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README.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
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<body>
<h1 id="faers-pharmacovigilance">FAERS-Pharmacovigilance</h1>
<ul>
<li><a href="#introduction">Introduction</a></li>
<li><a href="#installation">Installation</a></li>
<li><a href="#pharmacovigilance-analysis-using-faers">Pharmacovigilance
Analysis using FAERS</a>
<ul>
<li><a href="#check-metadata-of-faers">Check metadata of FAERS</a></li>
<li><a href="#download-and-parse-quarterly-data-files-from-faers">Download and
Parse quarterly data files from FAERS</a></li>
<li><a href="#standardize-and-de-duplication">Standardize and
De-duplication</a></li>
<li><a href="#pharmacovigilance-analysis">Pharmacovigilance
analysis</a></li>
</ul></li>
<li><a href="#sessioninfo">sessionInfo</a></li>
</ul>
<h2 id="introduction">Introduction</h2>
<p>The FDA Adverse Event Reporting System (FAERS) stands as a database
dedicated to the monitoring of post-marketing drug safety and exercises
a notable influence over FDA safety guidance documents, including the
modification of drug labels. The quantity of cases stored within FAERS
has experienced an exponential surge due to the refinement of submission
techniques and adherence to standardized data protocols, making it a
pivotal asset for the realm of regulatory science. While FAERS has
predominantly focused on safety signal detection, the faers package acts
as the intermediary, seamlessly bridging the gap between the FAERS
database and the programming language R. Moreover, the faers package
provides a unified methodology for the seamless execution of
pharmacovigilance analysis, facilitating the integration of genetic
tools in R. With an ultimate ambition towards precision medicine, it
aspires to scrutinize the vast expanse of the human genome, revealing
drug pathways that may be intricately tied to potentially functional,
population-differentiated polymorphisms.</p>
<h2 id="installation">Installation</h2>
<p>To install from Bioconductor, use the following code:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">requireNamespace</span>(<span class="st">"BiocManager"</span>, <span class="at">quietly =</span> <span class="cn">TRUE</span>)) {</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"BiocManager"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>}</span>
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="st">"faers"</span>)</span></code></pre></div>
<p>You can install the development version of <code>faers</code> from <a href="https://github.com/Yunuuuu/faers">GitHub</a> with:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">requireNamespace</span>(<span class="st">"pak"</span>)) {</span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"pak"</span>,</span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a> <span class="at">repos =</span> <span class="fu">sprintf</span>(</span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a> <span class="st">"https://r-lib.github.io/p/pak/devel/%s/%s/%s"</span>,</span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a> .Platform<span class="sc">$</span>pkgType, <span class="fu">R.Version</span>()<span class="sc">$</span>os, <span class="fu">R.Version</span>()<span class="sc">$</span>arch</span>
<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a> )</span>
<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a> )</span>
<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a>}</span>
<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a>pak<span class="sc">::</span><span class="fu">pkg_install</span>(<span class="st">"Yunuuuu/faers"</span>)</span></code></pre></div>
<h2 id="pharmacovigilance-analysis-using-faers">Pharmacovigilance
Analysis using FAERS</h2>
<p>FAERS is a database for the spontaneous reporting of adverse events
and medication errors involving human drugs and therapeutic biological
products. This package accelarate the process of Pharmacovigilance
Analysis using FAERS.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">library</span>(faers)</span></code></pre></div>
<h3 id="check-metadata-of-faers">Check metadata of FAERS</h3>
<p>This will return a data.table reporting years, period, quarter, and
file urls and file sizes. By default, this will use the cached file in
<code>tools::R_user_dir("faers", "cache")</code>. If it doesn’t exist,
the internal will parse metadata in <a href="https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html">https://fis.fda.gov/extensions/FPD-QDE-FAERS/FPD-QDE-FAERS.html</a></p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">faers_meta</span>()</span></code></pre></div>
<p>An metadata copy was associated with the package, just set
<code>internal = TRUE</code>.</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">faers_meta</span>(<span class="at">internal =</span> <span class="cn">TRUE</span>)</span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="co">#> → Using internal FAERS metadata</span></span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co">#> Snapshot time: 2024-09-19 00:18:06.64623</span></span>
<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="co">#> year quarter period</span></span>
<span id="cb5-5"><a href="#cb5-5" tabindex="-1"></a><span class="co">#> <int> <char> <char></span></span>
<span id="cb5-6"><a href="#cb5-6" tabindex="-1"></a><span class="co">#> 1: 2024 q2 April - June</span></span>
<span id="cb5-7"><a href="#cb5-7" tabindex="-1"></a><span class="co">#> 2: 2024 q1 January - March</span></span>
<span id="cb5-8"><a href="#cb5-8" tabindex="-1"></a><span class="co">#> 3: 2023 q4 October - December</span></span>
<span id="cb5-9"><a href="#cb5-9" tabindex="-1"></a><span class="co">#> 4: 2023 q3 July - September</span></span>
<span id="cb5-10"><a href="#cb5-10" tabindex="-1"></a><span class="co">#> 5: 2023 q2 April - June</span></span>
<span id="cb5-11"><a href="#cb5-11" tabindex="-1"></a><span class="co">#> 6: 2023 q1 January - March</span></span>
