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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -86,7 +86,7 @@ Content not found. Please use links in the navbar.
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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CLAUDE.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -263,7 +263,7 @@ _pkgdown.yml # pkgdown website configuration</code></pre>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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LICENSE-text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -302,7 +302,7 @@ END OF TERMS AND CONDITIONS
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -721,9 +721,9 @@ Carlo simulation:</p>
<th align="left">Piperacillin/tazobactam + Tobramycin</th> <th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead> </tr></thead>
<tbody><tr class="odd"> <tbody><tr class="odd">
<td align="left">70.2% (64.8-75.2%)</td> <td align="left">70% (64.4-75.3%)</td>
<td align="left">93.6% (92.2-95%)</td> <td align="left">93.6% (92.1-95%)</td>
<td align="left">89.9% (87-92.3%)</td> <td align="left">89.8% (87-92.3%)</td>
</tr></tbody> </tr></tbody>
</table> </table>
<p>The output tells you: <em>“given the species distribution in your <p>The output tells you: <em>“given the species distribution in your
@@ -764,51 +764,51 @@ accepts any column or expression:</p>
<tr class="odd"> <tr class="odd">
<td align="left">0-24</td> <td align="left">0-24</td>
<td align="left">F</td> <td align="left">F</td>
<td align="left">56.8% (29.9-81.3%)</td> <td align="left">57% (29.7-81.3%)</td>
<td align="left">70.7% (45.2-89%)</td> <td align="left">70.8% (45.2-88.9%)</td>
<td align="left">65.9% (42.3-86.6%)</td> <td align="left">66.1% (43-86.8%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">0-24</td> <td align="left">0-24</td>
<td align="left">M</td> <td align="left">M</td>
<td align="left">59.5% (31.2-85.5%)</td> <td align="left">59.7% (31.2-85.9%)</td>
<td align="left">76.1% (56.5-92%)</td> <td align="left">76.1% (57.1-91.7%)</td>
<td align="left">59.6% (31.7-85.1%)</td> <td align="left">59.5% (31.7-85.1%)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">25-49</td> <td align="left">25-49</td>
<td align="left">F</td> <td align="left">F</td>
<td align="left">67.7% (43.9-89.7%)</td> <td align="left">67.9% (44.6-89.7%)</td>
<td align="left">93.8% (87.4-98.1%)</td> <td align="left">93.8% (87.4-98.1%)</td>
<td align="left">87% (70.1-97%)</td> <td align="left">87% (70-97%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">25-49</td> <td align="left">25-49</td>
<td align="left">M</td> <td align="left">M</td>
<td align="left">56.9% (26.6-86.2%)</td> <td align="left">56.9% (26.6-86.2%)</td>
<td align="left">91% (82-97.2%)</td> <td align="left">91.1% (82-97.2%)</td>
<td align="left">76.6% (51.4-93.5%)</td> <td align="left">76.5% (51.4-93.5%)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">50-74</td> <td align="left">50-74</td>
<td align="left">F</td> <td align="left">F</td>
<td align="left">68% (54.1-81.8%)</td> <td align="left">68% (54.1-81.8%)</td>
<td align="left">96.9% (94.6-98.5%)</td> <td align="left">96.9% (94.6-98.5%)</td>
<td align="left">90.2% (82-96.2%)</td> <td align="left">90.3% (82-96.2%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">50-74</td> <td align="left">50-74</td>
<td align="left">M</td> <td align="left">M</td>
<td align="left">67% (56-78.5%)</td> <td align="left">67% (56-78.5%)</td>
<td align="left">96.7% (94.1-98.5%)</td> <td align="left">96.7% (94-98.5%)</td>
<td align="left">86.7% (77.3-94.4%)</td> <td align="left">86.7% (77.3-94.5%)</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left">75+</td> <td align="left">75+</td>
<td align="left">F</td> <td align="left">F</td>
<td align="left">73.1% (61.8-84.1%)</td> <td align="left">73.2% (61.9-84.2%)</td>
<td align="left">97.7% (95.9-99%)</td> <td align="left">97.7% (95.9-99%)</td>
<td align="left">92.8% (85.7-97.2%)</td> <td align="left">92.7% (85.6-97.2%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">75+</td> <td align="left">75+</td>
@@ -1424,7 +1424,7 @@ values:</p>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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articles/AMR.md
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@@ -656,7 +656,7 @@ wisca_result
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---| |:---|:---|:---|
| 70.2% (64.8-75.2%) | 93.6% (92.2-95%) | 89.9% (87-92.3%) | | 70% (64.4-75.3%) | 93.6% (92.1-95%) | 89.8% (87-92.3%) |
The output tells you: *“given the species distribution in your data, The output tells you: *“given the species distribution in your data,
there is an estimated X% probability that this regimen covers the there is an estimated X% probability that this regimen covers the
@@ -683,13 +683,13 @@ wisca_out
| age_group | gender | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | age_group | gender | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|:---| |:---|:---|:---|:---|:---|
| 0-24 | F | 56.8% (29.9-81.3%) | 70.7% (45.2-89%) | 65.9% (42.3-86.6%) | | 0-24 | F | 57% (29.7-81.3%) | 70.8% (45.2-88.9%) | 66.1% (43-86.8%) |
| 0-24 | M | 59.5% (31.2-85.5%) | 76.1% (56.5-92%) | 59.6% (31.7-85.1%) | | 0-24 | M | 59.7% (31.2-85.9%) | 76.1% (57.1-91.7%) | 59.5% (31.7-85.1%) |
| 25-49 | F | 67.7% (43.9-89.7%) | 93.8% (87.4-98.1%) | 87% (70.1-97%) | | 25-49 | F | 67.9% (44.6-89.7%) | 93.8% (87.4-98.1%) | 87% (70-97%) |
| 25-49 | M | 56.9% (26.6-86.2%) | 91% (82-97.2%) | 76.6% (51.4-93.5%) | | 25-49 | M | 56.9% (26.6-86.2%) | 91.1% (82-97.2%) | 76.5% (51.4-93.5%) |
| 50-74 | F | 68% (54.1-81.8%) | 96.9% (94.6-98.5%) | 90.2% (82-96.2%) | | 50-74 | F | 68% (54.1-81.8%) | 96.9% (94.6-98.5%) | 90.3% (82-96.2%) |
| 50-74 | M | 67% (56-78.5%) | 96.7% (94.1-98.5%) | 86.7% (77.3-94.4%) | | 50-74 | M | 67% (56-78.5%) | 96.7% (94-98.5%) | 86.7% (77.3-94.5%) |
| 75+ | F | 73.1% (61.8-84.1%) | 97.7% (95.9-99%) | 92.8% (85.7-97.2%) | | 75+ | F | 73.2% (61.9-84.2%) | 97.7% (95.9-99%) | 92.7% (85.6-97.2%) |
| 75+ | M | 74% (63.6-82.6%) | 97.9% (96-99%) | 94.7% (89.3-97.9%) | | 75+ | M | 74% (63.6-82.6%) | 97.9% (96-99%) | 94.7% (89.3-97.9%) |
Keep in mind that more granular stratification produces more relevant Keep in mind that more granular stratification produces more relevant

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articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -642,7 +642,7 @@ Python.</p>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -998,7 +998,7 @@ settings.</p>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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articles/EUCAST.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -319,7 +319,7 @@ reading</em>, and is basically a form of imputation:</p>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -236,7 +236,7 @@ automatically adds the right labels and even groups:</p>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -325,7 +325,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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articles/WISCA.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -341,7 +341,11 @@ traditional antibiogram remains fit for purpose.</p>
<span><span class="co">#&gt; <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span></span> <span><span class="co">#&gt; <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span></span>
<span></span> <span></span>
<span><span class="co"># Add a synthetic syndrome column for demonstration</span></span> <span><span class="co"># Add a synthetic syndrome column for demonstration</span></span>
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Non-UTI"</span><span class="op">)</span></span></code></pre></div> <span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"Non-UTI"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Keep only 10 most common microorganisms</span></span>
<span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span><span class="va">data</span>, n <span class="op">=</span> <span class="fl">10</span>, property <span class="op">=</span> <span class="st">"species"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span></code></pre></div>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="basic-wisca">Basic WISCA<a class="anchor" aria-label="anchor" href="#basic-wisca"></a> <h3 id="basic-wisca">Basic WISCA<a class="anchor" aria-label="anchor" href="#basic-wisca"></a>
@@ -357,9 +361,9 @@ traditional antibiogram remains fit for purpose.</p>
<th align="left">Gentamicin</th> <th align="left">Gentamicin</th>
</tr></thead> </tr></thead>
<tbody><tr class="odd"> <tbody><tr class="odd">
<td align="left">74.2% (72.1-76.1%)</td> <td align="left">76.8% (74.7-79.1%)</td>
<td align="left">78.4% (75.6-81.1%)</td> <td align="left">81.5% (78.9-84.1%)</td>
<td align="left">72.5% (70.4-74.6%)</td> <td align="left">82.9% (81-84.8%)</td>
</tr></tbody> </tr></tbody>
</table> </table>
</div> </div>
@@ -385,9 +389,9 @@ covers the pathogen:</p>
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th> <th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
</tr></thead> </tr></thead>
<tbody><tr class="odd"> <tbody><tr class="odd">
<td align="left">74.2% (72.2-76.1%)</td> <td align="left">76.8% (74.6-78.9%)</td>
<td align="left">88.8% (87.2-90.4%)</td> <td align="left">89.6% (88-91.1%)</td>
<td align="left">90.8% (89.4-92.2%)</td> <td align="left">93.7% (92.5-94.9%)</td>
</tr></tbody> </tr></tbody>
</table> </table>
</div> </div>
@@ -397,10 +401,11 @@ covers the pathogen:</p>
<p>Use <code>syndromic_group</code> to produce separate WISCA estimates <p>Use <code>syndromic_group</code> to produce separate WISCA estimates
per clinical stratum. You can pass a column name or any expression:</p> per clinical stratum. You can pass a column name or any expression:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span> <code class="sourceCode R"><span><span class="va">wisca_out</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span></span> <span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span></span>
<span><span class="op">)</span></span></code></pre></div> <span><span class="op">)</span></span>
<span><span class="va">wisca_out</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="12%"> <col width="12%">
@@ -417,15 +422,15 @@ per clinical stratum. You can pass a column name or any expression:</p>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Non-UTI</td> <td align="left">Non-UTI</td>
<td align="left">70.3% (67.9-72.7%)</td> <td align="left">72.5% (69.9-75.1%)</td>
<td align="left">86.8% (84.9-88.7%)</td> <td align="left">86.9% (84.8-89%)</td>
<td align="left">88.4% (86.4-90.2%)</td> <td align="left">91.4% (89.5-93%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">UTI</td> <td align="left">UTI</td>
<td align="left">80.3% (77-83.3%)</td> <td align="left">86% (82.5-89%)</td>
<td align="left">88.4% (85.7-90.8%)</td> <td align="left">94.8% (92.5-96.6%)</td>
<td align="left">91% (88.3-93.3%)</td> <td align="left">97.9% (96.3-99%)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -453,15 +458,15 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Non-UCI</td> <td align="left">Non-UCI</td>
<td align="left">70.4% (68-72.8%)</td> <td align="left">72.6% (69.9-75.3%)</td>
<td align="left">86.7% (84.6-88.7%)</td> <td align="left">87% (84.9-89.1%)</td>
<td align="left">88.5% (86.5-90.2%)</td> <td align="left">91.4% (89.7-92.9%)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">UCI</td> <td align="left">UCI</td>
<td align="left">80.3% (77.2-83.5%)</td> <td align="left">86% (82.7-89%)</td>
<td align="left">88.4% (85.5-90.8%)</td> <td align="left">94.8% (92.7-96.4%)</td>
<td align="left">91% (88.4-93.1%)</td> <td align="left">97.9% (96.5-99%)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@@ -482,6 +487,62 @@ preferred on stewardship grounds.</li>
clinically meaningful difference in coverage.</li> clinically meaningful difference in coverage.</li>
</ul> </ul>
</div> </div>
<div class="section level3">
<h3 id="plotting">Plotting<a class="anchor" aria-label="anchor" href="#plotting"></a>
</h3>
<p>WISCA results can be visualised in several ways. All plot functions
work on the output of <code><a href="../reference/antibiogram.html">wisca()</a></code> (or
<code>antibiogram(..., wisca = TRUE)</code>).</p>
<p>Below we use the <code>wisca_out</code> object that was generated
above.</p>
<div class="section level4">
<h4 id="coverage-with-credible-intervals">Coverage with credible intervals<a class="anchor" aria-label="anchor" href="#coverage-with-credible-intervals"></a>
</h4>
<p>The extended <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> method from the
<code>ggplot2()</code> package produces a point-and-interval plot
showing the coverage estimate and 95% credible interval for each
regimen, grouped by syndromic stratum. This is the most direct way to
compare regimens: overlapping intervals suggest clinical
non-inferiority, non-overlapping intervals indicate a meaningful
difference.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">wisca_out</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-6-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level4">
<h4 id="susceptibility-vs--incidence-weight">Susceptibility vs. incidence weight<a class="anchor" aria-label="anchor" href="#susceptibility-vs--incidence-weight"></a>
</h4>
<p><code><a href="../reference/antibiogram.html">wisca_plot()</a></code> produces a scatter plot of the Monte Carlo
simulation draws, showing each pathogen’s susceptibility (x-axis)
against its incidence weight (y-axis) for each regimen. Each dot
represents one of 1,000 simulated draws, so the spread reflects
posterior uncertainty. This plot reveals <em>why</em> a regimen achieves
its coverage: you can see which pathogens dominate the syndrome (high on
the y-axis), how susceptible they are (position on the x-axis), and how
uncertain both estimates are (spread of the cloud). The dashed vertical
lines denote the point estimates, i.e., the coverage percentages. The
ribbon behind the dashed lines denote the credible interval, which is
95% at default.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-7-1.png" class="r-plt" alt="" width="720"></p>
</div>
<div class="section level4">
<h4 id="posterior-coverage-distributions">Posterior coverage distributions<a class="anchor" aria-label="anchor" href="#posterior-coverage-distributions"></a>
</h4>
<p>Setting <code>wisca_plot_type = "posterior_coverage"</code> shows the
full posterior distribution of coverage for each regimen as a density
curve. This is the most complete representation of what the Bayesian
model produces: each curve shows the relative likelihood of each
coverage value across all 1,000 simulations. Narrow, tall peaks indicate
high certainty; wide, flat curves indicate greater uncertainty. Where
two curves overlap, the regimens cannot be confidently
distinguished.</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span>, wisca_plot_type <span class="op">=</span> <span class="st">"posterior_coverage"</span><span class="op">)</span></span></code></pre></div>
<p><img src="WISCA_files/figure-html/unnamed-chunk-8-1.png" class="r-plt" alt="" width="720"></p>
</div>
</div>
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a> <h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
@@ -554,7 +615,7 @@ by any clinical variable</li>
intervals that honestly communicate uncertainty</li> intervals that honestly communicate uncertainty</li>
</ul> </ul>
<p>It is available in the <code>AMR</code> package via either:</p> <p>It is available in the <code>AMR</code> package via either:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@@ -593,7 +654,7 @@ of weighted-incidence syndromic combination antibiograms (WISCA).
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

