phylorebelo: Greedy algorithm optimising the accumulation of Phylogenetic...

In davidnipperess/PDcalc: An implementation of the Phylogenetic Diversity (PD) calculus in R

Description

A heuristic algorithm that seeks to prioritise sites for conservation by optimising the accumulation of Phylogenetic Diversity (PD). PD will accumulate most rapidly when the samples are pooled in a particular sequence such that the gain in PD of each additional sample is maximised.

Usage

phylorebelo(x, phy, iterations = 1)

Arguments

x	is the community data given as a data.frame or matrix with species/OTUs as columns and samples/sites as rows (like in the vegan package). Columns are labelled with the names of the species/OTUs. Rows are labelled with the names of the samples/sites. Data can be either abundance or incidence (0/1). Column labels must match tip labels in the phylogenetic tree exactly!
phy	is a rooted phylogenetic tree with branch lengths stored as a phylo object (as in the ape package) with terminal nodes labelled with names matching those of the community data table. Note that the function trims away any terminal taxa not present in the community data table, so it is not necessary to do this beforehand.
iterations	is the number of iterations of the algorithm (to resolve ties). Default is 1.

Details

phylorebelo takes community data and a phylogenetic tree (rooted and with branch lengths) and calculates the optimal sequence of samples for accumulating Phylogenetic Diversity (PD). The algorithm starts by first selecting the sample with the highest PD. It will then choose the sample most complementary to the first (giving the largest gain in PD). Additional samples are chosen based on their complementarity to the set already chosen until all sites have been selected. At each step, ties are resolved by choosing at random from the available equally complementary options. The algorithm is an adaptation of that described by Rebelo & Siegfried (1992). The phylogenetic version implemented here is that used by Asmyhr et al. (2014).

Value

A list of two numeric matrices. The first matrix gives the optimised sequence (rank) of the samples as rows, with a column for each iteration of the algorithm. The second matrix is gives the corresponding gains in PD for each sample (row) and iteration.

References

• Asmyhr MG, Linke S, Hose G, & Nipperess DA. 2014. Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity. PLoS One 9: e115132

• Rebelo AG & Siegfried WR. 1992. Where should nature reserves be located in the Cape Floristic Region, South Africa? Models for the spatial configuration of a reserve network aimed at maximizing the protection of floral diversity. Conservation Biology 6: 243–252.

davidnipperess/PDcalc documentation built on July 7, 2021, 1:07 p.m.