<span id="cb5-12"><a href="#cb5-12" tabindex="-1"></a><span class="co">#> 7: 2022 q4 October - December</span></span>
<span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a><span class="co">#> 8: 2022 q3 July - September</span></span>
<span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a><span class="co">#> 9: 2022 q2 April - June</span></span>
<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a><span class="co">#> 10: 2022 q1 January - March</span></span>
<span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a><span class="co">#> 11: 2021 q4 October - December</span></span>
<span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="co">#> 12: 2021 q3 July - September</span></span>
<span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a><span class="co">#> 13: 2021 q2 April - June</span></span>
<span id="cb5-19"><a href="#cb5-19" tabindex="-1"></a><span class="co">#> 14: 2021 q1 January - March</span></span>
<span id="cb5-20"><a href="#cb5-20" tabindex="-1"></a><span class="co">#> 15: 2020 q4 October - December</span></span>
<span id="cb5-21"><a href="#cb5-21" tabindex="-1"></a><span class="co">#> 16: 2020 q3 July - September</span></span>
<span id="cb5-22"><a href="#cb5-22" tabindex="-1"></a><span class="co">#> 17: 2020 q2 April - June</span></span>
<span id="cb5-23"><a href="#cb5-23" tabindex="-1"></a><span class="co">#> 18: 2020 q1 January - March</span></span>
<span id="cb5-24"><a href="#cb5-24" tabindex="-1"></a><span class="co">#> 19: 2019 q4 October - December</span></span>
<span id="cb5-25"><a href="#cb5-25" tabindex="-1"></a><span class="co">#> 20: 2019 q3 July - September</span></span>
<span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a><span class="co">#> 21: 2019 q2 April - June</span></span>
<span id="cb5-27"><a href="#cb5-27" tabindex="-1"></a><span class="co">#> 22: 2019 q1 January - March</span></span>
<span id="cb5-28"><a href="#cb5-28" tabindex="-1"></a><span class="co">#> 23: 2018 q4 October - December</span></span>
<span id="cb5-29"><a href="#cb5-29" tabindex="-1"></a><span class="co">#> 24: 2018 q3 July - September</span></span>
<span id="cb5-30"><a href="#cb5-30" tabindex="-1"></a><span class="co">#> 25: 2018 q2 April - June</span></span>
<span id="cb5-31"><a href="#cb5-31" tabindex="-1"></a><span class="co">#> 26: 2018 q1 January - March</span></span>
<span id="cb5-32"><a href="#cb5-32" tabindex="-1"></a><span class="co">#> 27: 2017 q4 October - December</span></span>
<span id="cb5-33"><a href="#cb5-33" tabindex="-1"></a><span class="co">#> 28: 2017 q3 July - September</span></span>
<span id="cb5-34"><a href="#cb5-34" tabindex="-1"></a><span class="co">#> 29: 2017 q2 April - June</span></span>
<span id="cb5-35"><a href="#cb5-35" tabindex="-1"></a><span class="co">#> 30: 2017 q1 January - March</span></span>
<span id="cb5-36"><a href="#cb5-36" tabindex="-1"></a><span class="co">#> 31: 2016 q4 October - December</span></span>
<span id="cb5-37"><a href="#cb5-37" tabindex="-1"></a><span class="co">#> 32: 2016 q3 July - September</span></span>
<span id="cb5-38"><a href="#cb5-38" tabindex="-1"></a><span class="co">#> 33: 2016 q2 April - June</span></span>
<span id="cb5-39"><a href="#cb5-39" tabindex="-1"></a><span class="co">#> 34: 2016 q1 January - March</span></span>
<span id="cb5-40"><a href="#cb5-40" tabindex="-1"></a><span class="co">#> 35: 2015 q4 October - December</span></span>
<span id="cb5-41"><a href="#cb5-41" tabindex="-1"></a><span class="co">#> 36: 2015 q3 July - September</span></span>
<span id="cb5-42"><a href="#cb5-42" tabindex="-1"></a><span class="co">#> 37: 2015 q2 April - June</span></span>
<span id="cb5-43"><a href="#cb5-43" tabindex="-1"></a><span class="co">#> 38: 2015 q1 January - March</span></span>
<span id="cb5-44"><a href="#cb5-44" tabindex="-1"></a><span class="co">#> 39: 2014 q4 October - December</span></span>
<span id="cb5-45"><a href="#cb5-45" tabindex="-1"></a><span class="co">#> 40: 2014 q3 July - September</span></span>
<span id="cb5-46"><a href="#cb5-46" tabindex="-1"></a><span class="co">#> 41: 2014 q2 April - June</span></span>
<span id="cb5-47"><a href="#cb5-47" tabindex="-1"></a><span class="co">#> 42: 2014 q1 January - March</span></span>
<span id="cb5-48"><a href="#cb5-48" tabindex="-1"></a><span class="co">#> 43: 2013 q4 October - December</span></span>
<span id="cb5-49"><a href="#cb5-49" tabindex="-1"></a><span class="co">#> 44: 2013 q3 July - September</span></span>
<span id="cb5-50"><a href="#cb5-50" tabindex="-1"></a><span class="co">#> 45: 2013 q2 April - June</span></span>
<span id="cb5-51"><a href="#cb5-51" tabindex="-1"></a><span class="co">#> 46: 2013 q1 January - March</span></span>
<span id="cb5-52"><a href="#cb5-52" tabindex="-1"></a><span class="co">#> 47: 2012 q4 October - December</span></span>
<span id="cb5-53"><a href="#cb5-53" tabindex="-1"></a><span class="co">#> 48: 2012 q3 July - September</span></span>
<span id="cb5-54"><a href="#cb5-54" tabindex="-1"></a><span class="co">#> 49: 2012 q2 April - June</span></span>
<span id="cb5-55"><a href="#cb5-55" tabindex="-1"></a><span class="co">#> 50: 2012 q1 January - March</span></span>
<span id="cb5-56"><a href="#cb5-56" tabindex="-1"></a><span class="co">#> 51: 2011 q4 October - December</span></span>
<span id="cb5-57"><a href="#cb5-57" tabindex="-1"></a><span class="co">#> 52: 2011 q3 July - September</span></span>
<span id="cb5-58"><a href="#cb5-58" tabindex="-1"></a><span class="co">#> 53: 2011 q2 April - June</span></span>
<span id="cb5-59"><a href="#cb5-59" tabindex="-1"></a><span class="co">#> 54: 2011 q1 January - March</span></span>
<span id="cb5-60"><a href="#cb5-60" tabindex="-1"></a><span class="co">#> 55: 2010 q4 October - December</span></span>
<span id="cb5-61"><a href="#cb5-61" tabindex="-1"></a><span class="co">#> 56: 2010 q3 July - September</span></span>
<span id="cb5-62"><a href="#cb5-62" tabindex="-1"></a><span class="co">#> 57: 2010 q2 April - June</span></span>
<span id="cb5-63"><a href="#cb5-63" tabindex="-1"></a><span class="co">#> 58: 2010 q1 January - March</span></span>
