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

http://github.com/eastman/spacodiR
Unknown | 38 lines | 26 code | 12 blank | 0 comment | 0 complexity | 38690a243cddbf490863183fe7f23dd8 MD5 | raw file
 1\name{as.spacodi}
 2
 3\alias{as.spacodi}
 4
 5\title{converting between data formats for community phylogenetics}
 6
 7\usage{as.spacodi(data, outfile = NULL)}
 8
 9\arguments{
10  \item{data}{a species-by-plots matrix}
11  \item{outfile}{an optional text file to which to write output}
12}
13
14\details{This utility converts a species-by-plots matrix into a format readable by the external program \code{SPACoDi}, a Windows executable. 
15The user has the option to save an output file, defined by \code{outfile}. 
16}
17
18\value{an array, formatted for use in \code{SPACoDi} for Windows}
19
20\author{Jonathan Eastman}
21
22\seealso{\code{\link{as.phylocom}} for converting between \code{phylocom} and \code{SPACoDi} formats;
23see \code{\link{spacodi.calc}} for community diversity measures of empirical data}
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 and write to file
34as.spacodi(p.foo, outfile="spacodi.formatted.txt") -> s.foo
35s.foo		# re-converted SPACoDi dataset
36foo		# comparison with the original dataset
37
38}