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add_shuffle_portfolio.html
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add_shuffle_portfolio.html
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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 shuffle portfolio — add_shuffle_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 shuffle portfolio — add_shuffle_portfolio"><meta property="og:description" content="Generate a portfolio of solutions for a conservation planning
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add_top_portfolio() when the Gurobi software is not
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<h1>Add a shuffle portfolio</h1>
<small class="dont-index">Source: <a href="https://github.com/prioritizr/prioritizr/blob/HEAD/R/add_shuffle_portfolio.R" class="external-link"><code>R/add_shuffle_portfolio.R</code></a></small>
<div class="hidden name"><code>add_shuffle_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 randomly reordering the data prior to
solving the problem. This is recommended as a replacement for
<code><a href="add_top_portfolio.html">add_top_portfolio()</a></code> when the <em>Gurobi</em> software is not
available.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_shuffle_portfolio</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> number_solutions <span class="op">=</span> <span class="fl">10L</span>,</span>
<span> threads <span class="op">=</span> <span class="fl">1L</span>,</span>
<span> remove_duplicates <span class="op">=</span> <span class="cn">TRUE</span></span>
<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 attempts to generate
different solutions. Defaults to 10.</p></dd>
<dt>threads</dt>
<dd><p><code>integer</code> number of threads to use for the generating
the solution portfolio. Defaults to 1.</p></dd>
<dt>remove_duplicates</dt>
<dd><p><code>logical</code> should duplicate solutions
be removed? Defaults to <code>TRUE</code>.</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 of solutions often
results in different solutions, depending on optimality gap, but may
return duplicate solutions. In general, this strategy is most effective
when problems are quick to solve and multiple threads are available for
solving each problem separately.</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_gap_portfolio.html">add_gap_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">500</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="va">sim_pu_zones_stack</span>, <span class="va">sim_features_zones</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 shuffle portfolio</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">0.2</span><span class="op">)</span> <span class="op"><a href="pipe.html">%>%</a></span></span></span>
<span class="r-in"><span> <span class="fu">add_shuffle_portfolio</span><span class="op">(</span><span class="fl">10</span>, remove_duplicates <span class="op">=</span> <span class="cn">FALSE</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">0.2</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 10 solutions within 20% of optimality</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"># 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="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_shuffle_portfolio-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># build multi-zone conservation problem with shuffle portfolio</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"><a href="add_binary_decisions.html">add_binary_decisions</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">add_shuffle_portfolio</span><span class="op">(</span><span class="fl">10</span>, remove_duplicates <span class="op">=</span> <span class="cn">FALSE</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">0.2</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 the 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/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">s2</span>, max.level <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> List of 10</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_1 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_2 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_3 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_4 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_5 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_6 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_7 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_8 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_9 :Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> $ solution_10:Formal class 'RasterStack' [package "raster"] with 11 slots</span>
<span class="r-out co"><span class="r-pr">#></span> - attr(*, "objective")= Named num [1:10] 11667 11408 11268 11080 11752 ...</span>
<span class="r-out co"><span class="r-pr">#></span> ..- attr(*, "names")= chr [1:10] "solution_1" "solution_2" "solution_3" "solution_4" ...</span>
<span class="r-out co"><span class="r-pr">#></span> - attr(*, "status")= Named chr [1:10] "OPTIMAL" "OPTIMAL" "OPTIMAL" "OPTIMAL" ...</span>
<span class="r-out co"><span class="r-pr">#></span> ..- attr(*, "names")= chr [1:10] "solution_1" "solution_2" "solution_3" "solution_4" ...</span>
<span class="r-out co"><span class="r-pr">#></span> - attr(*, "runtime")= Named num [1:10] 0.031 0.016 0.033 0.016 0.016 ...</span>
<span class="r-out co"><span class="r-pr">#></span> ..- attr(*, "names")= chr [1:10] "solution_1" "solution_2" "solution_3" "solution_4" ...</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_shuffle_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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