* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -39,7 +39,7 @@
@@ -39,7 +39,7 @@
* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish
* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
* Fix for minor translation errors
@ -47,6 +47,10 @@
@@ -47,6 +47,10 @@
* Improved algorithm for generating random MICs with `random_mic()`
* Improved plot legends for MICs and disk diffusion values
* Improved speed of `as.ab()` and all `ab_*()` functions
* Added `fortify()` extensions for plotting methods
### Other
* This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated yearly from now on.
@ -206,40 +204,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -206,40 +204,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 70,760 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 6 October 2021 09:31:11 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds"class="external-link">R file</a> (2.2 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 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> (6.4 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.4 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> (14.9 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt">plain text file</a> (14.9 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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas">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> (18 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (18 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> (29.2 MB)</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (29.2 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>
<ahref="http://www.catalogueoflife.org">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>
<ahref="https://lpsn.dsmz.de">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">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>Included (sub)species per taxonomic kingdom:</p>
<tableclass="table">
<thead><trclass="header">
@ -426,39 +424,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -426,39 +424,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<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 โrefโ columns contains the scientific reference to the old taxonomic entries, i.e.ย of column <em>โfullnameโ</em>. For the scientific reference of the new names, i.e.ย of column <em>โfullname_newโ</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 5 October 2021 13:12:28 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav">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>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta">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>
<ahref="http://www.catalogueoflife.org">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>
<ahref="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<tableclass="table">
<thead><trclass="header">
@ -492,39 +490,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -492,39 +490,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 456 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 2 September 2021 11:50:06 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds"class="external-link">R file</a> (32 kB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds">R file</a> (32 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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav">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>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta">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>
<ahref="https://www.whocc.no/atc_ddd_index/">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">PubChem by the US National Library of Medicine</a></li>
@ -660,37 +658,37 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -660,37 +658,37 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<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 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav">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>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta">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>
<ahref="https://www.whocc.no/atc_ddd_index/">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">PubChem by the US National Library of Medicine</a></li>
@ -787,32 +785,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -787,32 +785,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 08:29:50 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds"class="external-link">R file</a> (69 kB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 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> (0.9 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 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> (3.5 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 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> (7.1 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 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> (5.1 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (5.1 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> (7 MB)</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 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_intrinsic_resistance/"class="external-link">โEUCAST Expert Rulesโ and โEUCAST Intrinsic Resistance and Unusual Phenotypesโ v3.2</a> (2020).</p>
<ahref="#source-4"class="anchor"></a>Source</h3>
<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_intrinsic_resistance/">โEUCAST Expert Rulesโ and โEUCAST Intrinsic Resistance and Unusual Phenotypesโ v3.2</a> (2020).</p>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<tableclass="table">
<thead><trclass="header">
@ -1002,32 +1000,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -1002,32 +1000,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<ahref="#interpretation-from-mic-values-disk-diameters-to-rsi"class="anchor"aria-hidden="true"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<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 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</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 5 October 2021 13:13:41 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds"class="external-link">R file</a> (37 kB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 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> (0.7 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 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> (1.8 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 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> (3.8 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 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> (2.4 MB)<br>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 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> (3.5 MB)</li>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
@ -1132,33 +1130,33 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -1132,33 +1130,33 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<ahref="#dosage-guidelines-from-eucast"class="anchor"aria-hidden="true"></a>Dosage guidelines from EUCAST</h2>
<ahref="#dosage-guidelines-from-eucast"class="anchor"></a>Dosage guidelines from EUCAST</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 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <ahref="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas">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>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav">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>