86
articles/WISCA.md
View File

@@ -214,6 +214,10 @@ data
# Add a synthetic syndrome column for demonstration # Add a synthetic syndrome column for demonstration
data$syndrome <- ifelse(data$mo %like% "coli", "UTI", "Non-UTI") data$syndrome <- ifelse(data$mo %like% "coli", "UTI", "Non-UTI")
# Keep only 10 most common microorganisms
data <- top_n_microorganisms(data, n = 10, property = "species")
#> ℹ Using column mo as input for `col_mo`.
``` ```
### Basic WISCA ### Basic WISCA
@@ -226,8 +230,8 @@ wisca(data,
``` ```
| Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin | | Amoxicillin/clavulanic acid | Ciprofloxacin | Gentamicin |
|:----------------------------|:-------------------|:-------------------| |:----------------------------|:-------------------|:-----------------|
| 74.2% (72.1-76.1%) | 78.4% (75.6-81.1%) | 72.5% (70.4-74.6%) | | 76.8% (74.7-79.1%) | 81.5% (78.9-84.1%) | 82.9% (81-84.8%) |
### Use combination regimens ### Use combination regimens
@@ -243,7 +247,7 @@ wisca(data,
| Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin | | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
|:---|:---|:---| |:---|:---|:---|
| 74.2% (72.2-76.1%) | 88.8% (87.2-90.4%) | 90.8% (89.4-92.2%) | | 76.8% (74.6-78.9%) | 89.6% (88-91.1%) | 93.7% (92.5-94.9%) |
### Stratify by syndrome ### Stratify by syndrome
@@ -252,16 +256,17 @@ stratum. You can pass a column name or any expression:
``` r ``` r
wisca(data, wisca_out <- wisca(data,
antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"), antimicrobials = c("AMC", "AMC + CIP", "AMC + GEN"),
syndromic_group = "syndrome" syndromic_group = "syndrome"
) )
wisca_out
``` ```
| Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin | | Syndromic Group | Amoxicillin/clavulanic acid | Amoxicillin/clavulanic acid + Ciprofloxacin | Amoxicillin/clavulanic acid + Gentamicin |
|:---|:---|:---|:---| |:---|:---|:---|:---|
| Non-UTI | 70.3% (67.9-72.7%) | 86.8% (84.9-88.7%) | 88.4% (86.4-90.2%) | | Non-UTI | 72.5% (69.9-75.1%) | 86.9% (84.8-89%) | 91.4% (89.5-93%) |
| UTI | 80.3% (77-83.3%) | 88.4% (85.7-90.8%) | 91% (88.3-93.3%) | | UTI | 86% (82.5-89%) | 94.8% (92.5-96.6%) | 97.9% (96.3-99%) |
The `AMR` package is available in 28 languages, which can all be used The `AMR` package is available in 28 languages, which can all be used
for the [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) for the [`wisca()`](https://amr-for-r.org/reference/antibiogram.md)
@@ -278,8 +283,8 @@ wisca(data,
| Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina | | Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/ácido clavulánico + Gentamicina |
|:---|:---|:---|:---| |:---|:---|:---|:---|
| Non-UCI | 70.4% (68-72.8%) | 86.7% (84.6-88.7%) | 88.5% (86.5-90.2%) | | Non-UCI | 72.6% (69.9-75.3%) | 87% (84.9-89.1%) | 91.4% (89.7-92.9%) |
| UCI | 80.3% (77.2-83.5%) | 88.4% (85.5-90.8%) | 91% (88.4-93.1%) | | UCI | 86% (82.7-89%) | 94.8% (92.7-96.4%) | 97.9% (96.5-99%) |
### Interpreting the output ### Interpreting the output
@@ -293,6 +298,71 @@ Each row shows the estimated empirical coverage for a regimen, with a
- **Non-overlapping credible intervals** indicate a clinically - **Non-overlapping credible intervals** indicate a clinically
meaningful difference in coverage. meaningful difference in coverage.
### Plotting
WISCA results can be visualised in several ways. All plot functions work
on the output of
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) (or
`antibiogram(..., wisca = TRUE)`).
Below we use the `wisca_out` object that was generated above.
#### Coverage with credible intervals
The extended
[`autoplot()`](https://ggplot2.tidyverse.org/reference/autoplot.html)
method from the `ggplot2()` package produces a point-and-interval plot
showing the coverage estimate and 95% credible interval for each
regimen, grouped by syndromic stratum. This is the most direct way to
compare regimens: overlapping intervals suggest clinical
non-inferiority, non-overlapping intervals indicate a meaningful
difference.
``` r
ggplot2::autoplot(wisca_out)
```
![](WISCA_files/figure-html/unnamed-chunk-6-1.png)
#### Susceptibility vs. incidence weight
[`wisca_plot()`](https://amr-for-r.org/reference/antibiogram.md)
produces a scatter plot of the Monte Carlo simulation draws, showing
each pathogen’s susceptibility (x-axis) against its incidence weight
(y-axis) for each regimen. Each dot represents one of 1,000 simulated
draws, so the spread reflects posterior uncertainty. This plot reveals
*why* a regimen achieves its coverage: you can see which pathogens
dominate the syndrome (high on the y-axis), how susceptible they are
(position on the x-axis), and how uncertain both estimates are (spread
of the cloud). The dashed vertical lines denote the point estimates,
i.e., the coverage percentages. The ribbon behind the dashed lines
denote the credible interval, which is 95% at default.
``` r
wisca_plot(wisca_out)
```
![](WISCA_files/figure-html/unnamed-chunk-7-1.png)
#### Posterior coverage distributions
Setting `wisca_plot_type = "posterior_coverage"` shows the full
posterior distribution of coverage for each regimen as a density curve.
This is the most complete representation of what the Bayesian model
produces: each curve shows the relative likelihood of each coverage
value across all 1,000 simulations. Narrow, tall peaks indicate high
certainty; wide, flat curves indicate greater uncertainty. Where two
curves overlap, the regimens cannot be confidently distinguished.
``` r
wisca_plot(wisca_out, wisca_plot_type = "posterior_coverage")
```
![](WISCA_files/figure-html/unnamed-chunk-8-1.png)
## Sensible defaults, which can be customised ## Sensible defaults, which can be customised
- `simulations = 1000`: number of Monte Carlo draws - `simulations = 1000`: number of Monte Carlo draws

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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -1327,7 +1327,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>MUP</em>, and <em>RIF</em>.</p> <em>MUP</em>, and <em>RIF</em>.</p>
<p>This data set is in R available as <code>example_isolates</code>, <p>This data set is in R available as <code>example_isolates</code>,
after you load the <code>AMR</code> package.</p> after you load the <code>AMR</code> package.</p>
<p>It was last updated on 9 February 2026 12:16:36 UTC. Find more info <p>It was last updated on 24 June 2026 16:36:47 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
here</a>.</p> here</a>.</p>
<p><strong>Example content</strong></p> <p><strong>Example content</strong></p>
@@ -2052,7 +2052,7 @@ inhibitors</td>
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
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View File

@@ -418,8 +418,8 @@ column names:
This data set is in R available as `example_isolates`, after you load This data set is in R available as `example_isolates`, after you load
the `AMR` package. the `AMR` package.
It was last updated on 9 February 2026 12:16:36 UTC. Find more info It was last updated on 24 June 2026 16:36:47 UTC. Find more info about
about the contents, (scientific) source, and structure of this [data set the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/example_isolates.html). here](https://amr-for-r.org/reference/example_isolates.html).
**Example content** **Example content**

4
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -72,7 +72,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
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View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -198,7 +198,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

