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objectives.html
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objectives.html
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<!DOCTYPE html>
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problem(). All conservation planning problems involve minimizing
or maximizing some kind of objective. For instance, the planner may require
a solution that conserves enough habitat for each species while minimizing
the overall cost of the reserve network. Alternatively, the planner may
require a solution that maximizes the number of conserved species while
ensuring that the cost of the reserve network does not exceed the budget."><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 an objective</h1>
<small class="dont-index">Source: <a href="https://github.com/prioritizr/prioritizr/blob/HEAD/R/objectives.R" class="external-link"><code>R/objectives.R</code></a></small>
<div class="hidden name"><code>objectives.Rd</code></div>
</div>
<div class="ref-description">
<p>An objective is used to specify the overall goal of a conservation planning
<code><a href="problem.html">problem()</a></code>. All conservation planning problems involve minimizing
or maximizing some kind of objective. For instance, the planner may require
a solution that conserves enough habitat for each species while minimizing
the overall cost of the reserve network. Alternatively, the planner may
require a solution that maximizes the number of conserved species while
ensuring that the cost of the reserve network does not exceed the budget.</p>
</div>
<div id="details">
<h2>Details</h2>
<p><strong>Please note that all conservation
planning problems formulated using the <span class="pkg">prioritizr</span> package require an
objective function---failing to do so will return an error
message when attempting to solve problem.</strong></p>
<p>The following objectives can be added to a conservation planning
<code><a href="problem.html">problem()</a></code>:</p>
<dl><dt><code><a href="add_min_set_objective.html">add_min_set_objective()</a></code></dt>
<dd><p>Minimize the cost of the
solution whilst ensuring that all targets are met. This objective is
similar to that used in <em>Marxan</em>.</p></dd>
<dt><code><a href="add_max_cover_objective.html">add_max_cover_objective()</a></code></dt>
<dd><p>Represent at least one
instance of as many features as possible within a given budget.</p></dd>
<dt><code><a href="add_max_features_objective.html">add_max_features_objective()</a></code></dt>
<dd><p>Fulfill as many targets as
possible while ensuring that the cost of the solution does not exceed a
budget.</p></dd>
<dt><code><a href="add_min_shortfall_objective.html">add_min_shortfall_objective()</a></code></dt>
<dd><p>Minimize the overall
(weighted sum) shortfall for as many targets as possible while ensuring
that the cost of the solution does not exceed a budget.</p></dd>
<dt><code><a href="add_min_largest_shortfall_objective.html">add_min_largest_shortfall_objective()</a></code></dt>
<dd><p>Minimize the
largest (maximum) shortfall among all targets while ensuring that
the cost of the solution does not exceed a budget.</p></dd>
<dt><code><a href="add_max_phylo_div_objective.html">add_max_phylo_div_objective()</a></code></dt>
<dd><p>Maximize the phylogenetic
diversity of the features represented in the solution subject to a
budget.</p></dd>
<dt><code><a href="add_max_phylo_end_objective.html">add_max_phylo_end_objective()</a></code></dt>
<dd><p>Maximize the phylogenetic
endemism of the features represented in the solution subject to a
budget.</p></dd>
<dt><code><a href="add_max_utility_objective.html">add_max_utility_objective()</a></code></dt>
<dd><p>Secure as much of the
features as possible without exceeding a budget.</p></dd>
</dl></div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p>Other overviews:
<code><a href="constraints.html">constraints</a></code>,
<code><a href="decisions.html">decisions</a></code>,
<code><a href="importance.html">importance</a></code>,
<code><a href="penalties.html">penalties</a></code>,
<code><a href="portfolios.html">portfolios</a></code>,
<code><a href="solvers.html">solvers</a></code>,
<code><a href="summaries.html">summaries</a></code>,
<code><a href="targets.html">targets</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"># 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_phylogeny</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create base problem</span></span></span>
<span class="r-in"><span><span class="va">p</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_relative_targets.html">add_relative_targets</a></span><span class="op">(</span><span class="fl">0.1</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"><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"># create problem with added minimum set objective</span></span></span>
<span class="r-in"><span><span class="va">p1</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></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></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added maximum coverage objective</span></span></span>
<span class="r-in"><span><span class="co"># note that this objective does not use targets</span></span></span>
<span class="r-in"><span><span class="va">p2</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_max_cover_objective.html">add_max_cover_objective</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"># create problem with added maximum feature representation objective</span></span></span>
<span class="r-in"><span><span class="va">p3</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_max_features_objective.html">add_max_features_objective</a></span><span class="op">(</span><span class="fl">1900</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added minimum shortfall objective</span></span></span>
<span class="r-in"><span><span class="va">p4</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_min_shortfall_objective.html">add_min_shortfall_objective</a></span><span class="op">(</span><span class="fl">1900</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added minimum largest shortfall objective</span></span></span>
<span class="r-in"><span><span class="va">p5</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_min_largest_shortfall_objective.html">add_min_largest_shortfall_objective</a></span><span class="op">(</span><span class="fl">1900</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added maximum phylogenetic diversity objective</span></span></span>
<span class="r-in"><span><span class="va">p6</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_max_phylo_div_objective.html">add_max_phylo_div_objective</a></span><span class="op">(</span><span class="fl">1900</span>, <span class="va">sim_phylogeny</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added maximum phylogenetic diversity objective</span></span></span>
<span class="r-in"><span><span class="va">p7</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_max_phylo_end_objective.html">add_max_phylo_end_objective</a></span><span class="op">(</span><span class="fl">1900</span>, <span class="va">sim_phylogeny</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># create problem with added maximum utility objective</span></span></span>
<span class="r-in"><span><span class="co"># note that this objective does not use targets</span></span></span>
<span class="r-in"><span><span class="va">p8</span> <span class="op"><-</span> <span class="va">p</span> <span class="op"><a href="pipe.html">%>%</a></span> <span class="fu"><a href="add_max_utility_objective.html">add_max_utility_objective</a></span><span class="op">(</span><span class="fl">1900</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># solve problems</span></span></span>
<span class="r-in"><span><span class="va">s</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="solve.html">solve</a></span><span class="op">(</span><span class="va">p1</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 class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p3</span><span class="op">)</span>, <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p4</span><span class="op">)</span>, <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p5</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span>, <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span>, <span class="fu"><a href="solve.html">solve</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>ignoring targets since the specified objective function doesn't use targets</span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>ignoring targets since the specified objective function doesn't use targets</span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>ignoring targets since the specified objective function doesn't use targets</span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>ignoring targets since the specified objective function doesn't use targets</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="va">s</span>, axes <span class="op">=</span> <span class="cn">FALSE</span>, box <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span> main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"min set"</span>, <span class="st">"max coverage"</span>, <span class="st">"max features"</span>,</span></span>
<span class="r-in"><span> <span class="st">"min shortfall"</span>, <span class="st">"min largest shortfall"</span>,</span></span>
<span class="r-in"><span> <span class="st">"max phylogenetic diversity"</span>,</span></span>
<span class="r-in"><span> <span class="st">"max phylogenetic endemism"</span>, <span class="st">"max utility"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="objectives-1.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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