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<h1>Preprocess spectral data according to user-designated method</h1>
<small class="dont-index">Source: <a href='https://github.com/GoreLab/waves/blob/master/R/DoPreprocessing.R'><code>R/DoPreprocessing.R</code></a></small>
<div class="hidden name"><code>DoPreprocessing.Rd</code></div>
</div>
<div class="ref-description">
<p>Preprocessing, also known as pretreatment, is often used to
increase the signal to noise ratio in vis-NIR datasets. The <em>waves</em>
function <code>DoPreprocessing</code> applies common spectral preprocessing
methods such as standard normal variate and the Savitzky-Golay filter.</p>
</div>
<pre class="usage"><span class='fu'>DoPreprocessing</span><span class='op'>(</span>
<span class='va'>df</span>,
test.data <span class='op'>=</span> <span class='cn'>NULL</span>,
preprocessing.method <span class='op'>=</span> <span class='fl'>1</span>,
wavelengths <span class='op'>=</span> <span class='fl'>740</span><span class='op'>:</span><span class='fl'>1070</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>df</th>
<td><p><code>data.frame</code> object containing spectral data. First column(s)
(optional) include metadata (with or without reference value column)
followed by spectral columns. Spectral column names must be formatted as
"X" followed by wavelength Include no other columns to right of spectra! No
missing values permitted.</p></td>
</tr>
<tr>
<th>test.data</th>
<td><p><code>data.frame</code> object with same format as train.data.
Will be appended to <code>df</code> during preprocessing so that the same
transformations are applied to each row. Default is <code>NULL</code>.</p></td>
</tr>
<tr>
<th>preprocessing.method</th>
<td><p>Number or list of numbers 1:13 corresponding to
desired pretreatment method(s):</p><ul>
<li><p>1 = raw data (default)</p></li>
<li><p>2 = standard normal variate (SNV)</p></li>
<li><p>3 = SNV and first derivative</p></li>
<li><p>4 = SNV and second derivative</p></li>
<li><p>5 = first derivative</p></li>
<li><p>6 = second derivative</p></li>
<li><p>7 = Savitzky–Golay filter (SG)</p></li>
<li><p>8 = SNV and SG</p></li>
<li><p>9 = gap segment derivative (window size = 11)</p></li>
<li><p>10 = SG and first derivative (window size = 5)</p></li>
<li><p>11 = SG and first derivative (window size = 11)</p></li>
<li><p>12 = SG and second derivative (window size = 5)</p></li>
<li><p>13 = SG and second derivative (window size = 11)</p></li>
</ul></td>
</tr>
<tr>
<th>wavelengths</th>
<td><p>List of wavelengths represented by each column in
<code>df</code>. Default is 740:1070.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Preprocessed <code>df</code>` (or list of <code>data.frame</code>s) with
reference column intact</p>
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='fu'>DoPreprocessing</span><span class='op'>(</span>df <span class='op'>=</span> <span class='va'>ikeogu.2017</span>, wavelengths <span class='op'>=</span> <span class='fl'>350</span><span class='op'>:</span><span class='fl'>2500</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span>,<span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span>
</div><div class='output co'>#> study.name sample.id DMC.oven TCC X350
#> 1 C16Mcal C16Mcal_1 39.62109 1.002029 0.4881079
#> 2 C16Mcal C16Mcal_2 35.52017 17.034718 0.5727389
#> 3 C16Mcal C16Mcal_3 42.04462 21.616243 0.5989934
#> 4 C16Mcal C16Mcal_4 39.00999 2.428640 0.5169374
#> 5 C16Mcal C16Mcal_5 33.44273 24.012182 0.5189608</div></pre>
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