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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9026</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</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">
@ -193,7 +193,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">26 June 2023</h4>
<h4 data-toc-skip class="date">08 July 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
@ -214,7 +214,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52 151 rows and 23 columns, containing the following
<p>A data set with 52 169 rows and 23 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -224,7 +224,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 11 May 2023 19:56:27 UTC. Find more info about
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
@ -250,7 +250,7 @@ data (SAS) file</a> (50.9 MB)<br>
transport (XPT) file</a> (48.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
SPSS Statistics data file</a> (17.7 MB)<br>
SPSS Statistics data file</a> (17.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
DTA file</a> (48.6 MB)</li>
@ -305,11 +305,11 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36 485</td>
<td align="center">36 499</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7 901</td>
<td align="center">7 905</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
@ -913,43 +913,43 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 42 599 rows and 12 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em>, <em>ecoff</em>, and
<p>A data set with 28 454 rows and 12 columns, containing the following
column names:<br><em>guideline</em>, <em>type</em>, <em>method</em>, <em>site</em>,
<em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>,
<em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em>, and
<em>uti</em>.</p>
<p>This data set is in R available as <code>clinical_breakpoints</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.rds" class="external-link">original
R Data Structure (RDS) file</a> (82 kB)<br>
R Data Structure (RDS) file</a> (57 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
text file</a> (4.4 MB)<br>
text file</a> (3.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
Excel workbook</a> (1.8 MB)<br>
Excel workbook</a> (1.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
Feather file</a> (1.6 MB)<br>
Feather file</a> (1.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
Parquet file</a> (0.2 MB)<br>
Parquet file</a> (92 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
data (SAS) file</a> (3.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
transport (XPT) file</a> (10.6 MB)<br>
transport (XPT) file</a> (7.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
SPSS Statistics data file</a> (5.8 MB)<br>
SPSS Statistics data file</a> (4.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
DTA file</a> (10.5 MB)</li>
DTA file</a> (7.5 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
@ -961,25 +961,26 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<div class="section level3">
<h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
</h3>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="7%">
<col width="4%">
<col width="3%">
<col width="8%">
<col width="14%">
<col width="7%">
<col width="3%">
<col width="9%">
<col width="7%">
<col width="6%">
<col width="3%">
<col width="4%">
<col width="3%">
<col width="7%">
<col width="14%">
<col width="6%">
<col width="2%">
<col width="15%">
<col width="8%">
<col width="8%">
<col width="4%">
<col width="4%">
<col width="7%">
<col width="7%">
<col width="3%">
</colgroup>
<thead><tr class="header">
<th align="center">guideline</th>
<th align="center">type</th>
<th align="center">method</th>
<th align="center">site</th>
<th align="center">mo</th>
@ -991,104 +992,103 @@ diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
<th align="center">disk_dose</th>
<th align="center">breakpoint_S</th>
<th align="center">breakpoint_R</th>
<th align="center">ecoff</th>
<th align="center">uti</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">F_ASPRG_MGTS</td>
<td align="center">Aspergillus fumigatus</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
<td align="center">A. xylosoxidans</td>
<td align="center">10ug</td>
<td align="center">26.000</td>
<td align="center">20.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_ASPRG_NIGR</td>
<td align="center">Aspergillus niger</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Aspergillus</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">MEM</td>
<td align="center">Meropenem</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">1.000</td>
<td align="center">4.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">F_CANDD_ALBC</td>
<td align="center">Candida albicans</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center">1.25ug/23.75ug</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_DBLN</td>
<td align="center">Candida dubliniensis</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">SXT</td>
<td align="center">Trimethoprim/sulfamethoxazole</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">0.125</td>
<td align="center">0.125</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">EUCAST 2023</td>
<td align="center">MIC</td>
<td align="center">human</td>
<td align="center">DISK</td>
<td align="center"></td>
<td align="center">F_CANDD_GLBR</td>
<td align="center">Candida glabrata</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center"></td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center">30ug/6ug</td>
<td align="center">26.000</td>
<td align="center">26.000</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">EUCAST 2023</td>
<td align="center">human</td>
<td align="center">MIC</td>
<td align="center"></td>
<td align="center">F_CANDD_KRUS</td>
<td align="center">Candida krusei</td>
<td align="center">B_ACHRMB_DNTR</td>
<td align="center">Achromobacter denitrificans</td>
<td align="center">2</td>
<td align="center">AMB</td>
<td align="center">Amphotericin B</td>
<td align="center">Candida</td>
<td align="center"></td>
<td align="center">1</td>
<td align="center">1</td>
<td align="center">TZP</td>
<td align="center">Piperacillin/tazobactam</td>