232
index.html
View File

@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,7 +84,8 @@
</div> </div>
<ul> <ul>
<li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li> <li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
<li>Peer-reviewed, used in over 175 countries, available in 28 languages</li> <li>
<strong>Peer-reviewed</strong>, used in over 175 countries, available in 28 languages</li>
<li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li> <li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li>
<li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li> <li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
<li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li> <li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
@@ -95,7 +96,7 @@
</li> </li>
</ul> </ul>
<blockquote> <blockquote>
<p>Now available for Python too! <a href="./articles/AMR_for_Python.html">Click here</a> to read more.</p> <p>Available for Python too! <a href="./articles/AMR_for_Python.html">Click here</a> to read more.</p>
</blockquote> </blockquote>
<div style="display: flex; font-size: 0.8em;"> <div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;"> <p style="text-align:left; width: 50%;">
@@ -112,7 +113,7 @@
</h2> </h2>
<p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> 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. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p> <p>The <code>AMR</code> package is a peer-reviewed, <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> 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. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) 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>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) 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="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p> <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level3"> <div class="section level3">
<h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a> <h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
</h3> </h3>
@@ -169,131 +170,114 @@
<div class="section level3"> <div class="section level3">
<h3 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a> <h3 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
</h3> </h3>
<p>The <code>AMR</code> package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).</p> <p>The <code>AMR</code> package supports four types of antibiograms, with support for 28 languages. If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
<p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p> <p><strong>For empirical therapy guidance (i.e., coverage estimates), use WISCA</strong> (Weighted-Incidence Syndromic Combination Antibiogram). When a clinician starts empirical treatment, the causative pathogen is unknown. The relevant question is not <em>“what percentage of E. coli is susceptible?”</em> but <em>“what is the probability that this regimen will cover whatever pathogen is causing the infection?”</em>. WISCA answers that question directly, weighting susceptibility by pathogen incidence and providing credible intervals via Bayesian simulation. See <code><a href="articles/WISCA.html">vignette("WISCA")</a></code> for the full explanation.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span> <span> minimum <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="co"># Recommended threshold: &gt;=30</span></span>
<span><span class="co">#&gt; (amikacin), and KAN (kanamycin)</span></span> <span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div> <table class="table">
<table style="width:100%;" class="table">
<colgroup> <colgroup>
<col width="14%"> <col width="33%">
<col width="14%"> <col width="33%">
<col width="14%"> <col width="33%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="14%">
</colgroup> </colgroup>
<thead><tr> <thead><tr>
<th align="left">Pathogen</th> <th align="left">Piperacillin/tazobactam</th>
<th align="left">Amikacin</th> <th align="left">Piperacillin/tazobactam + Gentamicin</th>
<th align="left">Gentamicin</th> <th align="left">Piperacillin/tazobactam + Tobramycin</th>
<th align="left">Imipenem</th> </tr></thead>
<th align="left">Kanamycin</th> <tbody><tr>
<th align="left">Meropenem</th> <td align="left">70.1% (64.9-75.7%)</td>
<th align="left">Tobramycin</th> <td align="left">93.6% (92.2-95%)</td>
<td align="left">89.8% (86.7-92.3%)</td>
</tr></tbody>
</table>
<p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="co"># Recommended threshold: &gt;=30</span></span>
<span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="25%">
<col width="25%">
<col width="25%">
<col width="25%">
</colgroup>
<thead><tr>
<th align="left">Syndromic Group</th>
<th align="left">Piperacillin/tazobactam</th>
<th align="left">Piperacillin/tazobactam + Gentamicin</th>
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr> <tr>
<td align="left">CoNS</td> <td align="left">Clinical</td>
<td align="left">0% (0-8%,N=43)</td> <td align="left">74.5% (69.3-80.1%)</td>
<td align="left">86% (82-90%,N=309)</td> <td align="left">93.7% (92-95.1%)</td>
<td align="left">52% (37-67%,N=48)</td> <td align="left">90.5% (87.1-93.1%)</td>
<td align="left">0% (0-8%,N=43)</td>
<td align="left">52% (37-67%,N=48)</td>
<td align="left">22% (12-35%,N=55)</td>
</tr> </tr>
<tr> <tr>
<td align="left"><em>E. coli</em></td> <td align="left">ICU</td>
<td align="left">100% (98-100%,N=171)</td> <td align="left">56.7% (48-65.5%)</td>
<td align="left">98% (96-99%,N=460)</td> <td align="left">86.7% (83.4-89.8%)</td>
<td align="left">100% (99-100%,N=422)</td> <td align="left">82.9% (78.2-87.3%)</td>
<td align="left">NA</td>
<td align="left">100% (99-100%,N=418)</td>
<td align="left">97% (96-99%,N=462)</td>
</tr> </tr>
<tr> <tr>
<td align="left"><em>E. faecalis</em></td> <td align="left">Outpatient</td>
<td align="left">0% (0-9%,N=39)</td> <td align="left">57.8% (46.4-69.7%)</td>
<td align="left">0% (0-9%,N=39)</td> <td align="left">76.5% (70.1-82.2%)</td>
<td align="left">100% (91-100%,N=38)</td> <td align="left">67.9% (57.9-77.5%)</td>
<td align="left">0% (0-9%,N=39)</td>
<td align="left">NA</td>
<td align="left">0% (0-9%,N=39)</td>
</tr>
<tr>
<td align="left"><em>K. pneumoniae</em></td>
<td align="left">NA</td>
<td align="left">90% (79-96%,N=58)</td>
<td align="left">100% (93-100%,N=51)</td>
<td align="left">NA</td>
<td align="left">100% (93-100%,N=53)</td>
<td align="left">90% (79-96%,N=58)</td>
</tr>
<tr>
<td align="left"><em>P. aeruginosa</em></td>
<td align="left">NA</td>
<td align="left">100% (88-100%,N=30)</td>
<td align="left">NA</td>
<td align="left">0% (0-12%,N=30)</td>
<td align="left">NA</td>
<td align="left">100% (88-100%,N=30)</td>
</tr>
<tr>
<td align="left"><em>P. mirabilis</em></td>
<td align="left">NA</td>
<td align="left">94% (80-99%,N=34)</td>
<td align="left">94% (79-99%,N=32)</td>
<td align="left">NA</td>
<td align="left">NA</td>
<td align="left">94% (80-99%,N=34)</td>
</tr>
<tr>
<td align="left"><em>S. aureus</em></td>
<td align="left">NA</td>
<td align="left">99% (97-100%,N=233)</td>
<td align="left">NA</td>
<td align="left">NA</td>
<td align="left">NA</td>
<td align="left">98% (92-100%,N=86)</td>
</tr>
<tr>
<td align="left"><em>S. epidermidis</em></td>
<td align="left">0% (0-8%,N=44)</td>
<td align="left">79% (71-85%,N=163)</td>
<td align="left">NA</td>
<td align="left">0% (0-8%,N=44)</td>
<td align="left">NA</td>
<td align="left">51% (40-61%,N=89)</td>
</tr>
<tr>
<td align="left"><em>S. hominis</em></td>
<td align="left">NA</td>
<td align="left">92% (84-97%,N=80)</td>
<td align="left">NA</td>
<td align="left">NA</td>
<td align="left">NA</td>
<td align="left">85% (74-93%,N=62)</td>
</tr>
<tr>
<td align="left"><em>S. pneumoniae</em></td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left">NA</td>
<td align="left">0% (0-3%,N=117)</td>
<td align="left">NA</td>
<td align="left">0% (0-3%,N=117)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
<p>In combination antibiograms, it is clear that combined antimicrobials yield higher empiric coverage:</p> <p><strong>For AMR surveillance</strong>, traditional antibiograms remain the right tool for tracking resistance per species over time:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"TZP"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="20%">
<col width="20%">
<col width="20%">
<col width="20%">
<col width="20%">
</colgroup>
<thead><tr>
<th align="left">Pathogen</th>
<th align="left">Amoxicillin/clavulanic acid</th>
<th align="left">Imipenem</th>
<th align="left">Meropenem</th>
<th align="left">Piperacillin/tazobactam</th>
</tr></thead>
<tbody>
<tr>
<td align="left">Gram-negative</td>
<td align="left">76% (73-79%,N=726)</td>
<td align="left">99% (98-100%,N=631)</td>
<td align="left">100% (99-100%,N=626)</td>
<td align="left">88% (85-91%,N=641)</td>
</tr>
<tr>
<td align="left">Gram-positive</td>
<td align="left">76% (74-79%,N=1138)</td>
<td align="left">81% (75-85%,N=257)</td>
<td align="left">77% (70-82%,N=203)</td>
<td align="left">86% (82-89%,N=345)</td>
</tr>
</tbody>
</table>
<p>Combination antibiograms show the additional coverage gained by adding a second agent, stratified by species:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup> <colgroup>
<col width="25%"> <col width="25%">
@@ -322,8 +306,8 @@
</tr> </tr>
</tbody> </tbody>
</table> </table>
<p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> comes with support for 28 languages that are often detected automatically based on system language:</p> <p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> and <code><a href="reference/antibiogram.html">wisca()</a></code> come with support for 28 languages that are often detected automatically based on system language:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span> <span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
@@ -362,7 +346,7 @@
<h3 id="interpreting-and-plotting-mic-and-sir-values">Interpreting and plotting MIC and SIR values<a class="anchor" aria-label="anchor" href="#interpreting-and-plotting-mic-and-sir-values"></a> <h3 id="interpreting-and-plotting-mic-and-sir-values">Interpreting and plotting MIC and SIR values<a class="anchor" aria-label="anchor" href="#interpreting-and-plotting-mic-and-sir-values"></a>
</h3> </h3>
<p>The <code>AMR</code> package allows interpretation of MIC and disk diffusion values based on CLSI and EUCAST. Moreover, the <code>ggplot2</code> package is extended with new scale functions, to allow plotting of log2-distributed MIC values and SIR values.</p> <p>The <code>AMR</code> package allows interpretation of MIC and disk diffusion values based on CLSI and EUCAST. Moreover, the <code>ggplot2</code> package is extended with new scale functions, to allow plotting of log2-distributed MIC values and SIR values.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span></span> <span></span>
@@ -395,7 +379,7 @@
<h3 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a> <h3 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
</h3> </h3>
<p>For a manual approach, you can use the <code>resistance</code> or <code><a href="reference/proportion.html">susceptibility()</a></code> function:</p> <p>For a manual approach, you can use the <code>resistance</code> or <code><a href="reference/proportion.html">susceptibility()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># group by ward:</span></span> <span> <span class="co"># group by ward:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span> <span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -415,7 +399,7 @@
<span><span class="co">#&gt; 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span> <span><span class="co">#&gt; 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</span></span></code></pre></div> <span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</span></span></code></pre></div>
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p> <p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span> <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span> <span></span>
@@ -441,7 +425,7 @@
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span> <span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span> <span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div> <span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span> <code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span> <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span> <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
@@ -450,7 +434,7 @@
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span> <span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span> <span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div> <span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span> <code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span> <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span> <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
@@ -492,7 +476,7 @@
</h3> </h3>
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p> <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p> <p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p> <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.</p> <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest beta version.</p>
@@ -503,7 +487,7 @@
<p><a href="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main" alt="check-old"></a> <a href="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main" alt="check-recent"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p> <p><a href="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-old-tinytest.yaml/badge.svg?branch=main" alt="check-old"></a> <a href="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml" class="external-link"><img src="https://github.com/msberends/AMR/actions/workflows/check-current-testthat.yaml/badge.svg?branch=main" alt="check-recent"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
<p>Please read our <a href="https://github.com/msberends/AMR/wiki/Developer-Guideline" class="external-link">Developer Guideline here</a>.</p> <p>Please read our <a href="https://github.com/msberends/AMR/wiki/Developer-Guideline" class="external-link">Developer Guideline here</a>.</p>
<p>To install the latest and unpublished beta version:</p> <p>To install the latest and unpublished beta version:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span>, repos <span class="op">=</span> <span class="st">"beta.amr-for-r.org"</span><span class="op">)</span></span>
<span></span> <span></span>
<span><span class="co"># if this does not work, try to install directly from GitHub using the 'remotes' package:</span></span> <span><span class="co"># if this does not work, try to install directly from GitHub using the 'remotes' package:</span></span>
@@ -572,7 +556,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

