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<h1 class="title toc-ignore">Loading Raw and Processed Data</h1>
<h4 class="author"><em>Keith Baggerly</em></h4>
<h4 class="date"><em>2017-07-17</em></h4>
<p>I want to work through how to include raw and processed data files.</p>
<p>Let’s say we have a csv file, “basicData.csv”, which we want to summarize.</p>
<p>First, at the top level of the package (which has R/ and man/), we create a new folder for “inst/” (install) if this doesn’t already exist.</p>
<p>Next, within inst we similarly create a subfolder for “extdata”.</p>
<p>This is where raw data should be put.</p>
<p>We copy basicData.csv into inst/extdata.</p>
<p>Then, we recompile the package using “Ctrl-Shift-B”. This will add the csv file as a “system file” for the package.</p>
<p>Let’s see where this is now in sisbid3.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="st">"basicData.csv"</span>,
<span class="dt">package =</span> <span class="st">"sisbid3"</span>)</code></pre></div>
<pre><code>## [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sisbid3/extdata/basicData.csv"</code></pre>
<p>This is the path to where the csv file resides on your system. Now we want to load this data, process it, and store the processed version for later use.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">basicData <-<span class="st"> </span>
<span class="st"> </span><span class="kw">read.csv</span>(<span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="st">"basicData.csv"</span>,
<span class="dt">package =</span> <span class="st">"sisbid3"</span>))
basicData</code></pre></div>
<pre><code>## baseDataX baseDataY
## 1 1 2
## 2 2 4
## 3 3 6
## 4 4 7
## 5 5 11</code></pre>
<p>Now we want to save this as a processed (.Rda) file.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">use_data</span>(basicData)</code></pre></div>
<p>This creates “data/basicData.rda”. Now, as with all objects, we need to document the data. So, we go to R/, add “basicData.R”:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co">#' A small basic dataset</span>
<span class="co">#'</span>
<span class="co">#' This is just an example to see if I can get</span>
<span class="co">#' this to work</span>
<span class="co">#'</span>
<span class="co">#' @format A data frame with 5 rows and 2 columns</span>
<span class="co">#' \describe{</span>
<span class="co">#' \item{basicDataX}{simulated X values}</span>
<span class="co">#' \item{basicDataY}{simulated Y values}</span>
<span class="co">#' }</span>
<span class="co">#' @source I made this up</span>
<span class="st">"basicData"</span></code></pre></div>
<p>Invoke document (to document the dataset), and recompile the package using Ctrl-Shift-B. At this point, the basicData dataset is available at any time.</p>
<p>Now let’s consider a more realistic example.</p>
<p>Say we copy over the iomReview.csv to inst/extdata, and recompile the package so it’s findable using system.file.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="st">"iomReview.csv"</span>,
<span class="dt">package =</span> <span class="st">"sisbid3"</span>)</code></pre></div>
<pre><code>## [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sisbid3/extdata/iomReview.csv"</code></pre>
<p>Now we can load the contents into an R dataset called “vitD” and invoke “use_data”.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">vitD <-<span class="st"> </span>
<span class="st"> </span><span class="kw">read.csv</span>(<span class="kw">system.file</span>(<span class="st">"extdata"</span>,
<span class="st">"iomReview.csv"</span>,
<span class="dt">package =</span> <span class="st">"sisbid3"</span>))
vitD <-<span class="st"> </span>vitD[!<span class="kw">is.na</span>(vitD[,<span class="st">"N"</span>]),]
<span class="kw">use_data</span>(vitD)</code></pre></div>
<p>This creates “data/vitD.rda”.</p>
<p>We still need to document it. Here, the full documentation is in the “vitD.R” file available from the Module3 website, so we simply copy this file over to R/.</p>
<p>Then we invoke document (to document the dataset), and then recompile the package. The vitD object is now part of the package.</p>
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