<span id="cb5-64"><a href="#cb5-64" tabindex="-1"></a><span class="co">#> 59: 2009 q4 October - December</span></span>
<span id="cb5-65"><a href="#cb5-65" tabindex="-1"></a><span class="co">#> 60: 2009 q3 July - September</span></span>
<span id="cb5-66"><a href="#cb5-66" tabindex="-1"></a><span class="co">#> 61: 2009 q2 April - June</span></span>
<span id="cb5-67"><a href="#cb5-67" tabindex="-1"></a><span class="co">#> 62: 2009 q1 January - March</span></span>
<span id="cb5-68"><a href="#cb5-68" tabindex="-1"></a><span class="co">#> 63: 2008 q4 October - December</span></span>
<span id="cb5-69"><a href="#cb5-69" tabindex="-1"></a><span class="co">#> 64: 2008 q3 July - September</span></span>
<span id="cb5-70"><a href="#cb5-70" tabindex="-1"></a><span class="co">#> 65: 2008 q2 April - June</span></span>
<span id="cb5-71"><a href="#cb5-71" tabindex="-1"></a><span class="co">#> 66: 2008 q1 January - March</span></span>
<span id="cb5-72"><a href="#cb5-72" tabindex="-1"></a><span class="co">#> 67: 2007 q4 October - December</span></span>
<span id="cb5-73"><a href="#cb5-73" tabindex="-1"></a><span class="co">#> 68: 2007 q3 July - September</span></span>
<span id="cb5-74"><a href="#cb5-74" tabindex="-1"></a><span class="co">#> 69: 2007 q2 April - June</span></span>
<span id="cb5-75"><a href="#cb5-75" tabindex="-1"></a><span class="co">#> 70: 2007 q1 January - March</span></span>
<span id="cb5-76"><a href="#cb5-76" tabindex="-1"></a><span class="co">#> ascii_urls ascii_file_size</span></span>
<span id="cb5-77"><a href="#cb5-77" tabindex="-1"></a><span class="co">#> <char> <char></span></span>
<span id="cb5-78"><a href="#cb5-78" tabindex="-1"></a><span class="co">#> 1: https://fis.fda.gov/content/Exports/faers_ascii_2024q2.zip 63.9MB</span></span>
<span id="cb5-79"><a href="#cb5-79" tabindex="-1"></a><span class="co">#> 2: https://fis.fda.gov/content/Exports/faers_ascii_2024q1.zip 63.1MB</span></span>
<span id="cb5-80"><a href="#cb5-80" tabindex="-1"></a><span class="co">#> 3: https://fis.fda.gov/content/Exports/faers_ascii_2023Q4.zip 69.1MB</span></span>
<span id="cb5-81"><a href="#cb5-81" tabindex="-1"></a><span class="co">#> 4: https://fis.fda.gov/content/Exports/faers_ascii_2023Q3.zip 60.1MB</span></span>
<span id="cb5-82"><a href="#cb5-82" tabindex="-1"></a><span class="co">#> 5: https://fis.fda.gov/content/Exports/faers_ascii_2023q2.zip 64.5MB</span></span>
<span id="cb5-83"><a href="#cb5-83" tabindex="-1"></a><span class="co">#> 6: https://fis.fda.gov/content/Exports/faers_ascii_2023q1.zip 64.3MB</span></span>
<span id="cb5-84"><a href="#cb5-84" tabindex="-1"></a><span class="co">#> 7: https://fis.fda.gov/content/Exports/faers_ascii_2022Q4.zip 69MB</span></span>
<span id="cb5-85"><a href="#cb5-85" tabindex="-1"></a><span class="co">#> 8: https://fis.fda.gov/content/Exports/faers_ascii_2022Q3.zip 63.2MB</span></span>
<span id="cb5-86"><a href="#cb5-86" tabindex="-1"></a><span class="co">#> 9: https://fis.fda.gov/content/Exports/faers_ascii_2022q2.zip 63MB</span></span>
<span id="cb5-87"><a href="#cb5-87" tabindex="-1"></a><span class="co">#> 10: https://fis.fda.gov/content/Exports/faers_ascii_2022q1.zip 64.7MB</span></span>
<span id="cb5-88"><a href="#cb5-88" tabindex="-1"></a><span class="co">#> 11: https://fis.fda.gov/content/Exports/faers_ascii_2021Q4.zip 59MB</span></span>
<span id="cb5-89"><a href="#cb5-89" tabindex="-1"></a><span class="co">#> 12: https://fis.fda.gov/content/Exports/faers_ascii_2021Q3.zip 70MB</span></span>
<span id="cb5-90"><a href="#cb5-90" tabindex="-1"></a><span class="co">#> 13: https://fis.fda.gov/content/Exports/faers_ascii_2021Q2.zip 66MB</span></span>
<span id="cb5-91"><a href="#cb5-91" tabindex="-1"></a><span class="co">#> 14: https://fis.fda.gov/content/Exports/faers_ascii_2021Q1.zip 69MB</span></span>
<span id="cb5-92"><a href="#cb5-92" tabindex="-1"></a><span class="co">#> 15: https://fis.fda.gov/content/Exports/faers_ascii_2020Q4.zip 71MB</span></span>
<span id="cb5-93"><a href="#cb5-93" tabindex="-1"></a><span class="co">#> 16: https://fis.fda.gov/content/Exports/faers_ascii_2020Q3.zip 64MB</span></span>
<span id="cb5-94"><a href="#cb5-94" tabindex="-1"></a><span class="co">#> 17: https://fis.fda.gov/content/Exports/faers_ascii_2020Q2.zip 66MB</span></span>
<span id="cb5-95"><a href="#cb5-95" tabindex="-1"></a><span class="co">#> 18: https://fis.fda.gov/content/Exports/faers_ascii_2020Q1.zip 65MB</span></span>
<span id="cb5-96"><a href="#cb5-96" tabindex="-1"></a><span class="co">#> 19: https://fis.fda.gov/content/Exports/faers_ascii_2019Q4.zip 60MB</span></span>
<span id="cb5-97"><a href="#cb5-97" tabindex="-1"></a><span class="co">#> 20: https://fis.fda.gov/content/Exports/faers_ascii_2019Q3.zip 62MB</span></span>
<span id="cb5-98"><a href="#cb5-98" tabindex="-1"></a><span class="co">#> 21: https://fis.fda.gov/content/Exports/faers_ascii_2019Q2.zip 62MB</span></span>
<span id="cb5-99"><a href="#cb5-99" tabindex="-1"></a><span class="co">#> 22: https://fis.fda.gov/content/Exports/faers_ascii_2019Q1.zip 56MB</span></span>
<span id="cb5-100"><a href="#cb5-100" tabindex="-1"></a><span class="co">#> 23: https://fis.fda.gov/content/Exports/faers_ascii_2018q4.zip 60MB</span></span>
<span id="cb5-101"><a href="#cb5-101" tabindex="-1"></a><span class="co">#> 24: https://fis.fda.gov/content/Exports/faers_ascii_2018q3.zip 60MB</span></span>
<span id="cb5-102"><a href="#cb5-102" tabindex="-1"></a><span class="co">#> 25: https://fis.fda.gov/content/Exports/faers_ascii_2018q2.zip 60MB</span></span>
<span id="cb5-103"><a href="#cb5-103" tabindex="-1"></a><span class="co">#> 26: https://fis.fda.gov/content/Exports/faers_ascii_2018q1.zip 52MB</span></span>
<span id="cb5-104"><a href="#cb5-104" tabindex="-1"></a><span class="co">#> 27: https://fis.fda.gov/content/Exports/faers_ascii_2017q4.zip 41MB</span></span>
<span id="cb5-105"><a href="#cb5-105" tabindex="-1"></a><span class="co">#> 28: https://fis.fda.gov/content/Exports/faers_ascii_2017q3.zip 48MB</span></span>