95
index.md
View File

@@ -2,7 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- Peer-reviewed, used in over 175 countries, available in 28 languages - **Peer-reviewed**, used in over 175 countries, available in 28
languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -17,7 +18,7 @@
- 100% free of costs and dependencies, highly suitable for places with - 100% free of costs and dependencies, highly suitable for places with
**limited resources** **limited resources**
> Now available for Python too! [Click > Available for Python too! [Click
> here](https://amr-for-r.org/articles/AMR_for_Python.md) to read more. > here](https://amr-for-r.org/articles/AMR_for_Python.md) to read more.
[amr-for-r.org](https://amr-for-r.org/) [amr-for-r.org](https://amr-for-r.org/)
@@ -51,7 +52,7 @@ formed the basis of two PhD theses ([DOI
After installing this package, R knows [**~97 000 distinct microbial After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.md) (updated species**](https://amr-for-r.org/reference/microorganisms.md) (updated
June 2024) and all [**~620 antimicrobial and antiviral May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral clinical CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -154,43 +155,76 @@ in the `AMR` package make sure you get what you meant.
### Generating antibiograms ### Generating antibiograms
The `AMR` package supports generating traditional, combined, syndromic, The `AMR` package supports four types of antibiograms, with support for
and even weighted-incidence syndromic combination antibiograms (WISCA). 28 languages. If used inside [R Markdown](https://rmarkdown.rstudio.com)
or [Quarto](https://quarto.org), the table will be printed in the right
If used inside [R Markdown](https://rmarkdown.rstudio.com) or
[Quarto](https://quarto.org), the table will be printed in the right
output format automatically (such as markdown, LaTeX, HTML, etc.). output format automatically (such as markdown, LaTeX, HTML, etc.).
**For empirical therapy guidance (i.e., coverage estimates), use WISCA**
(Weighted-Incidence Syndromic Combination Antibiogram). When a clinician
starts empirical treatment, the causative pathogen is unknown. The
relevant question is not *“what percentage of E. coli is susceptible?”*
but *“what is the probability that this regimen will cover whatever
pathogen is causing the infection?”*. WISCA answers that question
directly, weighting susceptibility by pathogen incidence and providing
credible intervals via Bayesian simulation. See
[`vignette("WISCA")`](https://amr-for-r.org/articles/WISCA.md) for the
full explanation.
``` r
wisca(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
minimum = 10) # Recommended threshold: >=30
#> Warning: invalid microorganism code, NA generated
```
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
| 70.1% (64.9-75.7%) | 93.6% (92.2-95%) | 89.8% (86.7-92.3%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
``` r
wisca(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
syndromic_group = "ward",
minimum = 10) # Recommended threshold: >=30
#> Warning: invalid microorganism code, NA generated
```
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
| Clinical | 74.5% (69.3-80.1%) | 93.7% (92-95.1%) | 90.5% (87.1-93.1%) |
| ICU | 56.7% (48-65.5%) | 86.7% (83.4-89.8%) | 82.9% (78.2-87.3%) |
| Outpatient | 57.8% (46.4-69.7%) | 76.5% (70.1-82.2%) | 67.9% (57.9-77.5%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems())) mo_transform = "gramstain",
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK antimicrobials = c("AMC", carbapenems(), "TZP"))
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
``` ```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin | | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
|:---|:---|:---|:---|:---|:---|:---| |:---|:---|:---|:---|:---|
| CoNS | 0% (0-8%,N=43) | 86% (82-90%,N=309) | 52% (37-67%,N=48) | 0% (0-8%,N=43) | 52% (37-67%,N=48) | 22% (12-35%,N=55) | | Gram-negative | 76% (73-79%,N=726) | 99% (98-100%,N=631) | 100% (99-100%,N=626) | 88% (85-91%,N=641) |
| *E. coli* | 100% (98-100%,N=171) | 98% (96-99%,N=460) | 100% (99-100%,N=422) | NA | 100% (99-100%,N=418) | 97% (96-99%,N=462) | | Gram-positive | 76% (74-79%,N=1138) | 81% (75-85%,N=257) | 77% (70-82%,N=203) | 86% (82-89%,N=345) |
| *E. faecalis* | 0% (0-9%,N=39) | 0% (0-9%,N=39) | 100% (91-100%,N=38) | 0% (0-9%,N=39) | NA | 0% (0-9%,N=39) |
| *K. pneumoniae* | NA | 90% (79-96%,N=58) | 100% (93-100%,N=51) | NA | 100% (93-100%,N=53) | 90% (79-96%,N=58) |
| *P. aeruginosa* | NA | 100% (88-100%,N=30) | NA | 0% (0-12%,N=30) | NA | 100% (88-100%,N=30) |
| *P. mirabilis* | NA | 94% (80-99%,N=34) | 94% (79-99%,N=32) | NA | NA | 94% (80-99%,N=34) |
| *S. aureus* | NA | 99% (97-100%,N=233) | NA | NA | NA | 98% (92-100%,N=86) |
| *S. epidermidis* | 0% (0-8%,N=44) | 79% (71-85%,N=163) | NA | 0% (0-8%,N=44) | NA | 51% (40-61%,N=89) |
| *S. hominis* | NA | 92% (84-97%,N=80) | NA | NA | NA | 85% (74-93%,N=62) |
| *S. pneumoniae* | 0% (0-3%,N=117) | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) |
In combination antibiograms, it is clear that combined antimicrobials Combination antibiograms show the additional coverage gained by adding a
yield higher empiric coverage: second agent, stratified by species:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain",
mo_transform = "gramstain") antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
``` ```
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -199,9 +233,10 @@ antibiogram(example_isolates,
| Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) | | Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) |
Like many other functions in this package, Like many other functions in this package,
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) comes [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and
with support for 28 languages that are often detected automatically [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) come with
based on system language: support for 28 languages that are often detected automatically based on
system language:
``` r ``` r

95
llms.txt
View File

@@ -2,7 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- Peer-reviewed, used in over 175 countries, available in 28 languages - **Peer-reviewed**, used in over 175 countries, available in 28
languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -17,7 +18,7 @@
- 100% free of costs and dependencies, highly suitable for places with - 100% free of costs and dependencies, highly suitable for places with
**limited resources** **limited resources**
> Now available for Python too! [Click > Available for Python too! [Click
> here](https://amr-for-r.org/articles/AMR_for_Python.md) to read more. > here](https://amr-for-r.org/articles/AMR_for_Python.md) to read more.
[amr-for-r.org](https://amr-for-r.org/) [amr-for-r.org](https://amr-for-r.org/)
@@ -51,7 +52,7 @@ formed the basis of two PhD theses ([DOI
After installing this package, R knows [**~97 000 distinct microbial After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.md) (updated species**](https://amr-for-r.org/reference/microorganisms.md) (updated
June 2024) and all [**~620 antimicrobial and antiviral May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and drugs**](https://amr-for-r.org/reference/antimicrobials.md) by name and
code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral clinical CT), and knows all about valid SIR and MIC values. The integral clinical
@@ -154,43 +155,76 @@ in the `AMR` package make sure you get what you meant.
### Generating antibiograms ### Generating antibiograms
The `AMR` package supports generating traditional, combined, syndromic, The `AMR` package supports four types of antibiograms, with support for
and even weighted-incidence syndromic combination antibiograms (WISCA). 28 languages. If used inside [R Markdown](https://rmarkdown.rstudio.com)
or [Quarto](https://quarto.org), the table will be printed in the right
If used inside [R Markdown](https://rmarkdown.rstudio.com) or
[Quarto](https://quarto.org), the table will be printed in the right
output format automatically (such as markdown, LaTeX, HTML, etc.). output format automatically (such as markdown, LaTeX, HTML, etc.).
**For empirical therapy guidance (i.e., coverage estimates), use WISCA**
(Weighted-Incidence Syndromic Combination Antibiogram). When a clinician
starts empirical treatment, the causative pathogen is unknown. The
relevant question is not *“what percentage of E. coli is susceptible?”*
but *“what is the probability that this regimen will cover whatever
pathogen is causing the infection?”*. WISCA answers that question
directly, weighting susceptibility by pathogen incidence and providing
credible intervals via Bayesian simulation. See
[`vignette("WISCA")`](https://amr-for-r.org/articles/WISCA.md) for the
full explanation.
``` r
wisca(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
minimum = 10) # Recommended threshold: >=30
#> Warning: invalid microorganism code, NA generated
```
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
| 70.1% (64.9-75.7%) | 93.6% (92.2-95%) | 89.8% (86.7-92.3%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
``` r
wisca(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
syndromic_group = "ward",
minimum = 10) # Recommended threshold: >=30
#> Warning: invalid microorganism code, NA generated
```
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
| Clinical | 74.5% (69.3-80.1%) | 93.7% (92-95.1%) | 90.5% (87.1-93.1%) |
| ICU | 56.7% (48-65.5%) | 86.7% (83.4-89.8%) | 82.9% (78.2-87.3%) |
| Outpatient | 57.8% (46.4-69.7%) | 76.5% (70.1-82.2%) | 67.9% (57.9-77.5%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c(aminoglycosides(), carbapenems())) mo_transform = "gramstain",
#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK antimicrobials = c("AMC", carbapenems(), "TZP"))
#> (amikacin), and KAN (kanamycin)
#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem) #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
``` ```
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin | | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
|:---|:---|:---|:---|:---|:---|:---| |:---|:---|:---|:---|:---|
| CoNS | 0% (0-8%,N=43) | 86% (82-90%,N=309) | 52% (37-67%,N=48) | 0% (0-8%,N=43) | 52% (37-67%,N=48) | 22% (12-35%,N=55) | | Gram-negative | 76% (73-79%,N=726) | 99% (98-100%,N=631) | 100% (99-100%,N=626) | 88% (85-91%,N=641) |
| *E. coli* | 100% (98-100%,N=171) | 98% (96-99%,N=460) | 100% (99-100%,N=422) | NA | 100% (99-100%,N=418) | 97% (96-99%,N=462) | | Gram-positive | 76% (74-79%,N=1138) | 81% (75-85%,N=257) | 77% (70-82%,N=203) | 86% (82-89%,N=345) |
| *E. faecalis* | 0% (0-9%,N=39) | 0% (0-9%,N=39) | 100% (91-100%,N=38) | 0% (0-9%,N=39) | NA | 0% (0-9%,N=39) |
| *K. pneumoniae* | NA | 90% (79-96%,N=58) | 100% (93-100%,N=51) | NA | 100% (93-100%,N=53) | 90% (79-96%,N=58) |
| *P. aeruginosa* | NA | 100% (88-100%,N=30) | NA | 0% (0-12%,N=30) | NA | 100% (88-100%,N=30) |
| *P. mirabilis* | NA | 94% (80-99%,N=34) | 94% (79-99%,N=32) | NA | NA | 94% (80-99%,N=34) |
| *S. aureus* | NA | 99% (97-100%,N=233) | NA | NA | NA | 98% (92-100%,N=86) |
| *S. epidermidis* | 0% (0-8%,N=44) | 79% (71-85%,N=163) | NA | 0% (0-8%,N=44) | NA | 51% (40-61%,N=89) |
| *S. hominis* | NA | 92% (84-97%,N=80) | NA | NA | NA | 85% (74-93%,N=62) |
| *S. pneumoniae* | 0% (0-3%,N=117) | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) | NA | 0% (0-3%,N=117) |
In combination antibiograms, it is clear that combined antimicrobials Combination antibiograms show the additional coverage gained by adding a
yield higher empiric coverage: second agent, stratified by species:
``` r ``` r
antibiogram(example_isolates, antibiogram(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), mo_transform = "gramstain",
mo_transform = "gramstain") antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
``` ```
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
@@ -199,9 +233,10 @@ antibiogram(example_isolates,
| Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) | | Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) |
Like many other functions in this package, Like many other functions in this package,
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) comes [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and
with support for 28 languages that are often detected automatically [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) come with
based on system language: support for 28 languages that are often detected automatically based on
system language:
``` r ``` r

2
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@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<svg id="Layer_1" data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 1375.95 263.65"> <svg id="Layer_1" data-name="Layer 1" xmlns="http://www.w3.org/2000/svg" viewBox="-49.78 -9.45 1469.40 284.96">
<defs> <defs>
<style> <style>
.cls-1 { .cls-1 {
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 3.6 KiB

After

Width:  |  Height:  |  Size: 3.6 KiB

14
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View File

@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,15 +49,15 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9063" id="amr-3019063">AMR 3.0.1.9063<a class="anchor" aria-label="anchor" href="#amr-3019063"></a></h2> <h2 class="pkg-version" data-toc-text="3.0.1.9065" id="amr-3019065">AMR 3.0.1.9065<a class="anchor" aria-label="anchor" href="#amr-3019065"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p> <p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4"> <div class="section level4">
<h4 id="breaking-changes-3-0-1-9063">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9063"></a></h4> <h4 id="breaking-changes-3-0-1-9065">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9065"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li> <ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li> <li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="new-3-0-1-9063">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9063"></a></h4> <h4 id="new-3-0-1-9065">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9065"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li> <ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li> <li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li> <li>
@@ -74,7 +74,7 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li> <li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="fixed-3-0-1-9063">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9063"></a></h4> <h4 id="fixed-3-0-1-9065">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9065"></a></h4>
<ul><li> <ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> <code><a href="../reference/as.sir.html">as.sir()</a></code>
<ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li> <ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
@@ -101,7 +101,7 @@
</li> </li>
</ul></div> </ul></div>
<div class="section level4"> <div class="section level4">
<h4 id="updated-3-0-1-9063">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9063"></a></h4> <h4 id="updated-3-0-1-9065">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9065"></a></h4>
<ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li> <ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
<li> <li>
<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li> <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li>
@@ -337,7 +337,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

2
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@@ -1,6 +1,6 @@
# Changelog # Changelog
## AMR 3.0.1.9063 ## AMR 3.0.1.9065
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

2
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html PCA: PCA.html
WHONET: WHONET.html WHONET: WHONET.html
WISCA: WISCA.html WISCA: WISCA.html
last_built: 2026-06-24T08:28Z last_built: 2026-06-24T17:02Z
urls: urls:
reference: https://amr-for-r.org/reference reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles article: https://amr-for-r.org/articles

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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,7 +67,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -109,7 +109,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

10
reference/AMR.html
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@@ -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 formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375 and doi:10.33612/diss.192486375
). ).
