ecospat.calculate.pd: Calculate Phylogenetic Diversity Measures

Description

Calculate all phylogenetic diversity measures listed in Schweiger et al., 2008 (see full reference below).

Usage

ecospat.calculate.pd (tree, data, method="spanning", type="clade", root=FALSE, 
average=FALSE, verbose=FALSE)

Arguments

tree

The phylogenetic tree

data

A presence or absence (binary) matrix for each species (columns) in each location or grid cell (rows)

method

The method to use. Options are "pairwise", "topology", and "spanning". Default is "spanning".

type

Phylogenetic measure from those listed in Schweiger et al 2008. Options are "Q", "P", "W", "clade", "species", "J", "F", "AvTD","TTD", "Dd". Default is "clade".

root

Phylogenetic diversity can either be rooted or unrooted. Details in Schweiger et al 2008. Default is FALSE.

average

Phylogenetic diversity can either be averaged or not averaged. Details in Schweiger et al 2008. Default is FALSE.

verbose

Boolean indicating whether to print progress output during calculation. Default is FALSE.

Value

This function returns a list of phylogenetic diversity values for each of the grid cells in the presence/absence matrix

Details

Given a phylogenetic tree and a presence/absence matrix this script calculates phylogenetic diversity of a group of species across a given set of grid cells or locations. The library "ape" is required to read the tree in R. Command is "read.tree" or "read.nexus". Options of type: "P" is a normalized mearure of "Q". "clade" is "PDnode" when root= FALSE, and is "PDroot" ehn root =TRUE. "species" is "AvPD".

References

Schweiger, O., S. Klotz, W. Durka and I. Kuhn. 2008. A comparative test of phylogenetic diversity indices. Oecologia, 157, 485-495.

Pio, D.V., O. Broennimann, T.G. Barraclough, G. Reeves, A.G. Rebelo, W. Thuiller, A. Guisan and N. Salamin. 2011. Spatial predictions of phylogenetic diversity in conservation decision making. Conservation Biology, 25, 1229-1239.

Pio, D.V., R. Engler, H.P. Linder, A. Monadjem, F.P.D. Cotterill, P.J. Taylor, M.C. Schoeman, B.W. Price, M.H. Villet, G. Eick, N. Salamin and A. Guisan. 2014. Climate change effects on animal and plant phylogenetic diversity in southern Africa. Global Change Biology, 20, 1538-1549.

Examples

Run this code

# NOT RUN {
fpath <- system.file("extdata", "ecospat.testTree.tre", package="ecospat")
tree <-read.tree(fpath)
data <- ecospat.testData[9:52] 

pd <- ecospat.calculate.pd(tree, data, method = "spanning", type = "species", root = FALSE, 
average = FALSE, verbose = TRUE )

plot(pd)
# }

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