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<!DOCTYPE html>
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<h1><em>Marxan</em> conservation problem</h1>
<small class="dont-index">Source: <a href="https://github.com/prioritizr/prioritizr/blob/HEAD/R/marxan_problem.R" class="external-link"><code>R/marxan_problem.R</code></a></small>
<div class="hidden name"><code>marxan_problem.Rd</code></div>
</div>
<div class="ref-description">
<p>Create a conservation planning <code><a href="problem.html">problem()</a></code> following the
mathematical formulations used in <em>Marxan</em> (detailed in Beyer
<em>et al.</em> 2016). Note that these problems are solved using
exact algorithms and not simulated annealing (i.e., the <em>Marxan</em> software).</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">marxan_problem</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for default</span></span>
<span><span class="fu">marxan_problem</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for data.frame</span></span>
<span><span class="fu">marxan_problem</span><span class="op">(</span><span class="va">x</span>, <span class="va">spec</span>, <span class="va">puvspr</span>, bound <span class="op">=</span> <span class="cn">NULL</span>, blm <span class="op">=</span> <span class="fl">0</span>, symmetric <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for character</span></span>
<span><span class="fu">marxan_problem</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p><code>character</code> file path for a <em>Marxan</em> input file (typically
called <code>"input.dat"</code>), or <code>data.frame</code> containing planning unit
data (typically called <code>"pu.dat"</code>). If the argument to <code>x</code> is a
<code>data.frame</code>, then each row corresponds to a different planning unit,
and it must have the following columns:</p>
<dl><dt>id</dt>
<dd><p><code>integer</code> unique identifier for each planning unit.
These identifiers are used in the argument to <code>puvspr</code>.</p></dd>
<dt>cost</dt>
<dd><p><code>numeric</code> cost of each planning unit.</p></dd>
<dt>status</dt>
<dd><p><code>integer</code> indicating if each planning unit
should not be locked in the solution (0) or if it should be locked in
(2) or locked out (3) of the solution. Although <em>Marxan</em> allows
planning units to be selected in the initial solution (using values of
1), these values have no effect here. This column is optional.</p></dd>
</dl></dd>
<dt>...</dt>
<dd><p>not used.</p></dd>
<dt>spec</dt>
<dd><p><code>data.frame</code> containing information on the features.
The argument to <code>spec</code> must follow the conventions used by
<em>Marxan</em> for the species data file (conventionally called
<code>"spec.dat"</code>). Each row corresponds to a different feature and
each column corresponds to different information about the features. It
must contain the columns listed below. Note that the argument to
<code>spec</code> must contain at least one column named <code>"prop"</code> or
<code>"amount"</code>---<strong>but not both columns with both of these
names</strong>---to specify the target for each feature.</p>
<dl><dt>id</dt>
<dd><p><code>integer</code> unique identifier for each feature
These identifiers are used in the argument to <code>puvspr</code>.</p></dd>
<dt>name</dt>
<dd><p><code>character</code> name for each feature.</p></dd>
<dt>prop</dt>
<dd><p><code>numeric</code> relative target for each feature
(optional).</p></dd>
'
<dt>amount</dt>
<dd><p><code>numeric</code> absolute target for each
feature (optional).</p></dd>
</dl></dd>
<dt>puvspr</dt>
<dd><p><code>data.frame</code> containing information on the amount of
each feature in each planning unit. The argument to
<code>puvspr</code> must follow the conventions used in the <em>Marxan</em> input
data file (conventionally called <code>"puvspr.dat"</code>). It must contain the
following columns:</p>
<dl><dt>pu</dt>
<dd><p><code>integer</code> planning unit identifier.</p></dd>
<dt>species</dt>
<dd><p><code>integer</code> feature identifier.</p></dd>
<dt>amount</dt>
<dd><p><code>numeric</code> amount of the feature in the
planning unit.</p></dd>
</dl></dd>
<dt>bound</dt>
<dd><p><code>NULL</code> object indicating that no boundary data
is required for the conservation planning problem, or a <code>data.frame</code>
containing information on the planning units' boundaries. The argument to
<code>bound</code> must follow the conventions used in the <em>Marxan</em> input
data file (conventionally called <code>"bound.dat"</code>). It must contain the
following columns:</p>
<dl><dt>id1</dt>
<dd><p><code>integer</code> planning unit identifier.</p></dd>
<dt>id2</dt>
<dd><p><code>integer</code> planning unit identifier.</p></dd>
<dt>boundary</dt>
<dd><p><code>numeric</code> length of shared boundary
between the planning units identified in the previous two columns.</p></dd>
</dl></dd>
<dt>blm</dt>
<dd><p><code>numeric</code> boundary length modifier. This argument only
has an effect when argument to <code>x</code> is a <code>data.frame</code>. The
default argument is zero.</p></dd>
<dt>symmetric</dt>
<dd><p><code>logical</code> does the boundary data (i.e., argument to
<code>bound</code>) describe symmetric relationships between planning units?