After installing this package, R knows ~97 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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 and the University Medical Center Groningen. After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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 and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package. The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
The AMR package is a peer-reviewed, 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. We are a team of many different researchers from around the globe to make this a successful and durable project! The AMR package is a peer-reviewed, 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. We are a team of many different researchers from around the globe to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03 This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375 and doi:10.33612/diss.192486375
). ).
After installing this package, R knows ~97 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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 and the University Medical Center Groningen. After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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 and the University Medical Center Groningen.
The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -70,7 +70,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
) 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 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> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
).</p> ).</p>
<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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> and the <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://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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> and the <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, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p> <p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div> </div>
@@ -148,7 +148,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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2
reference/AMR.md
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@@ -25,7 +25,7 @@ and
After installing this package, R knows [**~97 000 distinct microbial After installing this package, R knows [**~97 000 distinct microbial
species**](https://amr-for-r.org/reference/microorganisms.html) (updated species**](https://amr-for-r.org/reference/microorganisms.html) (updated
June 2024) and all [**~620 antimicrobial and antiviral May 2026) and all [**~620 antimicrobial and antiviral
drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED 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 CT), and knows all about valid SIR and MIC values. The integral clinical

4
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -87,7 +87,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -126,7 +126,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -203,7 +203,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -449,7 +449,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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4
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -208,7 +208,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -251,7 +251,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -129,7 +129,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -164,7 +164,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -229,7 +229,7 @@ may affect the computations for subsequent operations.</p></dd>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -102,7 +102,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
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@@ -446,7 +446,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 74.2% (72.1-76.1%) 88.8% (87.2-90.3%) 90.8% (89.3-92.1%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 74.2% (72.2-76.1%) 88.8% (87.1-90.3%) 90.8% (89.3-92.2%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Amoxicillin/clavulanic acid + Gentamicin`</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Amoxicillin/clavulanic acid + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@@ -465,7 +465,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 74.2% (72.2-76.1%) 88.8% (87.1-90.4%) 90.8% (89.4-92.2%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 74.1% (72.1-75.9%) 88.8% (87.1-90.3%) 90.8% (89.5-92.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Amoxicillin/clavulanic acid + Gentamicin`</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`Amoxicillin/clavulanic acid + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@@ -485,8 +485,8 @@ All antibiogram types adhere to previously described approaches (see Source), an
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span> <span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 74.5% (68.8-79.8%) 93.6% (91.9-95.1%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 74.7% (69-80.3%) 93.6% (91.9-95.1%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57.1% (48.2-65.9%) 86.7% (83.3-89.9%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 57% (48.2-66%) 86.7% (83.5-89.7%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 57.5% (46-68.7%) 76.5% (70.6-82.2%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 57.5% (46-68.7%) 76.5% (70.6-82.2%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
@@ -515,14 +515,14 @@ All antibiogram types adhere to previously described approaches (see Source), an
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Simulations: 1000 per stratum</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> age_group gender `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentami…¹</span> <span class="r-out co"><span class="r-pr">#&gt;</span> age_group gender `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentami…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 0-24 F 57.7% (29.5-82.6%) 70.5% (45.9-89.1%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 0-24 F 57.7% (29.5-82.1%) 70.5% (46.1-89%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 0-24 M 59.1% (33-84.2%) 76.1% (55.7-90.6%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 0-24 M 59.3% (33.1-84.2%) 76.2% (55.7-90.9%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 25-49 F 67.4% (43.3-90.5%) 93.8% (87.8-97.9%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 25-49 F 67.4% (43.3-90.4%) 93.8% (87.8-97.9%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 25-49 M 56.8% (27.5-86.5%) 90.9% (82.4-96.8%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 25-49 M 56.9% (27.1-86.5%) 90.9% (82.6-96.8%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 50-74 F 68% (53.3-82.3%) 96.9% (94.7-98.5%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 50-74 F 68.1% (53.3-82.6%) 96.9% (94.7-98.5%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 50-74 M 67.1% (56.5-77.5%) 96.8% (94.2-98.8%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 50-74 M 67.1% (56.3-77.3%) 96.8% (94.3-98.8%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> 75+ F 73.3% (62.9-83.6%) 97.7% (96-98.9%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> 75+ F 73.3% (62.9-83.7%) 97.7% (96.1-98.9%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> 75+ M 74% (64.2-83.1%) 97.9% (96.1-99.1%) </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> 75+ M 74% (64.1-82.9%) 97.9% (96-99%) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` &lt;chr&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,</span></span>
@@ -705,8 +705,8 @@ All antibiogram types adhere to previously described approaches (see Source), an
<span class="r-out co"><span class="r-pr">#&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span> <span class="r-out co"><span class="r-pr">#&gt;</span> |Syndromic Group |Piperacillin/tazobactam |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span> <span class="r-out co"><span class="r-pr">#&gt;</span> |:---------------|:-----------------------|</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |74.6% (68.9-80%) |</span> <span class="r-out co"><span class="r-pr">#&gt;</span> |Clinical |74.7% (68.7-79.8%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |57% (49.1-65.8%) |</span> <span class="r-out co"><span class="r-pr">#&gt;</span> |ICU |56.8% (48.9-65.7%) |</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |57.4% (45.6-68.4%) |</span> <span class="r-out co"><span class="r-pr">#&gt;</span> |Outpatient |57.4% (45.6-68.4%) |</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
@@ -744,7 +744,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

28
reference/antibiogram.md
View File

@@ -660,7 +660,7 @@ wisca(example_isolates,
#> # Simulations: 1000 per stratum #> # Simulations: 1000 per stratum
#> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…² #> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²
#> <chr> <chr> <chr> #> <chr> <chr> <chr>
#> 1 74.2% (72.1-76.1%) 88.8% (87.2-90.3%) 90.8% (89.3-92.1%) #> 1 74.2% (72.2-76.1%) 88.8% (87.1-90.3%) 90.8% (89.3-92.2%)
#> # ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`, #> # ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,
#> # ²​`Amoxicillin/clavulanic acid + Gentamicin` #> # ²​`Amoxicillin/clavulanic acid + Gentamicin`
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram, #> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
@@ -679,7 +679,7 @@ antibiogram(example_isolates,
#> # Simulations: 1000 per stratum #> # Simulations: 1000 per stratum
#> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…² #> `Amoxicillin/clavulanic acid` Amoxicillin/clavulanic …¹ Amoxicillin/clavulan…²
#> <chr> <chr> <chr> #> <chr> <chr> <chr>
#> 1 74.2% (72.2-76.1%) 88.8% (87.1-90.4%) 90.8% (89.4-92.2%) #> 1 74.1% (72.1-75.9%) 88.8% (87.1-90.3%) 90.8% (89.5-92.1%)
#> # ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`, #> # ℹ abbreviated names: ¹​`Amoxicillin/clavulanic acid + Ciprofloxacin`,
#> # ²​`Amoxicillin/clavulanic acid + Gentamicin` #> # ²​`Amoxicillin/clavulanic acid + Gentamicin`
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram, #> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
@@ -699,8 +699,8 @@ out
#> # Simulations: 1000 per stratum #> # Simulations: 1000 per stratum
#> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹ #> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹
#> <chr> <chr> <chr> #> <chr> <chr> <chr>
#> 1 Clinical 74.5% (68.8-79.8%) 93.6% (91.9-95.1%) #> 1 Clinical 74.7% (69-80.3%) 93.6% (91.9-95.1%)
#> 2 ICU 57.1% (48.2-65.9%) 86.7% (83.3-89.9%) #> 2 ICU 57% (48.2-66%) 86.7% (83.5-89.7%)
#> 3 Outpatient 57.5% (46-68.7%) 76.5% (70.6-82.2%) #> 3 Outpatient 57.5% (46-68.7%) 76.5% (70.6-82.2%)
#> # ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin` #> # ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`
#> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr> #> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr>
@@ -729,14 +729,14 @@ if (requireNamespace("dplyr")) {
#> # Simulations: 1000 per stratum #> # Simulations: 1000 per stratum
#> age_group gender `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentami…¹ #> age_group gender `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentami…¹
#> <chr> <chr> <chr> <chr> #> <chr> <chr> <chr> <chr>
#> 1 0-24 F 57.7% (29.5-82.6%) 70.5% (45.9-89.1%) #> 1 0-24 F 57.7% (29.5-82.1%) 70.5% (46.1-89%)
#> 2 0-24 M 59.1% (33-84.2%) 76.1% (55.7-90.6%) #> 2 0-24 M 59.3% (33.1-84.2%) 76.2% (55.7-90.9%)
#> 3 25-49 F 67.4% (43.3-90.5%) 93.8% (87.8-97.9%) #> 3 25-49 F 67.4% (43.3-90.4%) 93.8% (87.8-97.9%)
#> 4 25-49 M 56.8% (27.5-86.5%) 90.9% (82.4-96.8%) #> 4 25-49 M 56.9% (27.1-86.5%) 90.9% (82.6-96.8%)
#> 5 50-74 F 68% (53.3-82.3%) 96.9% (94.7-98.5%) #> 5 50-74 F 68.1% (53.3-82.6%) 96.9% (94.7-98.5%)
#> 6 50-74 M 67.1% (56.5-77.5%) 96.8% (94.2-98.8%) #> 6 50-74 M 67.1% (56.3-77.3%) 96.8% (94.3-98.8%)
#> 7 75+ F 73.3% (62.9-83.6%) 97.7% (96-98.9%) #> 7 75+ F 73.3% (62.9-83.7%) 97.7% (96.1-98.9%)
#> 8 75+ M 74% (64.2-83.1%) 97.9% (96.1-99.1%) #> 8 75+ M 74% (64.1-82.9%) 97.9% (96-99%)
#> # ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin` #> # ℹ abbreviated name: ¹​`Piperacillin/tazobactam + Gentamicin`
#> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr> #> # ℹ 1 more variable: `Piperacillin/tazobactam + Tobramycin` <chr>
#> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram, #> # Use `ggplot2::autoplot()` or base R `plot()` to create a plot of this antibiogram,
@@ -919,8 +919,8 @@ if (requireNamespace("knitr")) {
#> #>
#> |Syndromic Group |Piperacillin/tazobactam | #> |Syndromic Group |Piperacillin/tazobactam |
#> |:---------------|:-----------------------| #> |:---------------|:-----------------------|
#> |Clinical |74.6% (68.9-80%) | #> |Clinical |74.7% (68.7-79.8%) |
#> |ICU |57% (49.1-65.8%) | #> |ICU |56.8% (48.9-65.7%) |
#> |Outpatient |57.4% (45.6-68.4%) | #> |Outpatient |57.4% (45.6-68.4%) |

4
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
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reference/as.ab.html
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reference/as.av.html
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@@ -7,7 +7,7 @@
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reference/as.disk.html
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@@ -7,7 +7,7 @@
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reference/as.mic.html
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@@ -7,7 +7,7 @@
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reference/as.mo.html
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@@ -7,7 +7,7 @@
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reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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@@ -458,10 +458,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-24 <span style="color: #949494;">08:31:34</span> 1 MIC amoxicillin Escherich… human 8 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-24 <span style="color: #949494;">17:04:09</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-24 <span style="color: #949494;">08:31:35</span> 1 MIC cipro Escherich… human 0.256 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-24 <span style="color: #949494;">17:04:09</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-24 <span style="color: #949494;">08:31:35</span> 1 DISK tobra Escherich… human 16 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-24 <span style="color: #949494;">17:04:10</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-24 <span style="color: #949494;">08:31:36</span> 1 DISK genta Escherich… human 18 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-24 <span style="color: #949494;">17:04:10</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -718,7 +718,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
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reference/as.sir.md
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@@ -705,10 +705,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18 #> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given #> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr> #> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-06-24 08:31:34 1 MIC amoxicillin Escherich… human 8 #> 1 2026-06-24 17:04:09 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-24 08:31:35 1 MIC cipro Escherich… human 0.256 #> 2 2026-06-24 17:04:09 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-24 08:31:35 1 DISK tobra Escherich… human 16 #> 3 2026-06-24 17:04:10 1 DISK tobra Escherich… human 16
#> 4 2026-06-24 08:31:36 1 DISK genta Escherich… human 18 #> 4 2026-06-24 17:04:10 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>, #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>, #> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr> #> # breakpoint_S_R <chr>, site <chr>

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reference/atc_online.html
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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@@ -142,7 +142,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/av_property.html
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@@ -7,7 +7,7 @@
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@@ -263,7 +263,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/availability.html
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@@ -7,7 +7,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@@ -297,7 +297,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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@@ -7,7 +7,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/dosage.html
