<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9007</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9012</span>
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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. 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>
<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 67,151 rows and 16 columns, containing the following column names:<br><em>‘mo’, ‘fullname’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, ‘species’, ‘subspecies’, ‘rank’, ‘ref’, ‘species_id’, ‘source’, ‘prevalence’, ‘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 28 July 2020 20:52:40 CEST.</p>
<p>It was last updated on 28 July 2020 20:52:40 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:<br><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>‘fullname’, ‘fullname_new’, ‘ref’, ‘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 28 May 2020 11:17:56 CEST.</p>
<p>It was last updated on 28 May 2020 11:17:56 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>A data set with 12,708 rows and 4 columns, containing the following column names:<br><em>fullname, fullname_new, ref, 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>A data set with 456 rows and 14 columns, containing the following column names:<br><em>‘ab’, ‘atc’, ‘cid’, ‘name’, ‘group’, ‘atc_group1’, ‘atc_group2’, ‘abbreviations’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘iv_units’, ‘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 31 July 2020 12:12:13 CEST.</p>
<p>It was last updated on 31 July 2020 12:12:13 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>‘atc’, ‘cid’, ‘name’, ‘atc_group’, ‘synonyms’, ‘oral_ddd’, ‘oral_units’, ‘iv_ddd’, ‘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 23 November 2019 19:03:43 CET.</p>
<p>It was last updated on 29 August 2020 21:36:44 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antivirals.html">here</a>.</p>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc, cid, name, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units</em>.</p>
<p>It was last updated on 14 August 2020 14:18:20 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
<p>The data set is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on ‘EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes’, version 3.1, 2016.</p>
<ahref="#interpretation-from-mic-values-disk-diameters-to-rsi"class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>‘guideline’, ‘method’, ‘site’, ‘mo’, ‘ab’, ‘ref_tbl’, ‘disk_dose’, ‘breakpoint_S’, ‘breakpoint_R’, ‘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 29 July 2020 13:12:34 CEST.</p>
<p>It was last updated on 29 July 2020 13:12:34 CEST. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020).</p>
<p>A data set with 18,650 rows and 10 columns, containing the following column names:<br><em>guideline, method, site, mo, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti</em>.</p>
<li><p>Function <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> now returns the genus for input where the species is unknown</p></li>
<li><p>BORSA is now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g.<code><ahref="../reference/mo_property.html">mo_genus("BORSA")</a></code> will return “Staphylococcus”</p></li>
<li><p>Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies: <code>tibble</code> printing support for classes <code><rsi></code>, <code><mic></code>, <code><disk></code>, <code><ab></code> and <code><mo></code>. When using <code>tibble</code>s containing antimicrobial columns (class <code><rsi></code>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class <code><mo></code>) will emphasise on the genus and species, not on the kingdom.</p></li>
<li><p>Names of antiviral agents in data set <code>antivirals</code> now have a starting capital letter, like it is the case in the <code>antibiotics</code> data set</p></li>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9011</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9012</span>
</span>
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