If the boundary data contain asymmetric connectivity data,
this parameter should be set to <code>FALSE</code>.
Defaults to <code>TRUE</code>.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p><code><a href="problem.html">problem()</a></code> (i.e., <code><a href="ConservationProblem-class.html">ConservationProblem</a></code>) object.</p>
</div>
<div id="details">
<h2>Details</h2>
<p>This function is provided as a convenient wrapper for solving
<em>Marxan</em> problems using the <span class="pkg">prioritizr</span> package.
Please note that it requires installation of the <span class="pkg">data.table</span> package
to import <em>Marxan</em> data files.</p>
</div>
<div id="notes">
<h2>Notes</h2>
<p>In previous versions, this function could not accommodate asymmetric
connectivity data. It has now been updated to handle asymmetric connectivity
data.</p>
</div>
<div id="references">
<h2>References</h2>
<p>Ball IR, Possingham HP, and Watts M (2009) <em>Marxan and relatives:
Software for spatial conservation prioritisation</em> in Spatial conservation
prioritisation: Quantitative methods and computational tools. Eds Moilanen
A, Wilson KA, and Possingham HP. Oxford University Press, Oxford, UK.</p>
<p>Beyer HL, Dujardin Y, Watts ME, and Possingham HP (2016) Solving
conservation planning problems with integer linear programming.
<em>Ecological Modelling</em>, 228: 14--22.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p>For more information on the correct format for
for <em>Marxan</em> input data, see the
<a href="https://marxansolutions.org" class="external-link">official <em>Marxan</em> website</a> and Ball
<em>et al.</em> (2009).</p></div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># create Marxan problem using Marxan input file</span></span></span>
<span class="r-in"><span><span class="co"># (note this example requires the data.table package to be installed)</span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="va">input_file</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/input.dat"</span>, package <span class="op">=</span> <span class="st">"prioritizr"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">p1</span> <span class="op"><-</span> <span class="fu">marxan_problem</span><span class="op">(</span><span class="va">input_file</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="add_default_solver.html">add_default_solver</a></span><span class="op">(</span>verbose <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># solve problem</span></span></span>
<span class="r-in"><span><span class="va">s1</span> <span class="op"><-</span> <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p1</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># print solution</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">s1</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id cost status xloc yloc locked_in locked_out solution_1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 3 0.000 0 1116623 -4493479 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 2 30 7527.275 3 1110623 -4496943 FALSE TRUE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 3 56 37349.075 0 1092623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 4 58 16959.021 0 1116623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 5 84 34220.256 0 1098623 -4503872 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 6 85 178907.584 0 1110623 -4503872 FALSE FALSE 0</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create Marxan problem using data.frames that have been loaded into R</span></span></span>
<span class="r-in"><span><span class="co"># (note this example also requires the data.table package to be installed)</span></span></span>
<span class="r-in"><span><span class="co">## load in planning unit data</span></span></span>
<span class="r-in"><span><span class="va">pu_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/input/pu.dat"</span>, package <span class="op">=</span> <span class="st">"prioritizr"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">pu_dat</span> <span class="op"><-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://Rdatatable.gitlab.io/data.table/reference/fread.html" class="external-link">fread</a></span><span class="op">(</span><span class="va">pu_path</span>, data.table <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">pu_dat</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id cost status xloc yloc</span>
<span class="r-out co"><span class="r-pr">#></span> 1 3 0.000 0 1116623 -4493479</span>
<span class="r-out co"><span class="r-pr">#></span> 2 30 7527.275 3 1110623 -4496943</span>
<span class="r-out co"><span class="r-pr">#></span> 3 56 37349.075 0 1092623 -4500408</span>
<span class="r-out co"><span class="r-pr">#></span> 4 58 16959.021 0 1116623 -4500408</span>
<span class="r-out co"><span class="r-pr">#></span> 5 84 34220.256 0 1098623 -4503872</span>
<span class="r-out co"><span class="r-pr">#></span> 6 85 178907.584 0 1110623 -4503872</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## load in feature data</span></span></span>
<span class="r-in"><span><span class="va">spec_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/input/spec.dat"</span>, package <span class="op">=</span> <span class="st">"prioritizr"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">spec_dat</span> <span class="op"><-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://Rdatatable.gitlab.io/data.table/reference/fread.html" class="external-link">fread</a></span><span class="op">(</span><span class="va">spec_path</span>, data.table <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">spec_dat</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id prop spf name</span>
<span class="r-out co"><span class="r-pr">#></span> 1 10 0.3 1 bird1</span>
<span class="r-out co"><span class="r-pr">#></span> 2 11 0.3 1 nvis2</span>
<span class="r-out co"><span class="r-pr">#></span> 3 12 0.3 1 nvis8</span>