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@@ -7,7 +7,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@@ -99,7 +99,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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4
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,7 +86,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
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@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -381,7 +381,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
reference/g.test.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -228,7 +228,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

110
reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -154,29 +154,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span> <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 20 43 19 12 43 41 12 28 30 15 41 18 34 6 15 9 29 8 45 16 43 10 14 9 42</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 28 47 7 7 6 17 9 4 37 11 43 43 14 38 26 38 12 39 49 18 15 27 5 22 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 48 8 28 24 4 31 45 20 43 47 4 30 2 15 22 15 19 32 27 4 11 12 3 2 28</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [26] 36 11 18 22 41 42 38 33 35 18 45 11 30 40 31 46 19 24 18 17 16 43 46 1 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 35 2 42 27 7 3 17 45 46 11 13 37 25 36 37 17 47 1 32 21 20 35 41 31 32</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [51] 2 18 34 45 21 3 45 12 48 30 10 13 29 40 48 30 2 20 9 19 14 36 19 32 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 24 21 33 48 25 40 42 39 6 23 5 11 35 13 33 16 38 18 49 44 2 48 26 9 3</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [76] 10 44 20 4 4 36 8 48 43 46 9 32 6 8 29 13 6 45 9 12 38 45 44 35 5</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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span> <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [61] TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE TRUE FALSE FALSE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></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="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">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span> <span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-20 F35553 51 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-07 710157 76 M Outpatie… <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-09-24 CF9318 29 M ICU <span style="color: #949494;">B_</span>CMPYL<span style="color: #949494;">_</span>JEJN <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-08-31 149442 80 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@@ -210,19 +208,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="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-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 018637 2005-09-28 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 005088 2017-09-28 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 022060 2004-05-04 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 010257 2004-04-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 032343 2003-06-09 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 080086 2007-10-26 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 080086 2010-08-08 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 083080 2012-04-16 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 126334 2009-11-26 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2008-07-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 149442 2002-08-31 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 141061 2014-10-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 14D826 2006-09-14 A TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 16DC39 2015-11-19 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 16F0F7 2010-01-17 C TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 204562 2010-07-03 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 179451 2007-09-15 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 22B987 2009-10-19 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 189795 2008-10-19 B TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 257844 2011-05-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></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="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>
@@ -236,19 +234,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="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-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [91]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2005-09-28 018637 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2017-09-28 005088 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU 2004-05-04 022060 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-04-03 010257 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2003-06-09 032343 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-10-26 080086 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2010-08-08 080086 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2012-04-16 083080 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Outpatient 2009-11-26 126334 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2008-07-22 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2002-08-31 149442 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-10-22 141061 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2006-09-14 14D826 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2015-11-19 16DC39 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-01-17 16F0F7 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Outpatient 2010-07-03 204562 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2007-09-15 179451 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2009-10-19 22B987 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-10-19 189795 1 TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2011-05-22 257844 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></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="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>
@@ -264,9 +262,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span> <span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 55 14 33 43</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 60 13 39 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 33 11 23 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 26 11 23 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 6 5 5 5</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 5 5 5 5</span>
<span class="r-in"><span></span></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"># 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> <span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@@ -284,7 +282,7 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span> <span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span> <span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</span></span></span>
@@ -295,19 +293,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="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-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [94]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span> <span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 189795 <span style="color: #949494;">B_</span>AERCC<span style="color: #949494;">_</span>URNQ Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> D91230 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 5C1947 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F5F794 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D22254 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 419655 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 018637 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 010257 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 483195 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E60130 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>OXYT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 324415 <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 693505 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 671180 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E1C9D4 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 59B5BD <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 762305 <span style="color: #949494;">B_</span>PROTS<span style="color: #949494;">_</span>MRBL Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 443847 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 545388 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>HMNS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 690B42 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E02001 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
@@ -317,7 +315,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
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reference/get_episode.md
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@@ -178,29 +178,27 @@ x
df <- example_isolates[sample(seq_len(2000), size = 100), ] df <- example_isolates[sample(seq_len(2000), size = 100), ]
get_episode(df$date, episode_days = 60) # indices get_episode(df$date, episode_days = 60) # indices
#> [1] 20 43 19 12 43 41 12 28 30 15 41 18 34 6 15 9 29 8 45 16 43 10 14 9 42 #> [1] 28 47 7 7 6 17 9 4 37 11 43 43 14 38 26 38 12 39 49 18 15 27 5 22 25
#> [26] 48 8 28 24 4 31 45 20 43 47 4 30 2 15 22 15 19 32 27 4 11 12 3 2 28 #> [26] 36 11 18 22 41 42 38 33 35 18 45 11 30 40 31 46 19 24 18 17 16 43 46 1 23
#> [51] 35 2 42 27 7 3 17 45 46 11 13 37 25 36 37 17 47 1 32 21 20 35 41 31 32 #> [51] 2 18 34 45 21 3 45 12 48 30 10 13 29 40 48 30 2 20 9 19 14 36 19 32 36
#> [76] 24 21 33 48 25 40 42 39 6 23 5 11 35 13 33 16 38 18 49 44 2 48 26 9 3 #> [76] 10 44 20 4 4 36 8 48 43 46 9 32 6 8 29 13 6 45 9 12 38 45 44 35 5
is_new_episode(df$date, episode_days = 60) # TRUE/FALSE is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
#> [1] TRUE TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE FALSE TRUE #> [1] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE
#> [13] TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE #> [13] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#> [25] TRUE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE #> [25] TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE
#> [37] FALSE TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE #> [37] FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE
#> [49] FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE #> [49] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE FALSE FALSE TRUE FALSE
#> [61] TRUE TRUE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE #> [61] TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE
#> [73] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE #> [73] FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> [85] TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE #> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [97] FALSE TRUE FALSE FALSE #> [97] FALSE FALSE FALSE FALSE
# filter on results from the third 60-day episode only, using base R # filter on results from the third 60-day episode only, using base R
df[which(get_episode(df$date, 60) == 3), ] df[which(get_episode(df$date, 60) == 3), ]
#> # A tibble: 3 × 46 #> # A tibble: 1 × 46
#> date patient age gender ward mo PEN OXA FLC AMX #> date patient age gender ward mo PEN OXA FLC AMX
#> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir> #> <date> <chr> <dbl> <chr> <chr> <mo> <sir> <sir> <sir> <sir>
#> 1 2002-10-20 F35553 51 M ICU B_STPHY_AURS S NA S NA #> 1 2002-06-07 710157 76 M Outpatie… B_STPHY_CONS S NA S NA
#> 2 2002-09-24 CF9318 29 M ICU B_CMPYL_JEJN NA NA NA NA
#> 3 2002-08-31 149442 80 F ICU B_STPHY_AURS R NA S R
#> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,
#> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> # CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,
#> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> # TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,
@@ -234,19 +232,19 @@ if (require("dplyr")) {
arrange(patient, condition, date) arrange(patient, condition, date)
} }
#> # A tibble: 100 × 4 #> # A tibble: 100 × 4
#> # Groups: patient, condition [97] #> # Groups: patient, condition [95]
#> patient date condition new_episode #> patient date condition new_episode
#> <chr> <date> <chr> <lgl> #> <chr> <date> <chr> <lgl>
#> 1 018637 2005-09-28 C TRUE #> 1 005088 2017-09-28 B TRUE
#> 2 022060 2004-05-04 C TRUE #> 2 010257 2004-04-03 C TRUE
#> 3 032343 2003-06-09 B TRUE #> 3 080086 2007-10-26 A TRUE
#> 4 080086 2010-08-08 C TRUE #> 4 083080 2012-04-16 B TRUE
#> 5 126334 2009-11-26 A TRUE #> 5 0E2483 2008-07-22 B TRUE
#> 6 149442 2002-08-31 C TRUE #> 6 141061 2014-10-22 B TRUE
#> 7 14D826 2006-09-14 A TRUE #> 7 16DC39 2015-11-19 A TRUE
#> 8 16F0F7 2010-01-17 C TRUE #> 8 204562 2010-07-03 B TRUE
#> 9 179451 2007-09-15 B TRUE #> 9 22B987 2009-10-19 C TRUE
#> 10 189795 2008-10-19 B TRUE #> 10 257844 2011-05-22 C TRUE
#> # ℹ 90 more rows #> # ℹ 90 more rows
if (require("dplyr")) { if (require("dplyr")) {
@@ -260,19 +258,19 @@ if (require("dplyr")) {
arrange(patient, ward, date) arrange(patient, ward, date)
} }
#> # A tibble: 100 × 5 #> # A tibble: 100 × 5
#> # Groups: ward, patient [94] #> # Groups: ward, patient [91]
#> ward date patient new_index new_logical #> ward date patient new_index new_logical
#> <chr> <date> <chr> <int> <lgl> #> <chr> <date> <chr> <int> <lgl>
#> 1 Clinical 2005-09-28 018637 1 TRUE #> 1 Clinical 2017-09-28 005088 1 TRUE
#> 2 ICU 2004-05-04 022060 1 TRUE #> 2 Clinical 2004-04-03 010257 1 TRUE
#> 3 Clinical 2003-06-09 032343 1 TRUE #> 3 Clinical 2007-10-26 080086 1 TRUE
#> 4 Clinical 2010-08-08 080086 1 TRUE #> 4 Clinical 2012-04-16 083080 1 TRUE
#> 5 Outpatient 2009-11-26 126334 1 TRUE #> 5 Clinical 2008-07-22 0E2483 1 TRUE
#> 6 ICU 2002-08-31 149442 1 TRUE #> 6 Clinical 2014-10-22 141061 1 TRUE
#> 7 Clinical 2006-09-14 14D826 1 TRUE #> 7 ICU 2015-11-19 16DC39 1 TRUE
#> 8 Clinical 2010-01-17 16F0F7 1 TRUE #> 8 Outpatient 2010-07-03 204562 1 TRUE
#> 9 ICU 2007-09-15 179451 1 TRUE #> 9 Clinical 2009-10-19 22B987 1 TRUE
#> 10 Clinical 2008-10-19 189795 1 TRUE #> 10 Clinical 2011-05-22 257844 1 TRUE
#> # ℹ 90 more rows #> # ℹ 90 more rows
if (require("dplyr")) { if (require("dplyr")) {
@@ -288,9 +286,9 @@ if (require("dplyr")) {
#> # A tibble: 3 × 5 #> # A tibble: 3 × 5
#> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30 #> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30
#> <chr> <int> <int> <int> <int> #> <chr> <int> <int> <int> <int>
#> 1 Clinical 55 14 33 43 #> 1 Clinical 60 13 39 49
#> 2 ICU 33 11 23 27 #> 2 ICU 26 11 23 24
#> 3 Outpatient 6 5 5 5 #> 3 Outpatient 5 5 5 5
# grouping on patients and microorganisms leads to the same # grouping on patients and microorganisms leads to the same
# results as first_isolate() when using 'episode-based': # results as first_isolate() when using 'episode-based':
@@ -308,7 +306,7 @@ if (require("dplyr")) {
identical(x, y) identical(x, y)
} }
#> [1] TRUE #> [1] FALSE
# but is_new_episode() has a lot more flexibility than first_isolate(), # but is_new_episode() has a lot more flexibility than first_isolate(),
# since you can now group on anything that seems relevant: # since you can now group on anything that seems relevant:
@@ -319,19 +317,19 @@ if (require("dplyr")) {
select(group_vars(.), flag_episode) select(group_vars(.), flag_episode)
} }
#> # A tibble: 100 × 4 #> # A tibble: 100 × 4
#> # Groups: patient, mo, ward [97] #> # Groups: patient, mo, ward [94]
#> patient mo ward flag_episode #> patient mo ward flag_episode
#> <chr> <mo> <chr> <lgl> #> <chr> <mo> <chr> <lgl>
#> 1 189795 B_AERCC_URNQ Clinical TRUE #> 1 D91230 B_STPHY_EPDR Clinical TRUE
#> 2 5C1947 B_ESCHR_COLI Clinical TRUE #> 2 F5F794 B_STPHY_AURS ICU TRUE
#> 3 D22254 B_ESCHR_COLI Clinical TRUE #> 3 419655 B_STPHY_EPDR Clinical TRUE
#> 4 018637 B_ESCHR_COLI Clinical TRUE #> 4 010257 B_ESCHR_COLI Clinical TRUE
#> 5 483195 B_ESCHR_COLI ICU TRUE #> 5 E60130 B_KLBSL_OXYT Clinical TRUE
#> 6 324415 B_PROTS_MRBL ICU TRUE #> 6 693505 B_STPHY_AURS ICU TRUE
#> 7 671180 B_ESCHR_COLI Clinical TRUE #> 7 E1C9D4 B_STPHY_CONS Clinical TRUE
#> 8 59B5BD B_ESCHR_COLI Clinical TRUE #> 8 762305 B_PROTS_MRBL Clinical TRUE
#> 9 443847 B_STPHY_CONS Clinical TRUE #> 9 545388 B_STPHY_HMNS Clinical TRUE
#> 10 690B42 B_ESCHR_COLI ICU TRUE #> 10 E02001 B_ESCHR_COLI Clinical TRUE
#> # ℹ 90 more rows #> # ℹ 90 more rows
# } # }
``` ```

