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corresponding x-axis values that are both stored in list-columns of a spectra
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tibble. A spectra tibble hosts spectra, x-axis vectors, metadata, and
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further linked data with standardized naming conventions. Data input for
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resampling can for example be generated with simplerspec::gather_spc().
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Resampling is a key harmonizing step to process and later model spectra
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measured at different resolutions and spectral ranges (i.e., different
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spectrometer devices and/or measurement settings)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<div class="page-header">
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<h1>Resample spectra in list-column to new x-axis interval</h1>
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<small class="dont-index">Source: <a href="https://github.com/philipp-baumann/simplerspec/blob/HEAD/R/resample-spc.R" class="external-link"><code>R/resample-spc.R</code></a></small>
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<div class="hidden name"><code>resample_spc.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>Resamples (interpolates) different spectra types with
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corresponding x-axis values that are both stored in list-columns of a spectra
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tibble. A spectra tibble hosts spectra, x-axis vectors, metadata, and
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further linked data with standardized naming conventions. Data input for
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resampling can for example be generated with <code><a href="gather_spc.html">simplerspec::gather_spc()</a></code>.
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Resampling is a key harmonizing step to process and later model spectra
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measured at different resolutions and spectral ranges (i.e., different
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spectrometer devices and/or measurement settings).</p>
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</div>
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<div id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">resample_spc</span><span class="op">(</span></span>
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<span> <span class="va">spc_tbl</span>,</span>
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<span> column_in <span class="op">=</span> <span class="st">"spc"</span>,</span>
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<span> x_unit <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"wavenumber"</span>, <span class="st">"wavelength"</span><span class="op">)</span>,</span>
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<span> wn_lower <span class="op">=</span> <span class="fl">500</span>,</span>
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<span> wn_upper <span class="op">=</span> <span class="fl">4000</span>,</span>
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<span> wn_interval <span class="op">=</span> <span class="fl">2</span>,</span>
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<span> wl_lower <span class="op">=</span> <span class="fl">350</span>,</span>
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<span> wl_upper <span class="op">=</span> <span class="fl">2500</span>,</span>
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<span> wl_interval <span class="op">=</span> <span class="fl">1</span>,</span>
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<span> interpol_method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"linear"</span>, <span class="st">"spline"</span><span class="op">)</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>spc_tbl</dt>
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<dd><p>Spectra data embedded in a tibble object (classes
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<code>"tbl_df", "tbl", "data.frame"</code>). The spectra tibble needs to contain at
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least of one of the the spectra columns <code>spc</code>, <code>spc_rs</code>, <code>spc_mean</code>,
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<code>spc_nocomp</code>, <code>sc_sm</code>, <code>sc_rf</code>, or <code>spc_pre</code> (list-columns with spectral
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<code>data.table</code>s), and <code>wavenumbers</code> or <code>wavelengths</code> (list-column with vectors
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of x-axis values corresponding to each spectrum). The help section <em>"Matching
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spectrum type and corresponding x-axis type"</em> describes the spectra types
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and corresponding x-axis types.</p></dd>
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<dt>column_in</dt>
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<dd><p>Character vector of length 1L or symbol/name
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specifying the name of list-column that contains the spectra to be resampled.</p></dd>
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<dt>x_unit</dt>
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<dd><p>Character vector of length 1L specifying the measurement unit
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of the x-axis values (list-column) of the input spectra in <code>spc_tbl</code>.
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Possible values are <code>"wavenumber"</code> (default) or <code>"wavelength"</code>. Wavenumber
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is a convenient unit of frequency in the mid-infrared spectral range,
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where wavelength is often used as spatial period for the visible and
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near-infrared range.</p></dd>
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<dt>wn_lower</dt>
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<dd><p>Numeric value of lowest wavenumber. This argument will only
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be used if <code>x_unit = "wavenumber"</code>. The value serves as starting value for
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 500 (i.e., in reciprocal centimeters).</p></dd>
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<dt>wn_upper</dt>
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<dd><p>Numeric value of highest wavenumber. This argument will only
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be used if <code>x_unit = "wavenumber</code>. The value will be used as last value of
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 4000 (i.e., in reciprocal centimeters).</p></dd>
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<dt>wn_interval</dt>
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<dd><p>Numeric value of the wavenumber increment for the new
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wavenumber sequence that the spectra will be resampled upon. Default value
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is 2 (i.e., in reciprocal centimeters).</p></dd>
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<dt>wl_lower</dt>
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<dd><p>Numeric value of lowest wavelength. This argument will only
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be used if <code>x_unit = "wavelength"</code>. The value serves as starting value of
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the new wavenumber sequence that the spectra will be resampled upon.
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Default value is 350 (i.e. in nanometers).</p></dd>
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<dt>wl_upper</dt>
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<dd><p>Numeric value of highest wavelength. This argument will only
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be used if <code>x_unit = "wavelength"</code>. The value will be used as last value of
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the new wavenumber sequence that the spectra will be resampled upon. Default
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value is 2500 (i.e., in nanometers).</p></dd>
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<dt>wl_interval</dt>
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<dd><p>Numeric value of the wavelength increment for the new
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wavenumber sequence that the spectra will be resampled upon. This argument
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will only be used if <code>x_unit = "wavelength"</code>. Default value is 1 (i.e., in
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nanometers).</p></dd>
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<dt>interpol_method</dt>
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<dd><p>Character of <code>"linear"</code> (default) or <code>"spline"</code> with
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the interpolation method. <code>"spline"</code> uses a cubic spline to interpolate the
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input spectra at given x-axis values to new equispaced x-axis intervals.</p></dd>
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</dl></div>
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<div id="value">
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<h2>Value</h2>
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<p>A spectra tibble (<code>spc_tbl</code>) containing two added list-columns:</p><ul><li><p><code>spc_rs:</code> Resampled spectra as list of <code>data.table</code>s</p></li>
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<li><p><code>wavenumbers_rs</code> or <code>wavelengths_rs</code>: Resampled x-axis values as list of
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numeric vectors</p></li>
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</ul></div>
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<div id="matching-spectrum-type-and-corresponding-x-axis-type">
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<h2>Matching spectrum type and corresponding x-axis type</h2>
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<p>The combinations of input spectrum types (<code>column_in</code>) and
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corresponding x-axis types are generated from a simple lookup list. The
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following key-value(s) pairs can be matched at given key, which is the column
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name from <code>column_in</code> containing the spectra.</p><ul><li><p><code>"spc"</code> : <code>"wavenumbers"</code> or <code>"wavelengths"</code> (raw spectra)</p></li>
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<li><p><code>"spc_rs"</code> : <code>"wavenumbers_rs"</code> or <code>"wavelengths_rs"</code>) (resampled spectra)</p></li>
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<li><p><code>"spc_mean"</code> : <code>"wavenumbers_rs"</code> or <code>"wavelengths_rs"</code> (mean spectra)</p></li>
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<li><p><code>"spc_nocomp"</code> <code>"wavenumbers"</code> or <code>"wavelengths"</code> (spectra prior
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atmospheric compensation)</p></li>
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<li><p><code>"sc_sm" : c("wavenumbers_sc_sm", "wavelengths_sc_sm")</code> (single channel
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sample spectra)</p></li>
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<li><p><code>"sc_rf" : c("wavenumbers_sc_rf", "wavelengths_sc_rf")</code> (single channel
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reference spectra)</p></li>
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<li><p><code>"spc_pre" : "xvalues_pre"</code> (preprocessed spectra)</p></li>
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</ul></div>
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