<li>Download as <ahref="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta">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">โEUCAST Clinical Breakpoint Tablesโ v11.0</a> (2021).</p>
<p>Currently included dosages in the data set are meant for: <ahref="https://www.eucast.org/clinical_breakpoints/">โEUCAST Clinical Breakpoint Tablesโ v11.0</a> (2021).</p>
@ -1255,13 +1253,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -1255,13 +1253,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<footer><divclass="copyright">
<p></p>
<p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/"class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
<p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<divclass="pkgdown">
<p></p>
<p>Site built with <ahref="https://pkgdown.r-lib.org/"class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
<p>Site built with <ahref="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</footer>
@ -1270,7 +1266,5 @@ If you are reading this page from within R, please <a href="https://msberends.gi
@@ -1270,7 +1266,5 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p><code>AMR</code> is a free, open-source and independent <spanstyle="R">R</span> package 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 antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, <spanstyle="R">R</span> knows ~70,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, <spanstyle="R">R</span> knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <spanstyle="R">R</span> package and works on Windows, macOS and Linux with all versions of <spanstyle="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <spanstyle="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
@ -310,11 +302,11 @@ The Netherlands
@@ -310,11 +302,11 @@ The Netherlands
<footer>
<divclass="copyright">
<p><p>Developed by <ahref="https://www.rug.nl/staff/m.s.berends/"class="external-link">Matthijs S. Berends</a>, <ahref="https://www.rug.nl/staff/c.f.luz/"class="external-link">Christian F. Luz</a>, <ahref="https://www.rug.nl/staff/a.w.friedrich/"class="external-link">Alexander W. Friedrich</a>, <ahref="https://www.rug.nl/staff/b.sinha/"class="external-link">Bhanu N. M. Sinha</a>, <ahref="https://www.rug.nl/staff/c.j.albers/"class="external-link">Casper J. Albers</a>, <ahref="https://www.rug.nl/staff/c.glasner/"class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<divclass="pkgdown">
<p><p>Site built with <ahref="https://pkgdown.r-lib.org/"class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <ahref="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -323,8 +315,6 @@ The Netherlands
@@ -323,8 +315,6 @@ The Netherlands
<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><ahref='as.ab.html'>as.ab()</a></code> or one of the <code><ahref='ab_property.html'>ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</p>
<h3class='hasAnchor'id='for-the-'><aclass='anchor'aria-hidden='true'href='#for-the-'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br/> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br/> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br/> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br/> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><ahref='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><ahref='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3class='hasAnchor'id='list-antibiotics-'><aclass='anchor'aria-hidden='true'href='#list-antibiotics-'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br/> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br/> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br/> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br/> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><ahref='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><ahref='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3class='hasAnchor'id='-data-set-a-'><aclass='anchor'aria-hidden='true'href='#-data-set-a-'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br/> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br/> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br/> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br/> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><ahref='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><ahref='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3class='hasAnchor'id='list-data-frame-'><aclass='anchor'aria-hidden='true'href='#list-data-frame-'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br/> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br/> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br/> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br/> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><ahref='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><ahref='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3class='hasAnchor'id='-with-observations-and-variables-'><aclass='anchor'aria-hidden='true'href='#-with-observations-and-variables-'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<h3class='hasAnchor'id='arguments'><aclass='anchor'href='#arguments'></a>For the antibiotics data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
@ -346,59 +266,7 @@
@@ -346,59 +266,7 @@
</ul>
<h3class='hasAnchor'id='for-the-'><aclass='anchor'aria-hidden='true'href='#for-the-'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
</ul>
<h3class='hasAnchor'id='list-antivirals-'><aclass='anchor'aria-hidden='true'href='#list-antivirals-'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
</ul>
<h3class='hasAnchor'id='-data-set-a-'><aclass='anchor'aria-hidden='true'href='#-data-set-a-'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
</ul>
<h3class='hasAnchor'id='list-data-frame-'><aclass='anchor'aria-hidden='true'href='#list-data-frame-'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br/> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br/> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br/> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br/> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br/> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br/> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br/> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br/> Units of <code>iv_ddd</code></p></li>
</ul>
<h3class='hasAnchor'id='-with-observations-and-variables-'><aclass='anchor'aria-hidden='true'href='#-with-observations-and-variables-'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<h3class='hasAnchor'id='arguments'><aclass='anchor'href='#arguments'></a>For the antivirals data set: a <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br/> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3class='hasAnchor'id='direct-download'><aclass='anchor'aria-hidden='true'href='#direct-download'></a>Direct download</h3>
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3class='hasAnchor'id='arguments'><aclass='anchor'href='#arguments'></a>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without <spanstyle="R">R</span> - you can find the files here:</p><ul>
@ -470,11 +338,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
@@ -470,11 +338,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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@ -483,8 +351,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
@@ -483,8 +351,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru