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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="@univgroningen"><!-- 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 566 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-data-frame-with-observations-and-variables-">For the antibiotics data set: a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 464 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antibiotics-data-set-a-data-frame-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 170 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 145 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-data-frame-with-observations-and-variables-">For the antivirals data set: a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 102 observations and 9 variables:<a class="anchor" aria-label="anchor" href="#for-the-antivirals-data-set-a-data-frame-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>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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<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>
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<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>
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</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 Compound ID (<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>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt</a></p></li>
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<li><p><a href="https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt" class="external-link">https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt</a></p></li>
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</ul><p>Files in <span style="R">R</span> format (with preserved data structure) can be found here:</p><ul><li><p><a href="https://github.com/msberends/AMR/raw/main/data/antibiotics.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/antibiotics.rda</a></p></li>
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<li><p><a href="https://github.com/msberends/AMR/raw/main/data/antivirals.rda" class="external-link">https://github.com/msberends/AMR/raw/main/data/antivirals.rda</a></p></li>
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</ul></div>
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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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="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">antibiotics</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> ab cid name group</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 AMA 4649 4-aminosalicylic acid Antimycobacterials</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 FCT 3366 5-fluorocytosine Antifungals/antimycotics</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 ACM 6450012 Acetylmidecamycin Macrolides/lincosamides</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 ASP 49787020 Acetylspiramycin Macrolides/lincosamides</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 ALS 8954 Aldesulfone sodium Other antibacterials</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 AMK 37768 Amikacin Aminoglycosides</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> atc atc_group1</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 J04AA01 Drugs for treatment of tuberculosis</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 D01AE21 Antifungals for topical use</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 J04BA03 Drugs for treatment of lepra</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 D06AX12, J01GB06, S01AA21 Aminoglycoside antibacterials</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> atc_group2 abbreviations</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 Aminosalicylic acid and derivatives </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 Other antifungals for topical use 5flc, fcu, fluo, fluy</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 <NA> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 <NA> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 Drugs for treatment of lepra </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 Other aminoglycosides ak, ami, amik, amk, an</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> synonyms</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 aminopar, aminosalicylic, aminosalicylic acid, aminosalyl, aminox, apacil, deapasil, entepas, ferrosan, gabbropas, helipidyl, hellipidyl, neopasalate, osacyl, pamacyl, pamisyl, paramycin, parasal, parasalicil, parasalindon, pasalon, pasara, pascorbic, pasdium, paser granules, paskalium, pasmed, pasnodia, pasolac, propasa, rezipas, teebacin, wln: zr cq dvq</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 alcobon, ancobon, ancotil, ancotyl, flucitosina, flucystine, flucytosin, flucytosine, flucytosinum, flucytosone, fluocytosine, fluorcytosine</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 acetylspiramycin, foromacidin b, spiramycin ii</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 adesulfone sodium, aldapsone, aldesulfona sodica, aldesulfone, aldesulfone sodique, aldesulfone sodium, diamidin, diasone, diasone sodium, diazon, novotrone, sodium aldesulphone, sodium sulfoxone, sulfoxone sodium</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 amicacin, amikacillin, amikacin, amikacin base, amikacin dihydrate, amikacin sulfate, amikacina, amikacine, amikacinum, amikavet, amikin, amiklin, amikozit, amukin, arikace, briclin, lukadin, mikavir, pierami, potentox</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> oral_ddd oral_units iv_ddd iv_units</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 12.00 g NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 NA <NA> NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 NA <NA> NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 NA <NA> NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 0.33 g NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 NA <NA> 1 g</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> loinc</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 10974-4, 23805-5, 25142-1, 25143-9, 3639-2, 46218-4</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 13546-7, 15098-7, 17798-0, 31097-9, 31098-7, 31099-5, 3319-1, 3320-9, 3321-7, 35669-1, 50802-8, 50803-6, 56628-1, 59378-0, 80972-3</span>
|
|
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">antivirals</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> atc cid name</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 J05AF06 441300 Abacavir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 J05AB01 135398513 Aciclovir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 J05AF08 60871 Adefovir dipivoxil</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 J05AE05 65016 Amprenavir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 J05AP06 16076883 Asunaprevir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 J05AE08 148192 Atazanavir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> atc_group</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 Nucleoside and nucleotide reverse transcriptase inhibitors</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 Nucleosides and nucleotides excl. reverse transcriptase inhibitors</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 Nucleoside and nucleotide reverse transcriptase inhibitors</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 Protease inhibitors</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 Antivirals for treatment of HCV infections</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 Protease inhibitors</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> synonyms</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 Abacavir, Abacavir sulfate, Ziagen</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 Acicloftal, Aciclovier, Aciclovir, Aciclovirum, Activir, AcycloFoam, Acycloguanosine, Acyclovir, Acyclovir Lauriad, ACYCLOVIR SODIUM, Avirax, Cargosil, Cyclovir, Genvir, Gerpevir, Hascovir, Herpevir, Maynar, Poviral, Sitavig, Sitavir, Vipral, Virolex, Viropump, Virorax, Zovirax, Zovirax topical, Zyclir</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 Adefovir di ester, Adefovir dipivoxil, Adefovir Dipivoxil, Adefovir dipivoxyl, Adefovir pivoxil, Adefovirdipivoxl, Bisadenine, BISADENINE, BisPMEA, Hepsera, Preveon, YouHeDing</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 Agenerase, Amprenavir, Amprenavirum, Prozei, Vertex</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 Asunaprevir, Sunvepra</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 Atazanavir, Atazanavir Base, Latazanavir, Reyataz, Zrivada</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> oral_ddd oral_units iv_ddd iv_units</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 1 0.6 g NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 2 4.0 g 4 g</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 3 10.0 mg NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 4 1.2 g NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 5 NA <NA> NA <NA></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> 6 0.3 g NA <NA></span>
|
|
</code></pre></div>
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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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