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(v1.7.1.9053) fortify() methods
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Data Sets with 558 Antimicrobial Drugs</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
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<div class="hidden name"><code>antibiotics.Rd</code></div>
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</div>
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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="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>antibiotics</span>
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<pre class="usage"><span class='va'>antibiotics</span>
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<span class='va'>antivirals</span></code></pre></div>
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<span class='va'>antivirals</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
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<ul>
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<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>
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<h3 class='hasAnchor' id='list-antibiotics-'><a class='anchor' aria-hidden='true' href='#list-antibiotics-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
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<ul>
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<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>
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<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
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<ul>
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<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>
|
||||
<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>
|
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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>
|
||||
<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>
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<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
|
||||
|
||||
<ul>
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<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>
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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>
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<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
|
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<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
|
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|
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<ul>
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<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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@ -346,59 +266,7 @@
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</ul>
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<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
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<ul>
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<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>
|
||||
<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>
|
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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>
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<h3 class='hasAnchor' id='list-antivirals-'><a class='anchor' aria-hidden='true' href='#list-antivirals-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
|
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|
||||
<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>
|
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<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antivirals data set: a <a href='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>
|
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<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antivirals data set: a <a href='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>
|
||||
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
|
||||
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='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>
|
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@ -422,7 +290,7 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</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><h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
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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><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</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>
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@ -470,11 +338,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<footer>
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<div class="copyright">
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
|
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
|
||||
</div>
|
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<div class="pkgdown">
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||||
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
|
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</div>
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</footer>
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@ -483,8 +351,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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</body>
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</html>
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Reference in New Issue
Block a user