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@@ -7,7 +7,7 @@
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
reference/join.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -189,7 +189,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
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4
reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -212,7 +212,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
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reference/kurtosis.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,9 +91,9 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <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> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.948511</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.947136</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-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06510041</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.05825893</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -101,7 +101,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
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4
reference/kurtosis.md
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@@ -45,7 +45,7 @@ kurtosis(x, na.rm = FALSE, excess = FALSE)
``` r ``` r
kurtosis(rnorm(10000)) kurtosis(rnorm(10000))
#> [1] 2.948511 #> [1] 2.947136
kurtosis(rnorm(10000), excess = TRUE) kurtosis(rnorm(10000), excess = TRUE)
#> [1] -0.06510041 #> [1] -0.05825893
``` ```

4
reference/like.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -188,7 +188,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

4
reference/mdro.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -269,7 +269,7 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

92
reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -110,31 +110,31 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span> <span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S I S I S I S I R</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S R I R R R R I I I</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833 0.9486833</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.3162278 -0.3162278 -0.3162278 2.8460499</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.9486833 -0.9486833 -0.9486833 -0.9486833</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span> <span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;mic&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.0001 0.0002 0.5 0.0005 0.004 0.001 0.016 0.0002 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.032 0.064 0.125 0.5 0.016 0.008 &lt;=0.0005 0.032 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.032 1 </span> <span class="r-out co"><span class="r-pr">#&gt;</span> [9] 0.5 1 </span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.40022677 -0.92906618 0.61049379 1.65463443</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -2.03386972 -0.20876566 0.99756251 1.30174652</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span> <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.40022677 -0.92906618 0.61049379 1.65463443</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] -2.03386972 -0.20876566 0.99756251 1.30174652</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span> <span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;disk&gt;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> Class <span style="color: #0000BB;">&lt;disk&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 30 42 50 16 27 12 13 28 32</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 48 45 48 40 44 9 39 49 39 29</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.37726856 0.00721083 0.87251045 1.44937686 -1.00230539 -0.20911407</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.74202711 0.49468474 0.74202711 0.08244746 0.41223728 -2.47342369</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.29073860 -1.21863029 -0.13700577 0.15142743</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.00000000 0.82447456 0.00000000 -0.82447456</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span> <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> <span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -145,35 +145,35 @@
<span class="r-in"><span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span> <span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 32 4 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 26 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 32 4 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 28 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 30 8 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 31 8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 16 4 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 30 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 33 4 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 32 8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 32 4 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 28 32 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 29 8 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 33 &lt;=2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 8 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 24 &lt;=2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 30 4 16</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 20 &lt;=2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 8 8</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 19 16 2</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"tobr"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.351732344 0.165816825 0.045278388 -1.048629829 0.209372918</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.31430391 0.09942875 0.25436185 0.26948082 0.08306514 0.24576214</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 0.165816825 0.001722296 0.606383651 0.078704640 0.127266630</span> <span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.26823618 -0.44796371 -1.15734233 0.07066724</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"gent"</span> and <span style="color: #0000BB;">"tobr"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"gent"</span> and <span style="color: #0000BB;">"tobr"</span></span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span> <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 32 4 8 -0.6978278</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 I S 20 &lt;=2 1 -1.1069930</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 32 4 8 -0.6978278</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 28 8 1 -0.3684440</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D S 16 4 8 -0.6978278</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 31 8 1 -0.3684440</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 32 4 8 -0.6978278</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 30 4 2 -0.2349174</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 30 8 8 0.2704180</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 24 &lt;=2 4 -0.1013907</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 29 8 8 0.2704180</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 32 8 2 0.1343571</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 20 8 8 0.2704180</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 26 4 4 0.2678838</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 33 4 16 0.3372705</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 G S 33 &lt;=2 &gt;=8 0.4014105</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 30 4 16 0.3372705</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 J R 19 16 2 0.5036316</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H I 31 8 16 1.3055163</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 F S 28 32 2 0.8729061</span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="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="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="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -186,16 +186,16 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Calculating mean AMR distance based on columns <span style="color: #0000BB;">"amox"</span>, <span style="color: #0000BB;">"cipr"</span>, <span style="color: #0000BB;">"gent"</span>, and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"tobr"</span></span> <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">"tobr"</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span> <span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 30 8 8 0.045278388 0.00000000</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 31 8 1 0.25436185 0.000000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 I I 30 4 16 0.078704640 0.03342625</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 F S 28 32 2 0.24576214 0.008599711</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 G I 29 8 8 0.001722296 0.04355609</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 G S 33 &lt;=2 &gt;=8 0.26823618 0.013874329</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J R 20 8 8 0.127266630 0.08198824</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 30 4 2 0.26948082 0.015118966</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B R 32 4 8 0.165816825 0.12053844</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 A R 26 4 4 0.31430391 0.059942062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 32 4 8 0.165816825 0.12053844</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 B R 28 8 1 0.09942875 0.154933106</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E S 33 4 16 0.209372918 0.16409453</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 E I 32 8 2 0.08306514 0.171296709</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A I 32 4 8 -0.351732344 0.39701073</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 J R 19 16 2 0.07066724 0.183694618</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H I 31 8 16 0.606383651 0.56110526</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 H I 24 &lt;=2 4 -0.44796371 0.702325561</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 D S 16 4 8 -1.048629829 1.09390822</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 I S 20 &lt;=2 1 -1.15734233 1.411704178</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="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span> <span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span> <span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -231,7 +231,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
</div> </div>
<div class="pkgdown-footer-right"> <div class="pkgdown-footer-right">

88
reference/mean_amr_distance.md
View File

@@ -85,31 +85,31 @@ suspicious.
sir <- random_sir(10) sir <- random_sir(10)
sir sir
#> Class <sir> #> Class <sir>
#> [1] S S I S I S I S I R #> [1] S R I R R R R I I I
mean_amr_distance(sir) mean_amr_distance(sir)
#> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 #> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 0.9486833 0.9486833
#> [7] -0.3162278 -0.3162278 -0.3162278 2.8460499 #> [7] 0.9486833 -0.9486833 -0.9486833 -0.9486833
mic <- random_mic(10) mic <- random_mic(10)
mic mic
#> Class <mic> #> Class <mic>
#> [1] <=0.0001 0.0002 0.5 0.0005 0.004 0.001 0.016 0.0002 #> [1] 0.032 0.064 0.125 0.5 0.016 0.008 <=0.0005 0.032
#> [9] 0.032 1 #> [9] 0.5 1
mean_amr_distance(mic) mean_amr_distance(mic)
#> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129 #> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368
#> [7] 0.40022677 -0.92906618 0.61049379 1.65463443 #> [7] -2.03386972 -0.20876566 0.99756251 1.30174652
# equal to the Z-score of their log2: # equal to the Z-score of their log2:
(log2(mic) - mean(log2(mic))) / sd(log2(mic)) (log2(mic) - mean(log2(mic))) / sd(log2(mic))
#> [1] -1.13933320 -0.92906618 1.44436742 -0.65110831 -0.02030726 -0.44084129 #> [1] -0.20876566 0.09541835 0.38919449 0.99756251 -0.51294967 -0.81713368
#> [7] 0.40022677 -0.92906618 0.61049379 1.65463443 #> [7] -2.03386972 -0.20876566 0.99756251 1.30174652
disk <- random_disk(10) disk <- random_disk(10)
disk disk
#> Class <disk> #> Class <disk>
#> [1] 49 30 42 50 16 27 12 13 28 32 #> [1] 48 45 48 40 44 9 39 49 39 29
mean_amr_distance(disk) mean_amr_distance(disk)
#> [1] 1.37726856 0.00721083 0.87251045 1.44937686 -1.00230539 -0.20911407 #> [1] 0.74202711 0.49468474 0.74202711 0.08244746 0.41223728 -2.47342369
#> [7] -1.29073860 -1.21863029 -0.13700577 0.15142743 #> [7] 0.00000000 0.82447456 0.00000000 -0.82447456
y <- data.frame( y <- data.frame(
id = LETTERS[1:10], id = LETTERS[1:10],
@@ -120,35 +120,35 @@ y <- data.frame(
) )
y y
#> id amox cipr gent tobr #> id amox cipr gent tobr
#> 1 A I 32 4 8 #> 1 A R 26 4 4
#> 2 B R 32 4 8 #> 2 B R 28 8 1
#> 3 C I 30 8 8 #> 3 C R 31 8 1
#> 4 D S 16 4 8 #> 4 D R 30 4 2
#> 5 E S 33 4 16 #> 5 E I 32 8 2
#> 6 F R 32 4 8 #> 6 F S 28 32 2
#> 7 G I 29 8 8 #> 7 G S 33 <=2 >=8
#> 8 H I 31 8 16 #> 8 H I 24 <=2 4
#> 9 I I 30 4 16 #> 9 I S 20 <=2 1
#> 10 J R 20 8 8 #> 10 J R 19 16 2
mean_amr_distance(y) mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> "tobr" #> "tobr"
#> [1] -0.351732344 0.165816825 0.045278388 -1.048629829 0.209372918 #> [1] 0.31430391 0.09942875 0.25436185 0.26948082 0.08306514 0.24576214
#> [6] 0.165816825 0.001722296 0.606383651 0.078704640 0.127266630 #> [7] 0.26823618 -0.44796371 -1.15734233 0.07066724
y$amr_distance <- mean_amr_distance(y, is.mic(y)) y$amr_distance <- mean_amr_distance(y, is.mic(y))
#> ℹ Calculating mean AMR distance based on columns "gent" and "tobr" #> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"
y[order(y$amr_distance), ] y[order(y$amr_distance), ]
#> id amox cipr gent tobr amr_distance #> id amox cipr gent tobr amr_distance
#> 1 A I 32 4 8 -0.6978278 #> 9 I S 20 <=2 1 -1.1069930
#> 2 B R 32 4 8 -0.6978278 #> 2 B R 28 8 1 -0.3684440
#> 4 D S 16 4 8 -0.6978278 #> 3 C R 31 8 1 -0.3684440
#> 6 F R 32 4 8 -0.6978278 #> 4 D R 30 4 2 -0.2349174
#> 3 C I 30 8 8 0.2704180 #> 8 H I 24 <=2 4 -0.1013907
#> 7 G I 29 8 8 0.2704180 #> 5 E I 32 8 2 0.1343571
#> 10 J R 20 8 8 0.2704180 #> 1 A R 26 4 4 0.2678838
#> 5 E S 33 4 16 0.3372705 #> 7 G S 33 <=2 >=8 0.4014105
#> 9 I I 30 4 16 0.3372705 #> 10 J R 19 16 2 0.5036316
#> 8 H I 31 8 16 1.3055163 #> 6 F S 28 32 2 0.8729061
if (require("dplyr")) { if (require("dplyr")) {
y %>% y %>%
@@ -161,16 +161,16 @@ if (require("dplyr")) {
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and #> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> "tobr" #> "tobr"
#> id amox cipr gent tobr amr_distance check_id_C #> id amox cipr gent tobr amr_distance check_id_C
#> 1 C I 30 8 8 0.045278388 0.00000000 #> 1 C R 31 8 1 0.25436185 0.000000000
#> 2 I I 30 4 16 0.078704640 0.03342625 #> 2 F S 28 32 2 0.24576214 0.008599711
#> 3 G I 29 8 8 0.001722296 0.04355609 #> 3 G S 33 <=2 >=8 0.26823618 0.013874329
#> 4 J R 20 8 8 0.127266630 0.08198824 #> 4 D R 30 4 2 0.26948082 0.015118966
#> 5 B R 32 4 8 0.165816825 0.12053844 #> 5 A R 26 4 4 0.31430391 0.059942062
#> 6 F R 32 4 8 0.165816825 0.12053844 #> 6 B R 28 8 1 0.09942875 0.154933106
#> 7 E S 33 4 16 0.209372918 0.16409453 #> 7 E I 32 8 2 0.08306514 0.171296709
#> 8 A I 32 4 8 -0.351732344 0.39701073 #> 8 J R 19 16 2 0.07066724 0.183694618
#> 9 H I 31 8 16 0.606383651 0.56110526 #> 9 H I 24 <=2 4 -0.44796371 0.702325561
#> 10 D S 16 4 8 -1.048629829 1.09390822 #> 10 I S 20 <=2 1 -1.15734233 1.411704178
if (require("dplyr")) { if (require("dplyr")) {
# support for groups # support for groups
example_isolates %>% example_isolates %>%