<span id="cb5-106"><a href="#cb5-106" tabindex="-1"></a><span class="co">#> 29: https://fis.fda.gov/content/Exports/faers_ascii_2017q2.zip 46MB</span></span>
<span id="cb5-107"><a href="#cb5-107" tabindex="-1"></a><span class="co">#> 30: https://fis.fda.gov/content/Exports/faers_ascii_2017q1.zip 48MB</span></span>
<span id="cb5-108"><a href="#cb5-108" tabindex="-1"></a><span class="co">#> 31: https://fis.fda.gov/content/Exports/faers_ascii_2016q4.zip 44MB</span></span>
<span id="cb5-109"><a href="#cb5-109" tabindex="-1"></a><span class="co">#> 32: https://fis.fda.gov/content/Exports/faers_ascii_2016q3.zip 46MB</span></span>
<span id="cb5-110"><a href="#cb5-110" tabindex="-1"></a><span class="co">#> 33: https://fis.fda.gov/content/Exports/faers_ascii_2016q2.zip 44MB</span></span>
<span id="cb5-111"><a href="#cb5-111" tabindex="-1"></a><span class="co">#> 34: https://fis.fda.gov/content/Exports/faers_ascii_2016q1.zip 46MB</span></span>
<span id="cb5-112"><a href="#cb5-112" tabindex="-1"></a><span class="co">#> 35: https://fis.fda.gov/content/Exports/faers_ascii_2015q4.zip 42MB</span></span>
<span id="cb5-113"><a href="#cb5-113" tabindex="-1"></a><span class="co">#> 36: https://fis.fda.gov/content/Exports/faers_ascii_2015q3.zip 47MB</span></span>
<span id="cb5-114"><a href="#cb5-114" tabindex="-1"></a><span class="co">#> 37: https://fis.fda.gov/content/Exports/faers_ascii_2015q2.zip 38MB</span></span>
<span id="cb5-115"><a href="#cb5-115" tabindex="-1"></a><span class="co">#> 38: https://fis.fda.gov/content/Exports/faers_ascii_2015q1.zip 39MB</span></span>
<span id="cb5-116"><a href="#cb5-116" tabindex="-1"></a><span class="co">#> 39: https://fis.fda.gov/content/Exports/faers_ascii_2014q4.zip 28MB</span></span>
<span id="cb5-117"><a href="#cb5-117" tabindex="-1"></a><span class="co">#> 40: https://fis.fda.gov/content/Exports/faers_ascii_2014q3.zip 28MB</span></span>
<span id="cb5-118"><a href="#cb5-118" tabindex="-1"></a><span class="co">#> 41: https://fis.fda.gov/content/Exports/faers_ascii_2014q2.zip 25MB</span></span>
<span id="cb5-119"><a href="#cb5-119" tabindex="-1"></a><span class="co">#> 42: https://fis.fda.gov/content/Exports/faers_ascii_2014q1.zip 30MB</span></span>
<span id="cb5-120"><a href="#cb5-120" tabindex="-1"></a><span class="co">#> 43: https://fis.fda.gov/content/Exports/faers_ascii_2013q4.zip 26MB</span></span>
<span id="cb5-121"><a href="#cb5-121" tabindex="-1"></a><span class="co">#> 44: https://fis.fda.gov/content/Exports/faers_ascii_2013q3.zip 22MB</span></span>
<span id="cb5-122"><a href="#cb5-122" tabindex="-1"></a><span class="co">#> 45: https://fis.fda.gov/content/Exports/faers_ascii_2013q2.zip 21MB</span></span>
<span id="cb5-123"><a href="#cb5-123" tabindex="-1"></a><span class="co">#> 46: https://fis.fda.gov/content/Exports/faers_ascii_2013q1.zip 25MB</span></span>
<span id="cb5-124"><a href="#cb5-124" tabindex="-1"></a><span class="co">#> 47: https://fis.fda.gov/content/Exports/faers_ascii_2012q4.zip 28MB</span></span>
<span id="cb5-125"><a href="#cb5-125" tabindex="-1"></a><span class="co">#> 48: https://fis.fda.gov/content/Exports/aers_ascii_2012q3.zip 16MB</span></span>
<span id="cb5-126"><a href="#cb5-126" tabindex="-1"></a><span class="co">#> 49: https://fis.fda.gov/content/Exports/aers_ascii_2012q2.zip 25MB</span></span>
<span id="cb5-127"><a href="#cb5-127" tabindex="-1"></a><span class="co">#> 50: https://fis.fda.gov/content/Exports/aers_ascii_2012q1.zip 26MB</span></span>
<span id="cb5-128"><a href="#cb5-128" tabindex="-1"></a><span class="co">#> 51: https://fis.fda.gov/content/Exports/aers_ascii_2011q4.zip 23MB</span></span>
<span id="cb5-129"><a href="#cb5-129" tabindex="-1"></a><span class="co">#> 52: https://fis.fda.gov/content/Exports/aers_ascii_2011q3.zip 23MB</span></span>
<span id="cb5-130"><a href="#cb5-130" tabindex="-1"></a><span class="co">#> 53: https://fis.fda.gov/content/Exports/aers_ascii_2011q2.zip 23MB</span></span>
<span id="cb5-131"><a href="#cb5-131" tabindex="-1"></a><span class="co">#> 54: https://fis.fda.gov/content/Exports/aers_ascii_2011q1.zip 21MB</span></span>
<span id="cb5-132"><a href="#cb5-132" tabindex="-1"></a><span class="co">#> 55: https://fis.fda.gov/content/Exports/aers_ascii_2010q4.zip 20MB</span></span>
<span id="cb5-133"><a href="#cb5-133" tabindex="-1"></a><span class="co">#> 56: https://fis.fda.gov/content/Exports/aers_ascii_2010q3.zip 22MB</span></span>
<span id="cb5-134"><a href="#cb5-134" tabindex="-1"></a><span class="co">#> 57: https://fis.fda.gov/content/Exports/aers_ascii_2010q2.zip 17MB</span></span>
<span id="cb5-135"><a href="#cb5-135" tabindex="-1"></a><span class="co">#> 58: https://fis.fda.gov/content/Exports/aers_ascii_2010q1.zip 16MB</span></span>
<span id="cb5-136"><a href="#cb5-136" tabindex="-1"></a><span class="co">#> 59: https://fis.fda.gov/content/Exports/aers_ascii_2009q4.zip 16MB</span></span>
<span id="cb5-137"><a href="#cb5-137" tabindex="-1"></a><span class="co">#> 60: https://fis.fda.gov/content/Exports/aers_ascii_2009q3.zip 16MB</span></span>
<span id="cb5-138"><a href="#cb5-138" tabindex="-1"></a><span class="co">#> 61: https://fis.fda.gov/content/Exports/aers_ascii_2009q2.zip 14MB</span></span>
<span id="cb5-139"><a href="#cb5-139" tabindex="-1"></a><span class="co">#> 62: https://fis.fda.gov/content/Exports/aers_ascii_2009q1.zip 13MB</span></span>
<span id="cb5-140"><a href="#cb5-140" tabindex="-1"></a><span class="co">#> 63: https://fis.fda.gov/content/Exports/aers_ascii_2008q4.zip 13MB</span></span>
<span id="cb5-141"><a href="#cb5-141" tabindex="-1"></a><span class="co">#> 64: https://fis.fda.gov/content/Exports/aers_ascii_2008q3.zip 13MB</span></span>
<span id="cb5-142"><a href="#cb5-142" tabindex="-1"></a><span class="co">#> 65: https://fis.fda.gov/content/Exports/aers_ascii_2008q2.zip 12MB</span></span>
<span id="cb5-143"><a href="#cb5-143" tabindex="-1"></a><span class="co">#> 66: https://fis.fda.gov/content/Exports/aers_ascii_2008q1.zip 12MB</span></span>