<span class="r-out co"><span class="r-pr">#></span> 4 13 0.3 1 nvis9</span>
<span class="r-out co"><span class="r-pr">#></span> 5 14 0.3 1 nvis14</span>
<span class="r-out co"><span class="r-pr">#></span> 6 15 0.3 1 nvis20</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## load in planning unit vs feature data</span></span></span>
<span class="r-in"><span><span class="va">puvspr_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/input/puvspr.dat"</span>,</span></span>
<span class="r-in"><span> package <span class="op">=</span> <span class="st">"prioritizr"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">puvspr_dat</span> <span class="op"><-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://Rdatatable.gitlab.io/data.table/reference/fread.html" class="external-link">fread</a></span><span class="op">(</span><span class="va">puvspr_path</span>, data.table <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">puvspr_dat</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> species pu amount</span>
<span class="r-out co"><span class="r-pr">#></span> 1 26 56 120.344884</span>
<span class="r-out co"><span class="r-pr">#></span> 2 26 58 45.167010</span>
<span class="r-out co"><span class="r-pr">#></span> 3 26 84 68.047375</span>
<span class="r-out co"><span class="r-pr">#></span> 4 26 85 9.735624</span>
<span class="r-out co"><span class="r-pr">#></span> 5 26 86 7.803476</span>
<span class="r-out co"><span class="r-pr">#></span> 6 26 111 478.327417</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## load in the boundary data</span></span></span>
<span class="r-in"><span><span class="va">bound_path</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata/input/bound.dat"</span>, package <span class="op">=</span> <span class="st">"prioritizr"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">bound_dat</span> <span class="op"><-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://Rdatatable.gitlab.io/data.table/reference/fread.html" class="external-link">fread</a></span><span class="op">(</span><span class="va">bound_path</span>, data.table <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">bound_dat</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id1 id2 boundary</span>
<span class="r-out co"><span class="r-pr">#></span> 1 3 3 16000</span>
<span class="r-out co"><span class="r-pr">#></span> 2 3 30 4000</span>
<span class="r-out co"><span class="r-pr">#></span> 3 3 58 4000</span>
<span class="r-out co"><span class="r-pr">#></span> 4 30 30 12000</span>
<span class="r-out co"><span class="r-pr">#></span> 5 30 58 4000</span>
<span class="r-out co"><span class="r-pr">#></span> 6 30 85 4000</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem without the boundary data</span></span></span>
<span class="r-in"><span><span class="va">p2</span> <span class="op"><-</span> <span class="fu">marxan_problem</span><span class="op">(</span><span class="va">pu_dat</span>, <span class="va">spec_dat</span>, <span class="va">puvspr_dat</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="add_default_solver.html">add_default_solver</a></span><span class="op">(</span>verbose <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># solve problem</span></span></span>
<span class="r-in"><span><span class="va">s2</span> <span class="op"><-</span> <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p2</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># print solution</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">s2</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id cost status xloc yloc locked_in locked_out solution_1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 3 0.000 0 1116623 -4493479 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 2 30 7527.275 3 1110623 -4496943 FALSE TRUE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 3 56 37349.075 0 1092623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 4 58 16959.021 0 1116623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 5 84 34220.256 0 1098623 -4503872 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 6 85 178907.584 0 1110623 -4503872 FALSE FALSE 0</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with the boundary data and a boundary length modifier</span></span></span>
<span class="r-in"><span><span class="co"># set to 5</span></span></span>
<span class="r-in"><span><span class="va">p3</span> <span class="op"><-</span> <span class="fu">marxan_problem</span><span class="op">(</span><span class="va">pu_dat</span>, <span class="va">spec_dat</span>, <span class="va">puvspr_dat</span>, <span class="va">bound_dat</span>, <span class="fl">5</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="add_default_solver.html">add_default_solver</a></span><span class="op">(</span>verbose <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># solve problem</span></span></span>
<span class="r-in"><span><span class="va">s3</span> <span class="op"><-</span> <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p3</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># print solution</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">s3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> id cost status xloc yloc locked_in locked_out solution_1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 3 0.000 0 1116623 -4493479 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 2 30 7527.275 3 1110623 -4496943 FALSE TRUE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 3 56 37349.075 0 1092623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 4 58 16959.021 0 1116623 -4500408 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 5 84 34220.256 0 1098623 -4503872 FALSE FALSE 0</span>
<span class="r-out co"><span class="r-pr">#></span> 6 85 178907.584 0 1110623 -4503872 FALSE FALSE 0</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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