optimalppp

optimalppp

Description

The optimalppp R package provides methods for prioritizing funding of conservation projects using the 'Protect Prioritization Protocol'. Projects can be prioritized by maximizing expected species richness or expected phylogenetic diversity. Prioritizations can be generated using a range of methods, such as exact algorithms which can identify optimal solutions, heuristic algorithms which have conventionally been used to identify solutions, and by randomly funding actions. This package also provides the functionality to visualize how well solutions maintain biodiversity.

To make the most of this package, the ggtree and gurobi R packages will need to be installed. Since the ggtree package is exclusively available at Bioconductor---and is not available on The Comprehensive R Archive Network---please execute the following command to install it: source("https://bioconductor.org/biocLite.R");biocLite("ggtree"). If the installation process fails, please consult the package's online documentation. To install the gurobi package, the Gurobi optimization suite will first need to be installed (see instructions for Linux, Mac OSX, and Windows operating systems). Although Gurobi is a commercial software, academics can obtain a special license for no cost. After installing the Gurobi optimization suite, the gurobi package can then be installed (see instructions for Linux, Mac OSX, and Windows operating systems).

Overview

This package provides functions for generating, evaluating, and visualizing prioritizations using 'expected weighted species richness' and 'expected phylogenetic diversity' metrics of conservation benefit. For convenience, the main functions in the package are listed below.

Expected weighted species richness:

ppp_exact_spp_solution

Prioritize conservation projects by maximizing expected weighted species richness using exact algorithms.

ppp_heuristic_spp_solution

Prioritize conservation projects by maximizing expected weighted species richness using heuristic algorithms.

ppp_manual_spp_solution

Manually prioritize conservation projects under expected weighted species richness.

ppp_random_spp_solution

Randomly prioritize conservation projects under expected weighted species richness.

Expected phylogenetic diversity:

ppp_exact_phylo_solution

Prioritize conservation projects by maximizing expected phylogenetic diversity with exact algorithms.

ppp_heuristic_phylo_solution

Prioritize conservation projects by maximizing expected phylogenetic diversity with heuristic algorithms.

ppp_manual_phylo_solution

Manually prioritize conservation projects under expected phylogenetic diversity.

ppp_random_phylo_solution

Randomly prioritize conservation projects under expected phylogenetic diversity.

See also

Please refer to the package vignette for more information and worked examples. This can be accessed using the code vignette("optimalppp").