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measurement metadata from a nested list into a spectra tibble, so that one
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row represents one spectral measurement. Spectra, x-axis values and metadata
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are mapped from the individual list elements (named after file name including
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the extension) and transformed into (list-)columns of a spectra tibble,
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which is an extended data frame. For each measurement, spectral data and
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metadata are combined into one row of the tidy data frame. In addition, the ID
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columns unique_id, file_id, and sample_id are extracted from
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"metadata" (data frame) list entries and returned as identifier columns of
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the spectra tibble. List-columns facilitate keeping related data together in
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a rectangular data structure. They can be manipulated easily during
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subsequent transformations, for example using the standardized functions of
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the simplerspec data processing pipeline.'><!-- 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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.1</span>
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<div class="col-md-9 contents">
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<div class="page-header">
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<h1>Gather measurements of different spectra types, corresponding x-axis values and metadata from nested list.</h1>
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<small class="dont-index">Source: <a href="https://github.com/philipp-baumann/simplerspec/blob/HEAD/R/gather-spc.R" class="external-link"><code>R/gather-spc.R</code></a></small>
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<div class="hidden name"><code>gather_spc.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>Gather spectra, corresponding x-axis values, and device and
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measurement metadata from a nested list into a spectra tibble, so that one
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row represents one spectral measurement. Spectra, x-axis values and metadata
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are mapped from the individual list elements (named after file name including
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the extension) and transformed into (list-)columns of a spectra tibble,
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which is an extended data frame. For each measurement, spectral data and
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metadata are combined into one row of the tidy data frame. In addition, the ID
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columns <code>unique_id</code>, <code>file_id</code>, and <code>sample_id</code> are extracted from
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<code>"metadata"</code> (data frame) list entries and returned as identifier columns of
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the spectra tibble. List-columns facilitate keeping related data together in
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a rectangular data structure. They can be manipulated easily during
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subsequent transformations, for example using the standardized functions of
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the simplerspec data processing pipeline.</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">gather_spc</span><span class="op">(</span><span class="va">data</span>, spc_types <span class="op">=</span> <span class="st">"spc"</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>data</dt>
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<dd><p>Recursive list named with filename (<code>file_id</code>) at first level
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entries, where each element containing a sample measurement has nested
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metadata (<code>"metadata"</code>), spectra types (see <code>spc_types</code>), corresponding
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x-axis values (see section <em>"Details on spectra data checks and matching"</em>).
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The <code>data</code> list is a structural convention to organize spectra and their
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metadata. It follows for example the list structure returned from the Bruker
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OPUS binary reader <code><a href="read_opus_univ.html">simplerspec::read_opus_univ()</a></code>.</p></dd>
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<dt>spc_types</dt>
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<dd><p>Character vector with the spectra types to be extracted
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from <code>data</code> list and gathered into list-columns. The spectra type names need
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to exactly follow the naming conventions, and the element names and contents
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need to be present at the second list hierarchy of <code>data</code>. These values are
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allowed:</p><ul><li><p><code>"spc"</code> (default): final raw spectra after atmospheric compensation, if
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performed (named <code>AB</code> in Bruker OPUS software; results from referencing
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sample to reference single channel reflectance and transforming to
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absorbance).</p></li>
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<li><p><code>"spc_nocomp"</code>: raw spectra without atmospheric correction</p></li>
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<li><p><code>"sc_sm"</code>: Single channel reflectance spectra of the samples</p></li>
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<li><p><code>"sc_rf"</code>: Single channel reflectance spectra of the reference (background
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spectra)</p></li>
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<li><p><code>"ig_sm"</code>: Interferograms of the sample spectra (currently only spectra
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without x-axis list-columns are matched and returned)</p></li>
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<li><p><code>"ig_rf"</code>: Interferograms of the reference spectra (currently only spectra
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without x-axis list-columns are matched and returned)</p></li>
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</ul></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>Spectra tibble (<code>spc_tbl</code> with classes <code>"tbl_df"</code>, <code>"tbl"</code>, and
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<code>"data.frame"</code>) with the following (list-)columns:</p><ul><li><p><code>"unique_id"</code>: Character vector with unique measurement identifier, likely
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a string with file names in combination with date and time (extracted from
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each <code>"metadata"</code> data frame column).</p></li>
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<li><p><code>"file_id"</code> : Character vector with file name including the extension
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(extracted from each <code>"metadata"</code> data frame column).</p></li>
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<li><p><code>"sample_id"</code>: Character vector with sample identifier. For Bruker OPUS
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binary files, this corresponds to the file name without the file extension
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in integer increments of sample replicate measurements.</p></li>
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<li><p>One or multiple of <code>"spc"</code>, <code>"spc_nocomp"</code>, <code>"sc_sm"</code>, or <code>"sc_rf"</code>:
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List(s) of data.table's containing spectra type(s).</p></li>
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<li><p>One or multiple of <code>"wavenumbers"</code>, <code>"wavelengths"</code>, <code>"x_values"</code>,
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<code>"wavenumbers_sc_sm"</code>, <code>"wavelengths_sc_sm"</code>, <code>"x_values_sc_sm"</code>,
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<code>"wavenumbers_sc_rf"</code>, <code>"wavelengths_sc_rf"</code>, or <code>"x_values_sc_rf"</code>:
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List(s) of numeric vectors with matched x-axis values (see <em>"Details on
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spectra data checks and matching"</em> below).</p></li>
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</ul></div>
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<div id="details-on-spectra-data-checks-and-matching">
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<h2>Details on spectra data checks and matching</h2>
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<p><code>gather_spc()</code> checks whether these conditions are met for each measurement
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in the list <code>data</code>:</p><ol><li><p>Make sure that the first level <code>data</code> elements are named (assumed to be
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the file name the data originate from), and remove missing measurements with
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an informative message.</p></li>
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<li><p>Remove any duplicated file names and raise a message if there are
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name duplicates at first level.</p></li>
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<li><p>Check whether <code>spc_types</code> inputs are supported (see argument <code>spc_types</code>)
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and present at the second level of the <code>data</code> list. If not, remove
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all data elements for incomplete spectral measurements.</p></li>
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<li><p>Match spectra types and possible corresponding x-axis types from
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a lookup list. For each selected spectrum type (left), at least one of
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the element names of the x-axis type (right) needs to be present for each
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measurement in the list <code>data</code>:</p><ul><li><p><code>"spc"</code> : <code>"wavenumbers"</code>, <code>"wavelengths"</code>, or <code>"x_values"</code></p></li>
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<li><p><code>"spc_nocomp"</code> : <code>"wavenumbers"</code>, <code>"wavelengths"</code>, or <code>"x_values"</code></p></li>
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<li><p><code>"sc_sm"</code> : <code>"wavenumbers_sc_sm"</code>, <code>"wavelengths_sc_sm"</code>, or
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<code>"x_values_sc_sm"</code></p></li>
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<li><p><code>"sc_rf"</code> : <code>"wavenumbers_sc_rf"</code>, <code>"wavelengths_sc_rf"</code>, or
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<code>"x_values_sc_rf"</code></p></li>
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</ul></li>
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<li><p>Check if <code>"metadata"</code> elements are present and remove data elements for
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measurements with missing or incorrectly named metadata elements
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(message).</p></li>
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</ol></div>
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