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/packages/archive/2010/04.2010/04.20.2010/spacodi/man/as.phylocom.Rd

http://github.com/eastman/spacodiR
Unknown | 41 lines | 27 code | 14 blank | 0 comment | 0 complexity | 058d6651839b0d745e5f3208d0dfa13e MD5 | raw file
 1\name{as.phylocom}
 2
 3\alias{as.phylocom}
 4
 5\title{converting between data formats for community phylogenetics}
 6
 7\usage{as.phylocom(data, outfile = NULL)}
 8\arguments{
 9  \item{data}{a species-by-plots matrix}
10  \item{outfile}{an optional text file to which to write output}
11}
12
13\details{This utility converts a species-by-plots matrix into \code{triplet} format, which is readable by the external program \code{phylocom}. 
14The user has the option to save an output file, defined by \code{outfile}. 
15}
16
17\value{an array, formatted for use in \code{phylocom}}
18
19\references{WEBB CO, DD ACKERLY and SW KEMBEL. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24:2098-2100.}
20
21\author{Jonathan Eastman}
22
23\seealso{\code{\link{as.spacodi}} for converting between \code{phylocom} and \code{SPACoDi} formats.}
24
25\examples{
26# generate a species-by-plots matrix
27foo <- r.plot(species=10,plots=6,missing.prop=0.15,sim.tree=FALSE)	
28
29# convert to phylocom format
30as.phylocom(foo) -> p.foo
31p.foo
32
33# convert back to spacodi format
34as.spacodi(p.foo) -> s.foo
35s.foo
36
37# save the converted dataset to working directory
38as.phylocom(s.foo, outfile="phylocom.in.triplet.txt")
39
40
41}