phylotools (version 0.1.2)

phylocom.comstruct: Calculating community phylogenetic structure using Phylocom

Description

This is a wrapper function for phylocom.

Usage

phylocom.comstruct(sample = "sample", phylo = "phylo",  swapmethod = 2, runs = 999, swaps = 1000,  aw = TRUE, file = "comstruct.txt")

Arguments

sample

Character string, the name of the sample file used in Phylocom

phylo

Character string, the name of the "phylo" file used in Phylocom

swapmethod

Swap method used in phylocom

runs

Times to generating null models

swaps

Times to swap

aw

Logical, if TRUE, the comdist will be computed in accounting of abundance. Otherwise, for presence - absence.

file

Result File that to be saved to .

References

Campbell Webb, David Ackerly, Steve Kembel (2010) Phylocom software for the analysis of phylogenetic community structure and character evolution (with phylomatic and ecovolve) User S Manual Version 4.1

See Also

phylocom.pd,phylocom.comdist

Examples

### Assume the file sample1 and phylo1 have been 
### saved to the R working directory.
### The phylocom executable file has been copied 
### to the same working directory
### Or could be invoked in console by command lines.
### in order to run phylocom in R, simply copy the 
### following command:

#   i = 1
#   phylocom.comstruct(sample = paste("sample",i, sep = ""),
#            phylo = paste("phylo",i, sep = ""), 
#            swapmethod = 2, runs = 999, swaps = 1000, aw = TRUE,  
#            file = paste("comstruct.aw",   i,".txt", sep = ""))