<td align="center">A. xylosoxidans</td>
<td align="center"></td>
<td align="center">4.000</td>
<td align="center">4.000</td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -1431,10 +1431,9 @@ DTA file</a> (0.1 MB)</li>
</h3>
<p>EUCAST breakpoints used in this package are based on the dosages in
this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v13.0</a> (2023).</p>
<p>Currently included dosages in the data set are meant for: <a href=""></a> (), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v11.0</a> (2021), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
Breakpoint Tables’ v12.0</a> (2022).</p>
</div>
<div class="section level3">
<h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@ -2059,6 +2058,189 @@ reality and can be used to practise AMR data analysis.</p>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="microorganisms-groups-species-groups-and-microbiological-complexes">
<code>microorganisms.groups</code>: Species Groups and
Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
</h2>
<p>A data set with 444 rows and 4 columns, containing the following
column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
<em>mo_name</em>.</p>
<p>This data set is in R available as
<code>microorganisms.groups</code>, after you load the <code>AMR</code>
package.</p>
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.rds" class="external-link">original
R Data Structure (RDS) file</a> (5 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
text file</a> (42 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
Excel workbook</a> (18 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
Feather file</a> (17 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.parquet" class="external-link">Apache
Parquet file</a> (12 kB)<br>
</li>
<li><em>(unavailable as SAS data (SAS) file)</em></li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
SPSS Statistics data file</a> (54 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
DTA file</a> (68 kB)</li>
</ul>
<div class="section level3">
<h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
</h3>
<p>This data set contains species groups and microbiological complexes,
which are used in the <code>clinical_breakpoints</code> data set.</p>
</div>
<div class="section level3">
<h3 id="example-content-8">Example content<a class="anchor" aria-label="anchor" href="#example-content-8"></a>
</h3>
<table class="table">
<colgroup>
<col width="17%">
<col width="15%">
<col width="35%">
<col width="31%">
</colgroup>
<thead><tr class="header">
<th align="center">mo_group</th>
<th align="center">mo</th>
<th align="center">mo_group_name</th>
<th align="center">mo_name</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_BMNN</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter baumannii</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_CLCC</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter calcoaceticus</td>
</tr>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_DJKS</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter dijkshoorniae</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_NSCM</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter nosocomialis</td>
</tr>
<tr class="odd">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_PITT</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter pittii</td>
</tr>
<tr class="even">
<td align="center">B_ACNTB_BMNN-C</td>
<td align="center">B_ACNTB_SFRT</td>
<td align="center">Acinetobacter baumannii complex</td>
<td align="center">Acinetobacter seifertii</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level2">
<h2 id="microorganisms-codes-common-laboratory-codes">
<code>microorganisms.codes</code>: Common Laboratory Codes<a class="anchor" aria-label="anchor" href="#microorganisms-codes-common-laboratory-codes"></a>
</h2>
<p>A data set with 4 957 rows and 2 columns, containing the following
column names:<br><em>code</em> and <em>mo</em>.</p>
<p>This data set is in R available as <code>microorganisms.codes</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 8 July 2023 15:30:05 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.codes.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.rds" class="external-link">original
R Data Structure (RDS) file</a> (22 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xlsx" class="external-link">Microsoft
Excel workbook</a> (91 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.feather" class="external-link">Apache
Feather file</a> (85 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.parquet" class="external-link">Apache
Parquet file</a> (57 kB)<br>
</li>
<li><em>(unavailable as SAS data (SAS) file)</em></li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.xpt" class="external-link">SAS
transport (XPT) file</a> (0 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.sav" class="external-link">IBM
SPSS Statistics data file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.codes.dta" class="external-link">Stata
DTA file</a> (0.1 MB)</li>
</ul>
<div class="section level3">
<h3 id="source-9">Source<a class="anchor" aria-label="anchor" href="#source-9"></a>
</h3>
<p>This data set contains commonly used codes for microorganisms, from
laboratory systems and <a href="https://whonet.org" class="external-link">WHONET</a>.</p>
</div>
<div class="section level3">
<h3 id="example-content-9">Example content<a class="anchor" aria-label="anchor" href="#example-content-9"></a>
</h3>
<table class="table">
<thead><tr class="header">
<th align="center">code</th>
<th align="center">mo</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">1011</td>
<td align="center">B_GRAMP</td>
</tr>
<tr class="even">
<td align="center">1012</td>
<td align="center">B_GRAMP</td>
</tr>
<tr class="odd">
<td align="center">1013</td>
<td align="center">B_GRAMN</td>
</tr>
<tr class="even">
<td align="center">1014</td>
<td align="center">B_GRAMN</td>
</tr>
<tr class="odd">
<td align="center">1015</td>
<td align="center">F_YEAST</td>
</tr>
<tr class="even">
<td align="center">103</td>
<td align="center">B_ESCHR_COLI</td>
</tr>
</tbody>
</table>
</div>
</div>
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