<span id="cb5-144"><a href="#cb5-144" tabindex="-1"></a><span class="co">#> 67: https://fis.fda.gov/content/Exports/aers_ascii_2007q4.zip 12MB</span></span>
<span id="cb5-145"><a href="#cb5-145" tabindex="-1"></a><span class="co">#> 68: https://fis.fda.gov/content/Exports/aers_ascii_2007q3.zip 9.9MB</span></span>
<span id="cb5-146"><a href="#cb5-146" tabindex="-1"></a><span class="co">#> 69: https://fis.fda.gov/content/Exports/aers_ascii_2007q2.zip 9.5MB</span></span>
<span id="cb5-147"><a href="#cb5-147" tabindex="-1"></a><span class="co">#> 70: https://fis.fda.gov/content/Exports/aers_ascii_2007q1.zip 9.6MB</span></span>
<span id="cb5-148"><a href="#cb5-148" tabindex="-1"></a><span class="co">#> xml_urls xml_file_size</span></span>
<span id="cb5-149"><a href="#cb5-149" tabindex="-1"></a><span class="co">#> <char> <char></span></span>
<span id="cb5-150"><a href="#cb5-150" tabindex="-1"></a><span class="co">#> 1: https://fis.fda.gov/content/Exports/faers_xml_2024q2.zip 126MB</span></span>
<span id="cb5-151"><a href="#cb5-151" tabindex="-1"></a><span class="co">#> 2: https://fis.fda.gov/content/Exports/faers_xml_2024q1.zip 128MB</span></span>
<span id="cb5-152"><a href="#cb5-152" tabindex="-1"></a><span class="co">#> 3: https://fis.fda.gov/content/Exports/faers_xml_2023Q4.zip 140MB</span></span>
<span id="cb5-153"><a href="#cb5-153" tabindex="-1"></a><span class="co">#> 4: https://fis.fda.gov/content/Exports/faers_xml_2023Q3.zip 123MB</span></span>
<span id="cb5-154"><a href="#cb5-154" tabindex="-1"></a><span class="co">#> 5: https://fis.fda.gov/content/Exports/faers_xml_2023q2.zip 130MB</span></span>
<span id="cb5-155"><a href="#cb5-155" tabindex="-1"></a><span class="co">#> 6: https://fis.fda.gov/content/Exports/faers_xml_2023q1.zip 133MB</span></span>
<span id="cb5-156"><a href="#cb5-156" tabindex="-1"></a><span class="co">#> 7: https://fis.fda.gov/content/Exports/faers_xml_2022Q4.zip 144MB</span></span>
<span id="cb5-157"><a href="#cb5-157" tabindex="-1"></a><span class="co">#> 8: https://fis.fda.gov/content/Exports/faers_xml_2022Q3.zip 132MB</span></span>
<span id="cb5-158"><a href="#cb5-158" tabindex="-1"></a><span class="co">#> 9: https://fis.fda.gov/content/Exports/faers_xml_2022q2.zip 140MB</span></span>
<span id="cb5-159"><a href="#cb5-159" tabindex="-1"></a><span class="co">#> 10: https://fis.fda.gov/content/Exports/faers_xml_2022q1.zip 136MB</span></span>
<span id="cb5-160"><a href="#cb5-160" tabindex="-1"></a><span class="co">#> 11: https://fis.fda.gov/content/Exports/faers_xml_2021Q4.zip 123MB</span></span>
<span id="cb5-161"><a href="#cb5-161" tabindex="-1"></a><span class="co">#> 12: https://fis.fda.gov/content/Exports/faers_xml_2021Q3.zip 132MB</span></span>
<span id="cb5-162"><a href="#cb5-162" tabindex="-1"></a><span class="co">#> 13: https://fis.fda.gov/content/Exports/faers_xml_2021Q2.zip 123MB</span></span>
<span id="cb5-163"><a href="#cb5-163" tabindex="-1"></a><span class="co">#> 14: https://fis.fda.gov/content/Exports/faers_xml_2021Q1.zip 130MB</span></span>
<span id="cb5-164"><a href="#cb5-164" tabindex="-1"></a><span class="co">#> 15: https://fis.fda.gov/content/Exports/faers_xml_2020Q4.zip 131MB</span></span>
<span id="cb5-165"><a href="#cb5-165" tabindex="-1"></a><span class="co">#> 16: https://fis.fda.gov/content/Exports/faers_xml_2020Q3.zip 121MB</span></span>
<span id="cb5-166"><a href="#cb5-166" tabindex="-1"></a><span class="co">#> 17: https://fis.fda.gov/content/Exports/faers_xml_2020Q2.zip 123MB</span></span>
<span id="cb5-167"><a href="#cb5-167" tabindex="-1"></a><span class="co">#> 18: https://fis.fda.gov/content/Exports/faers_xml_2020Q1.zip 125MB</span></span>
<span id="cb5-168"><a href="#cb5-168" tabindex="-1"></a><span class="co">#> 19: https://fis.fda.gov/content/Exports/faers_xml_2019Q4.zip 113MB</span></span>
<span id="cb5-169"><a href="#cb5-169" tabindex="-1"></a><span class="co">#> 20: https://fis.fda.gov/content/Exports/faers_xml_2019Q3.zip 118MB</span></span>
<span id="cb5-170"><a href="#cb5-170" tabindex="-1"></a><span class="co">#> 21: https://fis.fda.gov/content/Exports/faers_xml_2019Q2.zip 118MB</span></span>
<span id="cb5-171"><a href="#cb5-171" tabindex="-1"></a><span class="co">#> 22: https://fis.fda.gov/content/Exports/faers_xml_2019Q1.zip 103MB</span></span>
<span id="cb5-172"><a href="#cb5-172" tabindex="-1"></a><span class="co">#> 23: https://fis.fda.gov/content/Exports/faers_xml_2018q4.zip 112MB</span></span>
<span id="cb5-173"><a href="#cb5-173" tabindex="-1"></a><span class="co">#> 24: https://fis.fda.gov/content/Exports/faers_xml_2018q3.zip 112MB</span></span>
<span id="cb5-174"><a href="#cb5-174" tabindex="-1"></a><span class="co">#> 25: https://fis.fda.gov/content/Exports/faers_xml_2018q2.zip 112MB</span></span>
<span id="cb5-175"><a href="#cb5-175" tabindex="-1"></a><span class="co">#> 26: https://fis.fda.gov/content/Exports/faers_xml_2018q1.zip 94MB</span></span>
<span id="cb5-176"><a href="#cb5-176" tabindex="-1"></a><span class="co">#> 27: https://fis.fda.gov/content/Exports/faers_xml_2017q4.zip 76MB</span></span>
<span id="cb5-177"><a href="#cb5-177" tabindex="-1"></a><span class="co">#> 28: https://fis.fda.gov/content/Exports/faers_xml_2017q3.zip 91MB</span></span>
<span id="cb5-178"><a href="#cb5-178" tabindex="-1"></a><span class="co">#> 29: https://fis.fda.gov/content/Exports/faers_xml_2017q2.zip 86MB</span></span>
<span id="cb5-179"><a href="#cb5-179" tabindex="-1"></a><span class="co">#> 30: https://fis.fda.gov/content/Exports/faers_xml_2017q1.zip 91MB</span></span>
<span id="cb5-180"><a href="#cb5-180" tabindex="-1"></a><span class="co">#> 31: https://fis.fda.gov/content/Exports/faers_xml_2016q4.zip 82MB</span></span>
<span id="cb5-181"><a href="#cb5-181" tabindex="-1"></a><span class="co">#> 32: https://fis.fda.gov/content/Exports/faers_xml_2016q3.zip 87MB</span></span>
<span id="cb5-182"><a href="#cb5-182" tabindex="-1"></a><span class="co">#> 33: https://fis.fda.gov/content/Exports/faers_xml_2016q2.zip 81MB</span></span>
