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(v1.7.1.9026) updated DDDs
This commit is contained in:
@ -93,7 +93,7 @@
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</button>
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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">1.7.1.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9026</span>
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</span>
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</div>
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@ -223,13 +223,6 @@
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Source Code
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</a>
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</li>
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<li>
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
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Survey
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</a>
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</li>
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</ul>
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@ -316,7 +309,7 @@
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>ab_class</th>
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<td><p>an antimicrobial class, such as <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
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<td><p>an antimicrobial class or a part of it, such as <code>"carba"</code> and <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
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</tr>
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<tr>
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<th>only_rsi_columns</th>
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@ -343,7 +336,7 @@
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<p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a> such as <code><a href='https://tidyselect.r-lib.org/reference/everything.html'>everything()</a></code>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, see <em>Examples</em>.</p>
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<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
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<p>The <code>ab_class()</code> function can be used to filter/select on a manually defined antibiotic class. It searches for results in the <a href='antibiotics.html'>antibiotics</a> data set within the columns <code>name</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
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<p>The <code>ab_class()</code> function can be used to filter/select on a manually defined antibiotic class. It searches for results in the <a href='antibiotics.html'>antibiotics</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
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<p>The <code>ab_selector()</code> function can be used to internally filter the <a href='antibiotics.html'>antibiotics</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
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<p>The <code>administrable_per_os()</code> and <code>administrable_iv()</code> functions also rely on the <a href='antibiotics.html'>antibiotics</a> data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
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<h2 class="hasAnchor" id="full-list-of-supported-antibiotic-classes"><a class="anchor" href="#full-list-of-supported-antibiotic-classes"></a>Full list of supported (antibiotic) classes</h2>
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@ -432,6 +425,10 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='co'># and erythromycin is not a penicillin:</span>
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<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&</span> <span class='fu'>administrable_per_os</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
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<span class='co'># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span>
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<span class='co'># flexible. For instance, to select antibiotic columns with an oral DDD of at</span>
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<span class='co'># least 1 gram:</span>
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<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>ab_selector</span><span class='op'>(</span><span class='va'>oral_ddd</span> <span class='op'>></span> <span class='fl'>1</span> <span class='op'>&</span> <span class='va'>oral_units</span> <span class='op'>==</span> <span class='st'>"g"</span><span class='op'>)</span><span class='op'>]</span>
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<span class='co'># dplyr -------------------------------------------------------------------</span>
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<span class='co'># \donttest{</span>
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@ -6,7 +6,7 @@
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>Data Sets with 558 Antimicrobials — antibiotics • AMR (for R)</title>
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<title>Data Sets with 558 Antimicrobial Drugs — antibiotics • AMR (for R)</title>
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<!-- favicons -->
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script>
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<meta property="og:title" content="Data Sets with 558 Antimicrobials — antibiotics" />
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<meta property="og:title" content="Data Sets with 558 Antimicrobial Drugs — antibiotics" />
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<meta property="og:description" content="Two data sets containing all antibiotics/antimycotics and antivirals. 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." />
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary_large_image" />
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@ -93,7 +93,7 @@
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</button>
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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">1.7.1.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9026</span>
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</span>
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</div>
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@ -223,13 +223,6 @@
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Source Code
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</a>
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</li>
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<li>
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
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Survey
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</a>
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</li>
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</ul>
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@ -244,7 +237,7 @@
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<div class="row">
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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 Antimicrobials</h1>
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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/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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@ -273,9 +266,9 @@
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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</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 treatment</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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<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</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 treatment</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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<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</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 treatment</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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<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</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 treatment</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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<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</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 treatment</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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<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) 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>
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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>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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<script src="../extra.js"></script>
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<meta property="og:title" content="Get ATC Properties from WHOCC Website — atc_online_property" />
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<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit." />
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<meta property="og:description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit." />
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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<meta name="twitter:card" content="summary_large_image" />
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<meta name="twitter:creator" content="@msberends" />
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</button>
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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">1.7.1.9024</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9026</span>
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</span>
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</div>
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Source Code
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</a>
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</li>
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<li>
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<a href="../survey.html">
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<span class="fa fa-clipboard-list"></span>
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Survey
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</a>
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</li>
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</ul>
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</div>
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<div class="ref-description">
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<p>Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
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<p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
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</div>
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<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>atc_online_property</span><span class='op'>(</span>
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<span class='fu'>atc_online_groups</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
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<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span>
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<span class='fu'>atc_online_ddd_units</span><span class='op'>(</span><span class='va'>atc_code</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>atc_code</th>
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<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> or <a href='https://rdrr.io/r/base/character.html'>character</a> vector with ATC code(s) of antibiotic(s)</p></td>
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<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> (vector) with ATC code(s) of antibiotics, will be coerced with <code><a href='as.ab.html'>as.ab()</a></code> and <code><a href='ab_property.html'>ab_atc()</a></code> internally if not a valid ATC code</p></td>
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</tr>
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<tr>
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<th>property</th>
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@ -342,6 +337,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"curl"</span><span class='op'>)</span> <span class='op'>&&</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"rvest"</span><span class='op'>)</span> <span class='op'>&&</span> <span class='fu'><a href='https://rdrr.io/r/base/ns-load.html'>requireNamespace</a></span><span class='op'>(</span><span class='st'>"xml2"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='co'># oral DDD (Defined Daily Dose) of amoxicillin</span>
|
||||
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"O"</span><span class='op'>)</span>
|
||||
<span class='fu'>atc_online_ddd</span><span class='op'>(</span><span class='fu'><a href='ab_property.html'>ab_atc</a></span><span class='op'>(</span><span class='st'>"amox"</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
|
||||
<span class='fu'>atc_online_property</span><span class='op'>(</span><span class='st'>"J01CA04"</span>, <span class='st'>"DDD"</span>, <span class='st'>"P"</span><span class='op'>)</span>
|
||||
|
||||
@ -92,7 +92,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9025</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9026</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -311,7 +311,7 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
|
||||
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> <code><a href="atc_online.html">atc_online_ddd_units()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Get ATC Properties from WHOCC Website</p></td>
|
||||
</tr>
|
||||
@ -490,7 +490,7 @@
|
||||
<td>
|
||||
<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
|
||||
</td>
|
||||
<td><p>Data Sets with 558 Antimicrobials</p></td>
|
||||
<td><p>Data Sets with 558 Antimicrobial Drugs</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
|
||||
Reference in New Issue
Block a user