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extract_geocoverage.html
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extract_geocoverage.html
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<h1>Import template for geographic coverage</h1>
<small class="dont-index">Source: <a href='https://github.com/EDIorg/EMLassemblyline/blob/master/R/extract_geocoverage.R'><code>R/extract_geocoverage.R</code></a></small>
<div class="hidden name"><code>extract_geocoverage.Rd</code></div>
</div>
<div class="ref-description">
<p>Import template for defining geographic points and areas of a dataset.
The content of this template is automatically extracted from a data
table containing geographic coordinates.</p>
</div>
<pre class="usage"><span class='fu'>extract_geocoverage</span>(
<span class='no'>path</span>,
<span class='kw'>data.path</span> <span class='kw'>=</span> <span class='no'>path</span>,
<span class='no'>data.table</span>,
<span class='no'>lat.col</span>,
<span class='no'>lon.col</span>,
<span class='no'>site.col</span>,
<span class='kw'>write.file</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='kw'>NULL</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>path</th>
<td><p>(character) Path to the directory where the geographic coverage
template will be written.</p></td>
</tr>
<tr>
<th>data.path</th>
<td><p>(character) Path to the directory containing <code>data.table</code>.</p></td>
</tr>
<tr>
<th>data.table</th>
<td><p>(character) Name of table containing geographic coordinates
represented in decimal degrees, where latitudes south of the equator
and longitudes west of the prime meridian are negative.</p></td>
</tr>
<tr>
<th>lat.col</th>
<td><p>(character) Name of latitude column.</p></td>
</tr>
<tr>
<th>lon.col</th>
<td><p>(character) Name of longitude column.</p></td>
</tr>
<tr>
<th>site.col</th>
<td><p>(character) Name of site column, where site is the name of the location
specified by <code>lat.col</code> and <code>lon.col</code>.</p></td>
</tr>
<tr>
<th>x</th>
<td><p>(named list; optional) Alternative input to
<code>EMLassemblyline</code> functions. Use <code><a href='template_arguments.html'>template_arguments()</a></code> to
create <code>x</code>.</p></td>
</tr>
<tr>
<th>write.file</th>
<td><p>(logical; optional) Whether to write the geographic coverage template
to <code>path</code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<ul>
<li><p><strong>geographic_coverage.txt</strong> The geographic
coverage template. A tab delimited table.</p></li>
<li><p>If using <code>x</code>, then the geographic coverage template is
added to <strong>/x/templates</strong>.</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>An existing geographic coverage template will not be overwritten by
subsequent calls to <code>extract_geocoverage()</code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Set working directory</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/getwd'>setwd</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/tempfile'>tempdir</a></span>())
<span class='co'># Create data package directory "pkg_255"</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/files'>file.copy</a></span>(
<span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>'/examples/pkg_255'</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>'EMLassemblyline'</span>),
<span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>'.'</span>,
<span class='kw'>recursive</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>
)</div><div class='output co'>#> [1] TRUE</div><div class='input'>
<span class='co'># View directory contents (NOTE: geographic_coverage.txt doesn't exist)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list.files'>dir</a></span>(<span class='st'>'./pkg_255/metadata_templates'</span>)</div><div class='output co'>#> [1] "abstract.txt" "additional_info.txt"
#> [3] "attributes_decomp.txt" "attributes_nitrogen.txt"
#> [5] "custom_units.txt" "intellectual_rights.txt"
#> [7] "keywords.txt" "methods.txt"
#> [9] "personnel.txt" </div><div class='input'>
<span class='co'># Extract geographic coverage</span>
<span class='fu'>extract_geocoverage</span>(
<span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>'./pkg_255/metadata_templates'</span>,
<span class='kw'>data.path</span> <span class='kw'>=</span> <span class='st'>'./pkg_255/data_objects'</span>,
<span class='kw'>data.table</span> <span class='kw'>=</span> <span class='st'>'nitrogen.csv'</span>,
<span class='kw'>site.col</span> <span class='kw'>=</span> <span class='st'>'site_name'</span>,
<span class='kw'>lat.col</span> <span class='kw'>=</span> <span class='st'>'site_lat'</span>,
<span class='kw'>lon.col</span> <span class='kw'>=</span> <span class='st'>'site_lon'</span>
)</div><div class='output co'>#> <span class='message'>Creating geographic coverage template.</span></div><div class='output co'>#> <span class='warning'>Warning: 'extract_geocoverage' is deprecated.</span>
#> <span class='warning'>Use 'template_geographic_coverage' instead.</span>
#> <span class='warning'>See help("Deprecated") and help("EMLassemblyline-deprecated").</span></div><div class='output co'>#> <span class='message'>Writing geographic_coverage.txt to path</span></div><div class='output co'>#> <span class='message'>Done.</span></div><div class='input'>
<span class='co'># View directory contents (NOTE: geographic_coverage.txt exists)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list.files'>dir</a></span>(<span class='st'>'./pkg_255/metadata_templates'</span>)</div><div class='output co'>#> [1] "abstract.txt" "additional_info.txt"
#> [3] "attributes_decomp.txt" "attributes_nitrogen.txt"
#> [5] "custom_units.txt" "geographic_coverage.txt"
#> [7] "intellectual_rights.txt" "keywords.txt"
#> [9] "methods.txt" "personnel.txt" </div><div class='input'>
<span class='co'># Rerunning extract_geocoverage() does not overwrite files</span>
<span class='fu'>extract_geocoverage</span>(
<span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>'./pkg_255/metadata_templates'</span>,
<span class='kw'>data.path</span> <span class='kw'>=</span> <span class='st'>'./pkg_255/data_objects'</span>,
<span class='kw'>data.table</span> <span class='kw'>=</span> <span class='st'>'nitrogen.csv'</span>,
<span class='kw'>site.col</span> <span class='kw'>=</span> <span class='st'>'site_name'</span>,
<span class='kw'>lat.col</span> <span class='kw'>=</span> <span class='st'>'site_lat'</span>,
<span class='kw'>lon.col</span> <span class='kw'>=</span> <span class='st'>'site_lon'</span>
)</div><div class='output co'>#> <span class='message'>Creating geographic coverage template.</span></div><div class='output co'>#> <span class='warning'>Warning: 'extract_geocoverage' is deprecated.</span>
#> <span class='warning'>Use 'template_geographic_coverage' instead.</span>
#> <span class='warning'>See help("Deprecated") and help("EMLassemblyline-deprecated").</span></div><div class='output co'>#> <span class='message'>Writing geographic_coverage.txt to path</span></div><div class='output co'>#> <span class='message'>Done.</span></div><div class='input'>
<span class='co'># Clean up</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/unlink'>unlink</a></span>(
<span class='st'>'./pkg_255'</span>,
<span class='kw'>recursive</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>
)</div></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
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