<span id="cb5-183"><a href="#cb5-183" tabindex="-1"></a><span class="co">#> 34: https://fis.fda.gov/content/Exports/faers_xml_2016q1.zip 84MB</span></span>
<span id="cb5-184"><a href="#cb5-184" tabindex="-1"></a><span class="co">#> 35: https://fis.fda.gov/content/Exports/faers_xml_2015q4.zip 77MB</span></span>
<span id="cb5-185"><a href="#cb5-185" tabindex="-1"></a><span class="co">#> 36: https://fis.fda.gov/content/Exports/faers_xml_2015q3.zip 88MB</span></span>
<span id="cb5-186"><a href="#cb5-186" tabindex="-1"></a><span class="co">#> 37: https://fis.fda.gov/content/Exports/faers_xml_2015q2.zip 70MB</span></span>
<span id="cb5-187"><a href="#cb5-187" tabindex="-1"></a><span class="co">#> 38: https://fis.fda.gov/content/Exports/faers_xml_2015q1.zip 72MB</span></span>
<span id="cb5-188"><a href="#cb5-188" tabindex="-1"></a><span class="co">#> 39: https://fis.fda.gov/content/Exports/faers_xml_2014q4.zip 53MB</span></span>
<span id="cb5-189"><a href="#cb5-189" tabindex="-1"></a><span class="co">#> 40: https://fis.fda.gov/content/Exports/faers_xml_2014q3.zip 54MB</span></span>
<span id="cb5-190"><a href="#cb5-190" tabindex="-1"></a><span class="co">#> 41: https://fis.fda.gov/content/Exports/faers_xml_2014q2.zip 44MB</span></span>
<span id="cb5-191"><a href="#cb5-191" tabindex="-1"></a><span class="co">#> 42: https://fis.fda.gov/content/Exports/faers_xml_2014q1.zip 52MB</span></span>
<span id="cb5-192"><a href="#cb5-192" tabindex="-1"></a><span class="co">#> 43: https://fis.fda.gov/content/Exports/faers_xml_2013q4.zip 46MB</span></span>
<span id="cb5-193"><a href="#cb5-193" tabindex="-1"></a><span class="co">#> 44: https://fis.fda.gov/content/Exports/faers_xml_2013q3.zip 40MB</span></span>
<span id="cb5-194"><a href="#cb5-194" tabindex="-1"></a><span class="co">#> 45: https://fis.fda.gov/content/Exports/faers_xml_2013q2.zip 38MB</span></span>
<span id="cb5-195"><a href="#cb5-195" tabindex="-1"></a><span class="co">#> 46: https://fis.fda.gov/content/Exports/faers_xml_2013q1.zip 44MB</span></span>
<span id="cb5-196"><a href="#cb5-196" tabindex="-1"></a><span class="co">#> 47: https://fis.fda.gov/content/Exports/faers_xml_2012q4.zip 50MB</span></span>
<span id="cb5-197"><a href="#cb5-197" tabindex="-1"></a><span class="co">#> 48: https://fis.fda.gov/content/Exports/aers_sgml_2012q3.zip 21MB</span></span>
<span id="cb5-198"><a href="#cb5-198" tabindex="-1"></a><span class="co">#> 49: https://fis.fda.gov/content/Exports/aers_sgml_2012q2.zip 32MB</span></span>
<span id="cb5-199"><a href="#cb5-199" tabindex="-1"></a><span class="co">#> 50: https://fis.fda.gov/content/Exports/aers_sgml_2012q1.zip 33MB</span></span>
<span id="cb5-200"><a href="#cb5-200" tabindex="-1"></a><span class="co">#> 51: https://fis.fda.gov/content/Exports/aers_sgml_2011q4.zip 29MB</span></span>
<span id="cb5-201"><a href="#cb5-201" tabindex="-1"></a><span class="co">#> 52: https://fis.fda.gov/content/Exports/aers_sgml_2011q3.zip 29MB</span></span>
<span id="cb5-202"><a href="#cb5-202" tabindex="-1"></a><span class="co">#> 53: https://fis.fda.gov/content/Exports/aers_sgml_2011q2.zip 29MB</span></span>
<span id="cb5-203"><a href="#cb5-203" tabindex="-1"></a><span class="co">#> 54: https://fis.fda.gov/content/Exports/aers_sgml_2011q1.zip 26MB</span></span>
<span id="cb5-204"><a href="#cb5-204" tabindex="-1"></a><span class="co">#> 55: https://fis.fda.gov/content/Exports/aers_sgml_2010q4.zip 25MB</span></span>
<span id="cb5-205"><a href="#cb5-205" tabindex="-1"></a><span class="co">#> 56: https://fis.fda.gov/content/Exports/aers_sgml_2010q3.zip 28MB</span></span>
<span id="cb5-206"><a href="#cb5-206" tabindex="-1"></a><span class="co">#> 57: https://fis.fda.gov/content/Exports/aers_sgml_2010q2.zip 22MB</span></span>
<span id="cb5-207"><a href="#cb5-207" tabindex="-1"></a><span class="co">#> 58: https://fis.fda.gov/content/Exports/aers_sgml_2010q1.zip 20MB</span></span>
<span id="cb5-208"><a href="#cb5-208" tabindex="-1"></a><span class="co">#> 59: https://fis.fda.gov/content/Exports/aers_sgml_2009q4.zip 20MB</span></span>
<span id="cb5-209"><a href="#cb5-209" tabindex="-1"></a><span class="co">#> 60: https://fis.fda.gov/content/Exports/aers_sgml_2009q3.zip 19MB</span></span>
<span id="cb5-210"><a href="#cb5-210" tabindex="-1"></a><span class="co">#> 61: https://fis.fda.gov/content/Exports/aers_sgml_2009q2.zip 18MB</span></span>
<span id="cb5-211"><a href="#cb5-211" tabindex="-1"></a><span class="co">#> 62: https://fis.fda.gov/content/Exports/aers_sgml_2009q1.zip 16MB</span></span>
<span id="cb5-212"><a href="#cb5-212" tabindex="-1"></a><span class="co">#> 63: https://fis.fda.gov/content/Exports/aers_sgml_2008q4.zip 16MB</span></span>
<span id="cb5-213"><a href="#cb5-213" tabindex="-1"></a><span class="co">#> 64: https://fis.fda.gov/content/Exports/aers_sgml_2008q3.zip 16MB</span></span>
<span id="cb5-214"><a href="#cb5-214" tabindex="-1"></a><span class="co">#> 65: https://fis.fda.gov/content/Exports/aers_sgml_2008q2.zip 16MB</span></span>
<span id="cb5-215"><a href="#cb5-215" tabindex="-1"></a><span class="co">#> 66: https://fis.fda.gov/content/Exports/aers_sgml_2008q1.zip 15MB</span></span>
<span id="cb5-216"><a href="#cb5-216" tabindex="-1"></a><span class="co">#> 67: https://fis.fda.gov/content/Exports/aers_sgml_2007q4.zip 14MB</span></span>
<span id="cb5-217"><a href="#cb5-217" tabindex="-1"></a><span class="co">#> 68: https://fis.fda.gov/content/Exports/aers_sgml_2007q3.zip 13MB</span></span>
<span id="cb5-218"><a href="#cb5-218" tabindex="-1"></a><span class="co">#> 69: https://fis.fda.gov/content/Exports/aers_sgml_2007q2.zip 12MB</span></span>
<span id="cb5-219"><a href="#cb5-219" tabindex="-1"></a><span class="co">#> 70: https://fis.fda.gov/content/Exports/aers_sgml_2007q1.zip 12MB</span></span>
<span id="cb5-220"><a href="#cb5-220" tabindex="-1"></a><span class="co">#> [ reached getOption("max.print") -- omitted 13 rows ]</span></span></code></pre></div>
<h3 id="download-and-parse-quarterly-data-files-from-faers">Download and
Parse quarterly data files from FAERS</h3>
