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<p>All reference data (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply tab separated files that are machine-readable and suitable for input in any software program, such as laboratory information systems.</p>
<p>On this page, we explain how to download them and how the structure of the data sets look like.</p>
<pclass="dataset-within-r">
If you are reading this page from within R, please <ahref="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a>, which is automatically updated with every code change.
<p>A data set with 70,764 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</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>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <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 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds"class="external-link">R file</a> (1.3 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx"class="external-link">Excel file</a> (4.8 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt"class="external-link">plain text file</a> (13.1 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas"class="external-link">SAS file</a> (30.7 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav"class="external-link">SPSS file</a> (16.3 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta"class="external-link">Stata file</a> (27.5 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<ul>
<li>
<ahref="http://www.catalogueoflife.org"class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<li>
<ahref="https://lpsn.dsmz.de"class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <ahref="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009"class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e.of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e.of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds"class="external-link">R file</a> (0.2 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx"class="external-link">Excel file</a> (0.5 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt"class="external-link">plain text file</a> (1 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas"class="external-link">SAS file</a> (2.1 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav"class="external-link">SPSS file</a> (1.3 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta"class="external-link">Stata file</a> (2 MB)</li>
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
<ul>
<li>
<ahref="http://www.catalogueoflife.org"class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<li>
<ahref="https://lpsn.dsmz.de"class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds"class="external-link">R file</a> (33 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx"class="external-link">Excel file</a> (65 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt"class="external-link">plain text file</a> (0.1 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas"class="external-link">SAS file</a> (1.8 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav"class="external-link">SPSS file</a> (0.3 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta"class="external-link">Stata file</a> (0.3 MB)</li>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<ahref="https://www.whocc.no/atc_ddd_index/"class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><ahref="https://pubchem.ncbi.nlm.nih.gov"class="external-link">PubChem by the US National Library of Medicine</a></li>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds"class="external-link">R file</a> (5 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx"class="external-link">Excel file</a> (14 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt"class="external-link">plain text file</a> (16 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas"class="external-link">SAS file</a> (80 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav"class="external-link">SPSS file</a> (68 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta"class="external-link">Stata file</a> (67 kB)</li>
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<ahref="https://www.whocc.no/atc_ddd_index/"class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><ahref="https://pubchem.ncbi.nlm.nih.gov"class="external-link">PubChem by the US National Library of Medicine</a></li>
<h2id="interpretation-from-mic-values-disk-diameters-to-rsi">Interpretation from MIC values / disk diameters to R/SI<aclass="anchor"aria-label="anchor"href="#interpretation-from-mic-values-disk-diameters-to-rsi"></a>
</h2>
<p>A data set with 20,369 rows and 11 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> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds"class="external-link">R file</a> (49 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx"class="external-link">Excel file</a> (0.9 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt"class="external-link">plain text file</a> (2 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas"class="external-link">SAS file</a> (4 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav"class="external-link">SPSS file</a> (2.6 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta"class="external-link">Stata file</a> (3.8 MB)</li>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2011-2022) and EUCAST (2011-2022).</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds"class="external-link">R file</a> (78 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx"class="external-link">Excel file</a> (1.3 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt"class="external-link">plain text file</a> (5.1 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas"class="external-link">SAS file</a> (10.4 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav"class="external-link">SPSS file</a> (7.4 MB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta"class="external-link">Stata file</a> (10.2 MB)</li>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <ahref="https://www.eucast.org/expert_rules_and_expected_phenotypes/"class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.3</a> (2021).</p>
<h2id="dosage-guidelines-from-eucast">Dosage guidelines from EUCAST<aclass="anchor"aria-label="anchor"href="#dosage-guidelines-from-eucast"></a>
</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 21 August 2022 15:23:37 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds"class="external-link">R file</a> (3 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx"class="external-link">Excel file</a> (14 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt"class="external-link">plain text file</a> (15 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas"class="external-link">SAS file</a> (52 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav"class="external-link">SPSS file</a> (45 kB)<br>
</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta"class="external-link">Stata file</a> (44 kB)</li>
<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: <ahref="https://www.eucast.org/clinical_breakpoints/"class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
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<p><code>AMR</code> (for R). Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><atarget="_blank"href="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>.</p>
