 @@
|
||||
<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">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [100]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 438196 B_STPHY_COHN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> F37316 B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> D08278 B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 992282 B_STRPT_GRPA Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> D63414 B_PROTS_MRBL Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 450946 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> E95747 B_KLBSL_PNMN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 451990 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 175532 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 161373 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AFD3B1 B_STRPT_EQNS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E06844 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 59B5BD B_ESCHR_COLI ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 945BD5 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 314039 UNKNOWN Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 353710 B_STPHY_EPDR ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> A56264 B_STPHY_CPTS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> F41D7B B_STRPT_PNMN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 065187 B_STPHY_AURS ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 445249 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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>
|
||||
|
||||
@ -10,7 +10,7 @@
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@ -418,7 +418,7 @@
|
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|
||||
<code><a href="microorganisms.groups.html">microorganisms.groups</a></code>
|
||||
</dt>
|
||||
<dd>Data Set with 444 Microorganisms In Species Groups</dd>
|
||||
<dd>Data Set with 507 Microorganisms In Species Groups</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code>
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@ -199,9 +199,9 @@
|
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<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">#></span> [1] 2.959141</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2.955967</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">#></span> [1] -0.04474896</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.03244247</span>
|
||||
</code></pre></div>
|
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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@ -261,7 +261,8 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
|
||||
|
||||
|
||||
<p>Currently supported guidelines are (case-insensitive):</p><ul><li><p><code>guideline = "CMI2012"</code> (default)</p>
|
||||
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p></li>
|
||||
<p>Magiorakos AP, Srinivasan A <em>et al.</em> "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (<a href="https://doi.org/10.1111/j.1469-0691.2011.03570.x" class="external-link">doi:10.1111/j.1469-0691.2011.03570.x</a>
|
||||
)</p></li>
|
||||
<li><p><code>guideline = "EUCAST3.3"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
|
||||
<p>The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">link</a>)</p></li>
|
||||
<li><p><code>guideline = "EUCAST3.2"</code></p>
|
||||
|
||||
@ -10,7 +10,7 @@
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 444 Microorganisms In Species Groups</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 507 Microorganisms In Species Groups</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.groups.Rd</code></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 444 observations and 4 variables:</p><ul><li><p><code>mo_group</code><br> ID of the species group / microbiological complex</p></li>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 507 observations and 4 variables:</p><ul><li><p><code>mo_group</code><br> ID of the species group / microbiological complex</p></li>
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<li><p><code>mo</code><br> ID of the microorganism belonging in the species group / microbiological complex</p></li>
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<li><p><code>mo_group_name</code><br> Name of the species group / microbiological complex, as retrieved with <code><a href="mo_property.html">mo_name()</a></code></p></li>
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<li><p><code>mo_name</code><br> Name of the microorganism belonging in the species group / microbiological complex, as retrieved with <code><a href="mo_property.html">mo_name()</a></code></p></li>
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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@ -198,7 +198,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<div class="section level2">
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<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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.07297999</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] -0.01687014</span>
|
||||
</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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