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Use as.ab() or one of the ab_* functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) 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."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 585 Antimicrobial Drugs</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>antibiotics.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href="as.ab.html">as.ab()</a></code> or one of the <code><a href="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>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">antibiotics</span></span>
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<span></span>
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<span><span class="va">antivirals</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<div class="section">
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<h3 id="for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-">For the antibiotics data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 483 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-"></a></h3>
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<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>
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<li><p><code>cid</code><br> Compound ID as found in PubChem</p></li>
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<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO</p></li>
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<li><p><code>group</code><br> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
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<li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
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<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>
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<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>
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<li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
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<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
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<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 174 drugs</p></li>
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<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
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<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs</p></li>
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<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
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<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><a href="ab_property.html">ab_loinc()</a></code> to retrieve them quickly, see <code><a href="ab_property.html">ab_property()</a></code>.</p></li>
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</ul></div>
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<div class="section">
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<h3 id="for-the-antivirals-data-set-a-tibble-with-observations-and-variables-">For the antivirals data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 102 observations and 9 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-tibble-with-observations-and-variables-"></a></h3>
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<ul><li><p><code>atc</code><br> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
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<li><p><code>cid</code><br> Compound ID as found in PubChem</p></li>
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<li><p><code>name</code><br> Official name as used by WHONET/EARS-Net or the WHO</p></li>
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<li><p><code>atc_group</code><br> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
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<li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
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<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment</p></li>
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<li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
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<li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral treatment</p></li>
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<li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
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</ul></div>
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<p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 102 rows and 9 columns.</p>
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</div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<ul><li><p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <a href="https://www.whocc.no/atc_ddd_index/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p></li>
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<li><p>Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022). Accessed from <a href="https://loinc.org" class="external-link">https://loinc.org</a> on 30 October, 2022.</p></li>
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<li><p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<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>
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<p>Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column <code>cid</code>) and consequently only available where a CID is available.</p><div class="section">
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<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
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<p>Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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</div>
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<div class="section level2">
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<h2 id="whocc">WHOCC<a class="anchor" aria-label="anchor" href="#whocc"></a></h2>
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<p><img src="figures/logo_who.png" height="60" style='margin-bottom:"5"'><br>
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This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="external-link">https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm" class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a>).</p>
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<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
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<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
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<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href="https://www.whocc.no/copyright_disclaimer/." class="external-link">https://www.whocc.no/copyright_disclaimer/.</a></p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><a href="microorganisms.html">microorganisms</a>, <a href="intrinsic_resistant.html">intrinsic_resistant</a></p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antibiotics</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 483 × 14</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ab cid name group atc atc_g…¹ atc_g…² abbre…³ synon…⁴ oral_…⁵</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lis></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><named></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> AMA <span style="text-decoration: underline;">4</span>649 4-aminosal… Anti… <chr> Drugs … Aminos… <chr> <chr> 12 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ACM 6<span style="text-decoration: underline;">450</span>012 Acetylmide… Macr… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> ASP 49<span style="text-decoration: underline;">787</span>020 Acetylspir… Macr… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ALS <span style="text-decoration: underline;">8</span>954 Aldesulfon… Othe… <chr> Drugs … Drugs … <chr> <chr> 0.33</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> AMK <span style="text-decoration: underline;">37</span>768 Amikacin Amin… <chr> Aminog… Other … <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> AKF <span style="color: #BB0000;">NA</span> Amikacin/f… Amin… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> AMX <span style="text-decoration: underline;">33</span>613 Amoxicillin Beta… <chr> Beta-l… Penici… <chr> <chr> 1.5 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> AMC 23<span style="text-decoration: underline;">665</span>637 Amoxicilli… Beta… <chr> Beta-l… Combin… <chr> <chr> 1.5 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> AXS <span style="text-decoration: underline;">465</span>441 Amoxicilli… Beta… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <chr> <chr> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> AMB 5<span style="text-decoration: underline;">280</span>965 Amphoteric… Anti… <chr> Antimy… Antibi… <chr> <chr> 40 </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 473 more rows, 4 more variables: oral_units <chr>, iv_ddd <dbl>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># iv_units <chr>, loinc <list>, and abbreviated variable names ¹atc_group1,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²atc_group2, ³abbreviations, ⁴synonyms, ⁵oral_ddd</span></span>
|
||
<span class="r-in"><span><span class="va">antivirals</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 102 × 9</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> atc cid name atc_g…¹ synon…² oral_…³ oral_…⁴ iv_ddd iv_un…⁵</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> J05AF06 <span style="text-decoration: underline;">441</span>300 Abacavir Nucleo… <chr> 0.6 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> J05AB01 135<span style="text-decoration: underline;">398</span>513 Aciclovir Nucleo… <chr> 4 g 4 g </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> J05AF08 <span style="text-decoration: underline;">60</span>871 Adefovir di… Nucleo… <chr> 10 mg <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> J05AE05 <span style="text-decoration: underline;">65</span>016 Amprenavir Protea… <chr> 1.2 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> J05AP06 16<span style="text-decoration: underline;">076</span>883 Asunaprevir Antivi… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> J05AE08 <span style="text-decoration: underline;">148</span>192 Atazanavir Protea… <chr> 0.3 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> J05AR15 86<span style="text-decoration: underline;">583</span>336 Atazanavir … Antivi… <chr> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> J05AR23 <span style="color: #BB0000;">NA</span> Atazanavir … Antivi… <chr> 0.3 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> J05AP03 10<span style="text-decoration: underline;">324</span>367 Boceprevir Antivi… <chr> 2.4 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> J05AB15 <span style="text-decoration: underline;">446</span>727 Brivudine Nucleo… <chr> 0.125 g <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 92 more rows, and abbreviated variable names ¹atc_group, ²synonyms,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ³oral_ddd, ⁴oral_units, ⁵iv_units</span></span>
|
||
</code></pre></div>
|
||
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|
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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