phylocom.pd: Calculate phylogenetic diversity using Phylocom

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/phylocom.pd.R

Description

This is a wrapper function of phylocom for Calculate phylogenetic diversity using Phylocom

Usage

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phylocom.pd(sample = "sample", phylo = "phylo")

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

Value

PD data frame

Author(s)

Jinlong Zhang [email protected]

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.comstruct,phylocom.comdist

Examples

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### 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.
### inorder to run phylocom in R, simply copy the following command:
#   i = 1
#   PD.res <- phylocom.pd(sample = paste("sample",i, sep = ""), 
#          phylo = paste("phylo",i, sep = ""), 
#          )
#   PD.res
#            

Example output

Loading required package: seqRFLP
Loading required package: ape
Loading required package: picante
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Loading required package: nlme
Loading required package: spaa
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.4-0 (2016-08-29) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps

Attaching package: 'phylotools'

The following object is masked from 'package:ape':

    complement

phylotools documentation built on May 29, 2017, 1:41 p.m.