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<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Add a gap portfolio — add_gap_portfolio • prioritizr</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- docsearch --><script src="../docsearch.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.3/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous"><link href="../docsearch.css" rel="stylesheet"><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Add a gap portfolio — add_gap_portfolio"><meta property="og:description" content="Generate a portfolio of solutions for a conservation planning
problem() by finding a certain number of solutions that
are all within a pre-specified optimality gap. This method is useful for
generating multiple solutions that can be used to calculate selection
frequencies for moderate and large-sized problems (similar to
Marxan)."><meta property="og:image" content="https://prioritizr.net/logo.png"><!-- 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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<h1>Add a gap portfolio</h1>
<small class="dont-index">Source: <a href="https://github.com/prioritizr/prioritizr/blob/HEAD/R/add_gap_portfolio.R" class="external-link"><code>R/add_gap_portfolio.R</code></a></small>
<div class="hidden name"><code>add_gap_portfolio.Rd</code></div>
</div>
<div class="ref-description">
<p>Generate a portfolio of solutions for a conservation planning
<code><a href="problem.html">problem()</a></code> by finding a certain number of solutions that
are all within a pre-specified optimality gap. This method is useful for
generating multiple solutions that can be used to calculate selection
frequencies for moderate and large-sized problems (similar to
<em>Marxan</em>).</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_gap_portfolio</span><span class="op">(</span><span class="va">x</span>, <span class="va">number_solutions</span>, pool_gap <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p><code><a href="problem.html">problem()</a></code> (i.e., <code><a href="ConservationProblem-class.html">ConservationProblem</a></code>) object.</p></dd>
<dt>number_solutions</dt>
<dd><p><code>integer</code> number of solutions required.</p></dd>
<dt>pool_gap</dt>
<dd><p><code>numeric</code> gap to optimality for solutions in the portfolio.
This relative gap specifies a threshold worst-case performance for
solutions in the portfolio. For example, value of 0.1 will result in the
portfolio returning solutions that are within 10% of an optimal solution.
Note that the gap specified in the solver (i.e.,
<code><a href="add_gurobi_solver.html">add_gurobi_solver()</a></code> must be less than or equal to the gap
specified to generate the portfolio. Defaults to 0.1.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>Object (i.e., <code><a href="ConservationProblem-class.html">ConservationProblem</a></code>) with the portfolio
added to it.</p>
</div>
<div id="details">
<h2>Details</h2>
<p>This strategy for generating a portfolio requires problems to
be solved using the <em>Gurobi</em> software suite (i.e., using
<code><a href="add_gurobi_solver.html">add_gurobi_solver()</a></code>. Specifically, version 9.0.0 (or greater)
of the <span class="pkg">gurobi</span> package must be installed.
Note that the number of solutions returned may be less than the argument to
<code>number_solutions</code>, if the total number of solutions that
meet the optimality gap is less than the number of solutions requested.
Also, note that this portfolio function only works with problems
that have binary decisions (i.e., specified using
<code><a href="add_binary_decisions.html">add_binary_decisions()</a></code>).</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p>See <a href="portfolios.html">portfolios</a> for an overview of all functions for adding a portfolio.</p>
<p>Other portfolios:
<code><a href="add_cuts_portfolio.html">add_cuts_portfolio</a>()</code>,
<code><a href="add_extra_portfolio.html">add_extra_portfolio</a>()</code>,
<code><a href="add_shuffle_portfolio.html">add_shuffle_portfolio</a>()</code>,
<code><a href="add_top_portfolio.html">add_top_portfolio</a>()</code></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"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="co"># set seed for reproducibility</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">600</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># load data</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">sim_pu_raster</span>, <span class="va">sim_features</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create minimal problem with a portfolio containing 10 solutions within 20%</span></span></span>
<span class="r-in"><span><span class="co"># of optimality</span></span></span>
<span class="r-in"><span><span class="va">p1</span> <span class="op"><-</span> <span class="fu"><a href="problem.html">problem</a></span><span class="op">(</span><span class="va">sim_pu_raster</span>, <span class="va">sim_features</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_min_set_objective.html">add_min_set_objective</a></span><span class="op">(</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_relative_targets.html">add_relative_targets</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu">add_gap_portfolio</span><span class="op">(</span>number_solutions <span class="op">=</span> <span class="fl">5</span>, pool_gap <span class="op">=</span> <span class="fl">0.2</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>gap <span class="op">=</span> <span class="fl">0</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 and generate portfolio</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 number of solutions found</span></span></span>
<span class="r-in"><span><span class="fu"><a href="print.html">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">s1</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> [1] 5</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot solutions</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/raster/man/stack.html" class="external-link">stack</a></span><span class="op">(</span><span class="va">s1</span><span class="op">)</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>
<span class="r-plt img"><img src="add_gap_portfolio-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create multi-zone problem with a portfolio containing 10 solutions within</span></span></span>
<span class="r-in"><span><span class="co"># 20% of optimality</span></span></span>
<span class="r-in"><span><span class="va">p2</span> <span class="op"><-</span> <span class="fu"><a href="problem.html">problem</a></span><span class="op">(</span><span class="va">sim_pu_zones_stack</span>, <span class="va">sim_features_zones</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_min_set_objective.html">add_min_set_objective</a></span><span class="op">(</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_relative_targets.html">add_relative_targets</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">15</span>, <span class="fl">0.1</span>, <span class="fl">0.2</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">5</span>,</span></span>
<span class="r-in"><span> ncol <span class="op">=</span> <span class="fl">3</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu">add_gap_portfolio</span><span class="op">(</span>number_solutions <span class="op">=</span> <span class="fl">5</span>, pool_gap <span class="op">=</span> <span class="fl">0.2</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>gap <span class="op">=</span> <span class="fl">0</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 and generate portfolio</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 number of solutions found</span></span></span>
<span class="r-in"><span><span class="fu"><a href="print.html">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">s2</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> [1] 5</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot solutions in portfolio</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/raster/man/stack.html" class="external-link">stack</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">s2</span>, <span class="va">category_layer</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> main <span class="op">=</span> <span class="st">"solution"</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>
<span class="r-plt img"><img src="add_gap_portfolio-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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