<p>The FAERS Quarterly Data files contain raw data extracted from the
AERS database for the indicated time ranges. The quarterly data files,
which are available in ASCII or SGML formats, include:</p>
<ul>
<li><code>demo</code>: demographic and administrative information</li>
<li><code>drug</code>: drug information from the case reports</li>
<li><code>reac</code>: reaction information from the reports</li>
<li><code>outc</code>: patient outcome information from the reports</li>
<li><code>rpsr</code>: information on the source of the reports</li>
<li><code>ther</code>: drug therapy start dates and end dates for the
reported drugs</li>
<li><code>indi</code>: contains all “Medical Dictionary for Regulatory
Activities” (MedDRA) terms coded for the indications for use (diagnoses)
for the reported drugs</li>
</ul>
<p>Generally, we can use <code>faers()</code> function to download and
parse all quarterly data files from FAERS. Internally, the
<code>faers()</code> function seamlessly utilizes
<code>faers_download()</code> and <code>faers_parse()</code> to
preprocess each quarterly data file from the FAERS repository. The
default <code>format</code> was <code>ascii</code> and will return a
<code>FAERSascii</code> object. (xml format would also be okay , but
presently, the XML file receives only minimal support in the following
process.)</p>
<p>Some variables has been added into specific field. See
<code>?faers_parse</code> for details.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co"># Please make sure to replace dir with your own directory path, as the file</span></span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="co"># included in the package is a sampled version. </span></span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a>data1 <span class="ot"><-</span> <span class="fu">faers</span>(<span class="dv">2004</span>, <span class="st">"q1"</span>,</span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a> <span class="at">dir =</span> <span class="fu">system.file</span>(<span class="st">"extdata"</span>, <span class="at">package =</span> <span class="st">"faers"</span>),</span>
<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a> <span class="at">compress_dir =</span> <span class="fu">tempdir</span>()</span>
<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a>)</span>
<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="co">#> Finding 1 file already downloaded: 'aers_ascii_2004q1.zip'</span></span></code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a>data1</span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="co">#> FAERS data from 1 Quarterly ascii file</span></span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="co">#> Total reports: 100 (with duplicates)</span></span></code></pre></div>
<p>Furthermore, in cases where multiple quarterly data files are
requisite, the <code>faers_combine()</code> function is judiciously
employed.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a>data2 <span class="ot"><-</span> <span class="fu">faers</span>(<span class="fu">c</span>(<span class="dv">2004</span>, <span class="dv">2017</span>), <span class="fu">c</span>(<span class="st">"q1"</span>, <span class="st">"q2"</span>),</span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a> <span class="at">dir =</span> <span class="fu">system.file</span>(<span class="st">"extdata"</span>, <span class="at">package =</span> <span class="st">"faers"</span>),</span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a> <span class="at">compress_dir =</span> <span class="fu">tempdir</span>()</span>
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a>)</span>
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a><span class="co">#> Finding 2 files already downloaded: 'aers_ascii_2004q1.zip' and</span></span>
<span id="cb8-6"><a href="#cb8-6" tabindex="-1"></a><span class="co">#> 'faers_ascii_2017q2.zip'</span></span>
<span id="cb8-7"><a href="#cb8-7" tabindex="-1"></a><span class="co">#> → Combining all 2 <FAERS> Datas</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a>data2</span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="co">#> FAERS data from 2 Quarterly ascii files</span></span>
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a><span class="co">#> Total reports: 200 (with duplicates)</span></span></code></pre></div>
<p>You can use <code>faers_get()</code> to get specific field data, a
data.table will be returned.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="fu">faers_get</span>(data2, <span class="st">"demo"</span>)</span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="co">#> year quarter primaryid caseid i_f_code foll_seq image event_dt</span></span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a><span class="co">#> <int> <char> <char> <char> <char> <int> <char> <int></span></span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="co">#> 1: 2004 q1 4263764 4060920 I NA 4263764-6 20020101</span></span>
<span id="cb10-5"><a href="#cb10-5" tabindex="-1"></a><span class="co">#> 2: 2004 q1 4263927 4064250 I NA 4263927-X NA</span></span>
<span id="cb10-6"><a href="#cb10-6" tabindex="-1"></a><span class="co">#> 3: 2004 q1 4264001 4062524 I NA 4264001-9 20031218</span></span>
<span id="cb10-7"><a href="#cb10-7" tabindex="-1"></a><span class="co">#> 4: 2004 q1 4264319 4064506 I NA 4264319-X 20031216</span></span>
<span id="cb10-8"><a href="#cb10-8" tabindex="-1"></a><span class="co">#> 5: 2004 q1 4266745 4056689 I NA 4266745-1 20030529</span></span>
<span id="cb10-9"><a href="#cb10-9" tabindex="-1"></a><span class="co">#> --- </span></span>
<span id="cb10-10"><a href="#cb10-10" tabindex="-1"></a><span class="co">#> 196: 2017 q2 136874291 13687429 I NA <NA> NA</span></span>
<span id="cb10-11"><a href="#cb10-11" tabindex="-1"></a><span class="co">#> 197: 2017 q2 136987441 13698744 I NA <NA> 201706</span></span>
<span id="cb10-12"><a href="#cb10-12" tabindex="-1"></a><span class="co">#> 198: 2017 q2 137054551 13705455 I NA <NA> 20160103</span></span>
