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proximity_matrix.html
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proximity_matrix.html
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<h1>Proximity matrix</h1>
<small class="dont-index">Source: <a href='https://github.com/prioritizr/prioritizr/blob/master/R/proximity_matrix.R'><code>R/proximity_matrix.R</code></a></small>
<div class="hidden name"><code>proximity_matrix.Rd</code></div>
</div>
<div class="ref-description">
<p>Create a matrix showing which planning units are within a certain
spatial proximity to each other.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for Raster</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for SpatialPolygons</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for SpatialLines</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for SpatialPoints</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for sf</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span>
<span class='co'># S3 method for default</span>
<span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>distance</span><span class='op'>)</span></code></pre></div>
<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>x</th>
<td><p><code><a href='https://rdrr.io/pkg/raster/man/Raster-classes.html'>Raster</a></code>,
<code><a href='https://rdrr.io/pkg/sp/man/Spatial-class.html'>Spatial</a></code>, or <code><a href='https://r-spatial.github.io/sf/reference/sf.html'>sf::sf()</a></code> object
representing planning units.</p></td>
</tr>
<tr>
<th>distance</th>
<td><p><code>numeric</code> distance threshold. Planning units
that are further apart from each other than this threshold are
not treated as being within proximity of each other.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p><code><a href='https://rdrr.io/pkg/Matrix/man/dsCMatrix-class.html'>dsCMatrix</a></code> symmetric sparse matrix object.
Each row and column represents a planning unit.
Cells values indicate if the pair-wise distances between different
planning units are within the distance threshold or not (using ones and
zeros). To reduce computational burden, cells among the matrix diagonal are
set to zero. Furthermore, if the argument to <code>x</code> is a
<code><a href='https://rdrr.io/pkg/raster/man/Raster-classes.html'>Raster</a></code> object, then cells with <code>NA</code>
values are set to zero too.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Proximity calculations are performed using
<code><a href='https://r-spatial.github.io/sf/reference/geos_binary_pred.html'>sf::st_is_within_distance()</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='r-in'><span class='co'># load data</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>sim_pu_raster</span>, <span class='va'>sim_pu_sf</span>, <span class='va'>sim_pu_lines</span>, <span class='va'>sim_pu_points</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># create proximity matrix using raster data</span></span>
<span class='r-in'><span class='co'>## crop raster to 9 cells to provide a small example</span></span>
<span class='r-in'><span class='va'>r</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/raster/man/crop.html'>crop</a></span><span class='op'>(</span><span class='va'>sim_pu_raster</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>0.3</span>, <span class='fl'>0</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## make proximity matrix using a distance threshold of 2</span></span>
<span class='r-in'><span class='va'>cm_raster</span> <span class='op'><-</span> <span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>r</span>, distance <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># create proximity matrix using polygon (sf) data</span></span>
<span class='r-in'><span class='co'>## subset 9 polygons to provide a small example</span></span>
<span class='r-in'><span class='va'>ply</span> <span class='op'><-</span> <span class='va'>sim_pu_sf</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>, <span class='fl'>10</span><span class='op'>:</span><span class='fl'>12</span>, <span class='fl'>20</span><span class='op'>:</span><span class='fl'>22</span><span class='op'>)</span>, <span class='op'>]</span></span>
<span class='r-msg co'><span class='r-pr'>#></span> old-style crs object detected; please recreate object with a recent sf::st_crs()</span>
<span class='r-msg co'><span class='r-pr'>#></span> old-style crs object detected; please recreate object with a recent sf::st_crs()</span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## make proximity matrix using a distance threshold of 2</span></span>
<span class='r-in'><span class='va'>cm_ply</span> <span class='op'><-</span> <span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>ply</span>, distance <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># create proximity matrix using line (Spatial) data</span></span>
<span class='r-in'><span class='co'>## subset 9 lines to provide a small example</span></span>
<span class='r-in'><span class='va'>lns</span> <span class='op'><-</span> <span class='va'>sim_pu_lines</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>, <span class='fl'>10</span><span class='op'>:</span><span class='fl'>12</span>, <span class='fl'>20</span><span class='op'>:</span><span class='fl'>22</span><span class='op'>)</span>, <span class='op'>]</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## make proximity matrix</span></span>
<span class='r-in'><span class='va'>cm_lns</span> <span class='op'><-</span> <span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>lns</span>, distance <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## create proximity matrix using point (Spatial) data</span></span>
<span class='r-in'><span class='co'>## subset 9 points to provide a small example</span></span>
<span class='r-in'><span class='va'>pts</span> <span class='op'><-</span> <span class='va'>sim_pu_points</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>, <span class='fl'>10</span><span class='op'>:</span><span class='fl'>12</span>, <span class='fl'>20</span><span class='op'>:</span><span class='fl'>22</span><span class='op'>)</span>, <span class='op'>]</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># make proximity matrix</span></span>
<span class='r-in'><span class='va'>cm_pts</span> <span class='op'><-</span> <span class='fu'>proximity_matrix</span><span class='op'>(</span><span class='va'>pts</span>, distance <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'># plot data and the proximity matrices</span></span>
<span class='r-in'><span class='co'># \dontrun{</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/r/graphics/par.html'>par</a></span><span class='op'>(</span>mfrow <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>4</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## plot raster and proximity matrix</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='va'>r</span>, main <span class='op'>=</span> <span class='st'>"raster"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>, box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/as.matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='va'>cm_raster</span><span class='op'>)</span><span class='op'>)</span>, main <span class='op'>=</span> <span class='st'>"proximity matrix"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>,</span>
<span class='r-in'> box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## plot polygons and proximity matrix</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='va'>r</span>, main <span class='op'>=</span> <span class='st'>"polygons (sf)"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>, box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/as.matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='va'>cm_ply</span><span class='op'>)</span><span class='op'>)</span>, main <span class='op'>=</span> <span class='st'>"proximity matrix"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>,</span>
<span class='r-in'> box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## plot lines and proximity matrix</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='va'>r</span>, main <span class='op'>=</span> <span class='st'>"lines (Spatial)"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>, box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/as.matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='va'>cm_lns</span><span class='op'>)</span><span class='op'>)</span>, main <span class='op'>=</span> <span class='st'>"proximity matrix"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>,</span>
<span class='r-in'> box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'></span>
<span class='r-in'><span class='co'>## plot points and proximity matrix</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='va'>r</span>, main <span class='op'>=</span> <span class='st'>"points (Spatial)"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>, box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-in'><span class='fu'><a href='https://rdrr.io/pkg/raster/man/plot.html'>plot</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/raster.html'>raster</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/raster/man/as.matrix.html'>as.matrix</a></span><span class='op'>(</span><span class='va'>cm_pts</span><span class='op'>)</span><span class='op'>)</span>, main <span class='op'>=</span> <span class='st'>"proximity matrix"</span>, axes <span class='op'>=</span> <span class='cn'>FALSE</span>,</span>
<span class='r-in'> box <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></span>
<span class='r-plt'><img src='proximity_matrix-1.png' alt='' width='700' height='433' /></span>
<span class='r-in'><span class='co'># }</span></span>
</code></pre></div>
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