calcComPhyMets: Calculate Community Phylogenetic Metrics
In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description Usage Arguments Details References

One-stop function for calculating a range of community phylogenetic metrics from tree and community matrix.

1 2	calcComPhyMets(cmatrix, tree, min.spp = 2, metrics = c("PD1", "PD2", "PD3", "PSV", "PSD", "PSE", "PSC"))

`cmatrix`	community/trait data matrix (cols taxa, rows sites)
`tree`	phylogenetic tree (ape class)
`min.spp`	minimum number of species at site, default 2
`metric`	what metric to use as vector, default all metrics

Metrics calculated: PD (types 1, 2 and 3), PSV, PSD, PSE, PSC, and PSR. The PD metric in this function has 3 different types: PD1: considers the case if all other taxa from the phylogeny are dropped. In this way, type 1 is context independent but has a minimum number of taxa of 2. (This is the normal PD.) PD2: sums the lengths of all the edges connecting the specified taxa to the terminal node. PD3: sums the lengths of all the edges represented uniquely by the specified taxa.

No references yet! https://github.com/DomBennett/MoreTreeTools.

Faith, D. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1–10.

Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83 @examples data (catarrhines) cmatrix <- randCommData (catarrhines, nsites=20, nspp=10) res <- calcComPhyMets (cmatrix, catarrhines) print (res)

DomBennett/MoreTreeTools documentation built on May 6, 2019, 2:51 p.m.