<span id="cb10-13"><a href="#cb10-13" tabindex="-1"></a><span class="co">#> 199: 2017 q2 137055661 13705566 I NA <NA> NA</span></span>
<span id="cb10-14"><a href="#cb10-14" tabindex="-1"></a><span class="co">#> 200: 2017 q2 137086221 13708622 I NA <NA> NA</span></span>
<span id="cb10-15"><a href="#cb10-15" tabindex="-1"></a><span class="co">#> mfr_dt fda_dt rept_cod mfr_num</span></span>
<span id="cb10-16"><a href="#cb10-16" tabindex="-1"></a><span class="co">#> <int> <int> <char> <char></span></span>
<span id="cb10-17"><a href="#cb10-17" tabindex="-1"></a><span class="co">#> 1: 20031219 20040102 EXP USA031255171</span></span>
<span id="cb10-18"><a href="#cb10-18" tabindex="-1"></a><span class="co">#> 2: 20031209 20040102 EXP B0317710A</span></span>
<span id="cb10-19"><a href="#cb10-19" tabindex="-1"></a><span class="co">#> 3: 20031219 20040102 EXP JP-JNJFOC-20031204393</span></span>
<span id="cb10-20"><a href="#cb10-20" tabindex="-1"></a><span class="co">#> 4: 20031218 20040105 EXP MEDI-0001221</span></span>
<span id="cb10-21"><a href="#cb10-21" tabindex="-1"></a><span class="co">#> 5: 20040105 20040108 EXP FR-GLAXOSMITHKLINE-B0318977A</span></span>
<span id="cb10-22"><a href="#cb10-22" tabindex="-1"></a><span class="co">#> --- </span></span>
<span id="cb10-23"><a href="#cb10-23" tabindex="-1"></a><span class="co">#> 196: 20170612 20170624 EXP GB-TORRENT-00015363</span></span>
<span id="cb10-24"><a href="#cb10-24" tabindex="-1"></a><span class="co">#> 197: 20170623 20170628 EXP JP-PFIZER INC-2017277430</span></span>
<span id="cb10-25"><a href="#cb10-25" tabindex="-1"></a><span class="co">#> 198: 20170501 20170630 EXP US-BAYER-2017-084170</span></span>
<span id="cb10-26"><a href="#cb10-26" tabindex="-1"></a><span class="co">#> 199: 20140423 20170630 PER US-IPSEN BIOPHARMACEUTICALS, INC.-2014-2195</span></span>
<span id="cb10-27"><a href="#cb10-27" tabindex="-1"></a><span class="co">#> 200: 20151116 20170630 PER US-IPSEN BIOPHARMACEUTICALS, INC.-2015-08780</span></span>
<span id="cb10-28"><a href="#cb10-28" tabindex="-1"></a><span class="co">#> mfr_sndr age age_cod gender e_sub wt</span></span>
<span id="cb10-29"><a href="#cb10-29" tabindex="-1"></a><span class="co">#> <char> <num> <char> <char> <char> <num></span></span>
<span id="cb10-30"><a href="#cb10-30" tabindex="-1"></a><span class="co">#> 1: ELI LILLY AND COMPANY 68 YR F N 82.0</span></span>
<span id="cb10-31"><a href="#cb10-31" tabindex="-1"></a><span class="co">#> 2: GLAXOSMITHKLINE GLOBAL CLINICAL SAFETY 58 YR F N NA</span></span>
<span id="cb10-32"><a href="#cb10-32" tabindex="-1"></a><span class="co">#> 3: CENTOCOR, INC. 53 YR F N 36.8</span></span>
<span id="cb10-33"><a href="#cb10-33" tabindex="-1"></a><span class="co">#> 4: MEDIMUNE, INC. NA <NA> F N NA</span></span>
<span id="cb10-34"><a href="#cb10-34" tabindex="-1"></a><span class="co">#> 5: GLAXOSMITHKLINE 48 YR F Y NA</span></span>
<span id="cb10-35"><a href="#cb10-35" tabindex="-1"></a><span class="co">#> --- </span></span>
<span id="cb10-36"><a href="#cb10-36" tabindex="-1"></a><span class="co">#> 196: TORRENT NA <NA> <NA> Y NA</span></span>
<span id="cb10-37"><a href="#cb10-37" tabindex="-1"></a><span class="co">#> 197: PFIZER NA <NA> <NA> Y NA</span></span>
<span id="cb10-38"><a href="#cb10-38" tabindex="-1"></a><span class="co">#> 198: BAYER 84 YR M Y NA</span></span>
<span id="cb10-39"><a href="#cb10-39" tabindex="-1"></a><span class="co">#> 199: IPSEN NA <NA> F Y NA</span></span>
<span id="cb10-40"><a href="#cb10-40" tabindex="-1"></a><span class="co">#> 200: IPSEN 52 YR F Y NA</span></span>
<span id="cb10-41"><a href="#cb10-41" tabindex="-1"></a><span class="co">#> wt_cod rept_dt occp_cod death_dt to_mfr confid v23 caseversion</span></span>
<span id="cb10-42"><a href="#cb10-42" tabindex="-1"></a><span class="co">#> <char> <int> <char> <lgcl> <char> <char> <lgcl> <int></span></span>
<span id="cb10-43"><a href="#cb10-43" tabindex="-1"></a><span class="co">#> 1: KG 20031223 <NA> NA <NA> <NA> NA 0</span></span>
<span id="cb10-44"><a href="#cb10-44" tabindex="-1"></a><span class="co">#> 2: <NA> 20031219 <NA> NA <NA> <NA> NA 0</span></span>
<span id="cb10-45"><a href="#cb10-45" tabindex="-1"></a><span class="co">#> 3: KG 20031231 MD NA <NA> <NA> NA 0</span></span>
<span id="cb10-46"><a href="#cb10-46" tabindex="-1"></a><span class="co">#> 4: <NA> 20031231 MD NA <NA> <NA> NA 0</span></span>
<span id="cb10-47"><a href="#cb10-47" tabindex="-1"></a><span class="co">#> 5: <NA> 20040108 CN NA <NA> <NA> NA 0</span></span>
<span id="cb10-48"><a href="#cb10-48" tabindex="-1"></a><span class="co">#> --- </span></span>
<span id="cb10-49"><a href="#cb10-49" tabindex="-1"></a><span class="co">#> 196: <NA> 20170624 CN NA <NA> <NA> NA 1</span></span>
<span id="cb10-50"><a href="#cb10-50" tabindex="-1"></a><span class="co">#> 197: <NA> 20170628 MD NA <NA> <NA> NA 1</span></span>
<span id="cb10-51"><a href="#cb10-51" tabindex="-1"></a><span class="co">#> 198: <NA> 20170630 LW NA <NA> <NA> NA 1</span></span>
<span id="cb10-52"><a href="#cb10-52" tabindex="-1"></a><span class="co">#> 199: <NA> 20170630 OT NA <NA> <NA> NA 1</span></span>
<span id="cb10-53"><a href="#cb10-53" tabindex="-1"></a><span class="co">#> 200: <NA> 20170630 MD NA <NA> <NA> NA 1</span></span>
<span id="cb10-54"><a href="#cb10-54" tabindex="-1"></a><span class="co">#> age_in_years country_code sex init_fda_dt auth_num lit_ref</span></span>
<span id="cb10-55"><a href="#cb10-55" tabindex="-1"></a><span class="co">#> <num> <char> <char> <int> <char> <char></span></span>
<span id="cb10-56"><a href="#cb10-56" tabindex="-1"></a><span class="co">#> 1: 68 <NA> Female NA <NA> <NA></span></span>
<span id="cb10-57"><a href="#cb10-57" tabindex="-1"></a><span class="co">#> 2: 58 <NA> Female NA <NA> <NA></span></span>
<span id="cb10-58"><a href="#cb10-58" tabindex="-1"></a><span class="co">#> 3: 53 <NA> Female NA <NA> <NA></span></span>
<span id="cb10-59"><a href="#cb10-59" tabindex="-1"></a><span class="co">#> 4: NA <NA> Female NA <NA> <NA></span></span>