(v1.7.1.9022) rely on vctrs for ab selectors

2025-07-17 19:53:16 +02:00 · 2021-07-23 21:42:11 +02:00
parent 0ec81cc12e
commit 4e1efd902c
130 changed files with 3785 additions and 2960 deletions
--- a/docs/reference/antibiotics.html
+++ b/docs/reference/antibiotics.html
@ -55,6 +55,8 @@



+
+
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@ -66,9 +68,15 @@



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+    
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@ -82,7 +90,7 @@
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
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@ -90,14 +98,14 @@
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+    <span class="fa fa-question-circle"></span>
     
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@ -106,77 +114,77 @@
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-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
         
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+        <span class="fa fa-database"></span>
         
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+        <span class="fa fa-skull-crossbones"></span>
         
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+        <span class="fa fa-exchange-alt"></span>
         
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+        <span class="fa fa-bug"></span>
         
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-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
         
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+        <span class="fa fa-shipping-fast"></span>
         
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@ -185,14 +193,14 @@
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+    <span class="fa fa-book-open"></span>
     
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@ -215,7 +223,7 @@
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@ -242,15 +250,87 @@
    <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.</p>
    </div>

-    <pre class="usage"><span class='va'>antibiotics</span>
+    <div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>antibiotics</span>

-<span class='va'>antivirals</span></pre>
+<span class='va'>antivirals</span></code></pre></div>


    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    
-<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>
+<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>
+
+<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>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></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_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</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>
+<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>
+</ul>
+<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>
+
+<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>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></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_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</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>
+<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>
+</ul>
+<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>
+
+<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>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></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_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</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>
+<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>
+</ul>
+<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>
+<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>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></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_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</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>
+<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>
+</ul>
+<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>

 <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>
@ -270,7 +350,59 @@
 </ul>


-<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>
+<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>
+
+<ul>
+<li><p><code>atc</code><br /> ATC code (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='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>
+
+<ul>
+<li><p><code>atc</code><br /> ATC code (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='-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 code (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='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 code (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>

 <ul>
 <li><p><code>atc</code><br /> ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
@ -294,7 +426,7 @@
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <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) are 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>
+<p>Synonyms (i.e. trade names) are 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>


 <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>
@ -342,11 +474,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru

      <footer>
      <div class="copyright">
-  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+  <p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
 </div>

 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <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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      </footer>
@ -355,6 +487,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
  


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