4
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -190,7 +190,7 @@
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -113,7 +113,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/microorganisms.html
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@@ -1,6 +1,6 @@
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions. <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 96 982 Taxonomic Records of Microorganisms — microorganisms"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of seven domains. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of 15 kingdoms. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions. This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 7th of May, 2026) of seven domains. This data set is the backbone of this AMR package. MO codes can be looked up using as.mo() and microorganism properties can be looked up using any of the mo_* functions.
This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body> This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using this script), namely: List of Prokaryotic names with Standing in Nomenclature (LPSN) for bacteria, MycoBank for fungi, and Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL) for all others taxons."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -52,7 +52,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
</div> </div>
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>A data set containing the full microbial taxonomy (<strong>last updated: 7th of May, 2026</strong>) of 15 kingdoms. This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p> <p>A data set containing the full microbial taxonomy (<strong>last updated: 7th of May, 2026</strong>) of seven domains. This data set is the backbone of this <code>AMR</code> package. MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code> and microorganism properties can be looked up using any of the <code><a href="mo_property.html">mo_*</a></code> functions.</p>
<p>This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">this script</a>), namely: <em>List of Prokaryotic names with Standing in Nomenclature (LPSN)</em> for bacteria, <em>MycoBank</em> for fungi, and <em>Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)</em> for all others taxons.</p> <p>This data set is carefully crafted, yet made 100% reproducible from public and authoritative taxonomic sources (using <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_microorganisms.R" class="external-link">this script</a>), namely: <em>List of Prokaryotic names with Standing in Nomenclature (LPSN)</em> for bacteria, <em>MycoBank</em> for fungi, and <em>Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)</em> for all others taxons.</p>
</div> </div>
@@ -69,8 +69,8 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<li><p><code>domain</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is used for their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy. For all species outside the domains of Bacteria and Archaea, the <code>domain</code> and <code>kingdom</code> are identical.</p></li> <li><p><code>domain</code>, <code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism. Note that for fungi, <em>phylum</em> is used for their taxonomic <em>division</em>. Also, for fungi, <em>subkingdom</em> and <em>subdivision</em> were left out since they do not occur in the bacterial taxonomy. For all species outside the domains of Bacteria and Archaea, the <code>domain</code> and <code>kingdom</code> are identical.</p></li>
<li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li> <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
<li><p><code>ref</code><br> Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (<em>sp. nov.</em>), this is the original description author(s) and year. For species transferred to a different genus (<em>comb. nov.</em>), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. This field is directly retrieved from the source specified in the column <code>source</code>. Diacritics were removed to comply with CRAN, that only allows ASCII characters.</p></li> <li><p><code>ref</code><br> Abbreviated authority citation for the nomenclatural act that established the current name combination, following ICNP conventions. For species described in their current genus (<em>sp. nov.</em>), this is the original description author(s) and year. For species transferred to a different genus (<em>comb. nov.</em>), this is the reclassification author(s) and year. Emendations are excluded. For synonyms, this is the authority under which the synonym was originally published. This field is directly retrieved from the source specified in the column <code>source</code>. Diacritics were removed to comply with CRAN, that only allows ASCII characters.</p></li>
<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 1.3784 × 10<sup>6</sup>% of all 2 bacteria in the data set contain an oxygen tolerance.</p></li> <li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either <code>"aerobe"</code>, <code>"anaerobe"</code>, <code>"anaerobe/microaerophile"</code>, <code>"facultative anaerobe"</code>, <code>"likely facultative anaerobe"</code>, <code>"microaerophile"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 59.5% of all ~46 000 bacteria in the data set contain an oxygen tolerance.</p></li>
<li><p><code>morphology</code> <br> Morphology (cell shape), either <code>"cocci"</code>, <code>"coccobacilli"</code>, <code>"filamentous"</code>, <code>"likely cocci"</code>, <code>"likely coccobacilli"</code>, <code>"likely filamentous"</code>, <code>"likely rods"</code>, <code>"likely spirilla"</code>, <code>"rods"</code>, <code>"spirilla"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Genera that are clinically established as coccobacilli (the HACEK group and beyond, such as <em>Haemophilus</em> and <em>Acinetobacter</em>) are classified as such regardless of BacDive majority vote. Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus. Currently 1.3232 × 10<sup>6</sup>% of all 2 bacteria in the data set contain a morphology.</p></li> <li><p><code>morphology</code> <br> Morphology (cell shape), either <code>"cocci"</code>, <code>"coccobacilli"</code>, <code>"filamentous"</code>, <code>"likely cocci"</code>, <code>"likely coccobacilli"</code>, <code>"likely filamentous"</code>, <code>"likely rods"</code>, <code>"likely spirilla"</code>, <code>"rods"</code>, <code>"spirilla"</code>, or NA. These data were retrieved from BacDive (see <em>Source</em>). Genera that are clinically established as coccobacilli (the HACEK group and beyond, such as <em>Haemophilus</em> and <em>Acinetobacter</em>) are classified as such regardless of BacDive majority vote. Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus. Currently 57.1% of all ~46 000 bacteria in the data set contain a morphology.</p></li>
<li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li> <li><p><code>source</code><br> Either <code>"GBIF"</code>, <code>"LPSN"</code>, <code>"MycoBank"</code>, or <code>"manually added"</code> (see <em>Source</em>)</p></li>
<li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~36 000 records.</p></li> <li><p><code>lpsn</code><br> Identifier ('Record number') of List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set. <em><strong>This is a unique identifier</strong></em>, though available for only ~36 000 records.</p></li>
<li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li> <li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
@@ -96,12 +96,12 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2> <h2 id="included-taxa">Included Taxa<a class="anchor" aria-label="anchor" href="#included-taxa"></a></h2>
<p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All 2 (sub)species from the kingdoms of Archaea and Bacteria</p></li> <p>Included taxonomic data from <a href="https://lpsn.dsmz.de" class="external-link">LPSN</a>, <a href="https://www.mycobank.org" class="external-link">MycoBank</a>, and <a href="https://www.gbif.org" class="external-link">GBIF</a> are:</p><ul><li><p>All ~46 000 (sub)species from the domains of Archaea and Bacteria</p></li>
<li><p>~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li> <li><p>~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package. Only relevant fungi are covered (such as all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>~11 000 (sub)species from the kingdom of Protozoa</p></li> <li><p>~11 000 (sub)species from the kingdom of Protozoa</p></li>
<li><p>~2 000 (sub)species from ~60 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li> <li><p>~2 000 (sub)species from ~60 other relevant genera from the kingdom of Animalia (such as <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~31 000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li> <li><p>All ~31 000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li> <li><p>The complete taxonomic tree of all included (sub)species: from domain to subspecies</p></li>
<li><p>The identifier of the parent taxons</p></li> <li><p>The identifier of the parent taxons</p></li>
<li><p>The year and first author of the related scientific publication</p></li> <li><p>The year and first author of the related scientific publication</p></li>
</ul><div class="section"> </ul><div class="section">
@@ -179,7 +179,7 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
<footer><div class="pkgdown-footer-left"> <footer><div class="pkgdown-footer-left">
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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12
reference/microorganisms.md
View File

@@ -1,7 +1,7 @@
# Data Set with 96 982 Taxonomic Records of Microorganisms # Data Set with 96 982 Taxonomic Records of Microorganisms
A data set containing the full microbial taxonomy (**last updated: 7th A data set containing the full microbial taxonomy (**last updated: 7th
of May, 2026**) of 15 kingdoms. This data set is the backbone of this of May, 2026**) of seven domains. This data set is the backbone of this
`AMR` package. MO codes can be looked up using `AMR` package. MO codes can be looked up using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and microorganism [`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and microorganism
properties can be looked up using any of the properties can be looked up using any of the
@@ -69,7 +69,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 96
were retrieved from BacDive (see *Source*). Items that contain were retrieved from BacDive (see *Source*). Items that contain
"likely" are missing from BacDive and were extrapolated from other "likely" are missing from BacDive and were extrapolated from other
species within the same genus to guess the oxygen tolerance. Currently species within the same genus to guess the oxygen tolerance. Currently
1.3784 × 10⁶% of all 2 bacteria in the data set contain an oxygen 59.5% of all ~46 000 bacteria in the data set contain an oxygen
tolerance. tolerance.
- `morphology` - `morphology`
@@ -81,8 +81,8 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 96
(the HACEK group and beyond, such as *Haemophilus* and (the HACEK group and beyond, such as *Haemophilus* and
*Acinetobacter*) are classified as such regardless of BacDive majority *Acinetobacter*) are classified as such regardless of BacDive majority
vote. Items that contain "likely" are missing from BacDive and were vote. Items that contain "likely" are missing from BacDive and were
extrapolated from other species within the same genus. Currently extrapolated from other species within the same genus. Currently 57.1%
1.3232 × 10⁶% of all 2 bacteria in the data set contain a morphology. of all ~46 000 bacteria in the data set contain a morphology.
- `source` - `source`
Either `"GBIF"`, `"LPSN"`, `"MycoBank"`, or `"manually added"` (see Either `"GBIF"`, `"LPSN"`, `"MycoBank"`, or `"manually added"` (see
@@ -159,7 +159,7 @@ Included taxonomic data from [LPSN](https://lpsn.dsmz.de),
[MycoBank](https://www.mycobank.org), and [GBIF](https://www.gbif.org) [MycoBank](https://www.mycobank.org), and [GBIF](https://www.gbif.org)
are: are:
- All 2 (sub)species from the kingdoms of Archaea and Bacteria - All ~46 000 (sub)species from the domains of Archaea and Bacteria
- ~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a - ~36 000 species from the kingdom of Fungi. The kingdom of Fungi is a
very large taxon with almost 300,000 different (sub)species, of which very large taxon with almost 300,000 different (sub)species, of which
@@ -177,7 +177,7 @@ are:
- All ~31 000 previously accepted names of all included (sub)species - All ~31 000 previously accepted names of all included (sub)species
(these were taxonomically renamed) (these were taxonomically renamed)
- The complete taxonomic tree of all included (sub)species: from kingdom - The complete taxonomic tree of all included (sub)species: from domain
to subspecies to subspecies
- The identifier of the parent taxons - The identifier of the parent taxons

4
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -146,7 +146,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/mo_property.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9063</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</small>
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@@ -791,7 +791,7 @@
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@@ -147,7 +147,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p> <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/pca.html
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@@ -7,7 +7,7 @@
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@@ -189,7 +189,7 @@
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