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/packages/archive/2010/04.2010/04.29.2010/spacodi/man/as.picante.Rd

http://github.com/eastman/spacodiR
Unknown | 47 lines | 34 code | 13 blank | 0 comment | 0 complexity | c5d688df64080d20dfe235af0bc87a66 MD5 | raw file
 1\name{as.picante}
 2
 3\alias{as.picante}
 4
 5\title{converting between data formats for community phylogenetics}
 6
 7\usage{as.picante(data, outfile = NULL)}
 8
 9\arguments{
10  \item{data}{a community dataset in \code{phylocom} or \code{spacodi} format}
11  \item{outfile}{an optional text file to which to write output}
12}
13
14\details{This utility converts a community dataset (either from \code{phylocom} or \pkg{spacodi}) 
15into a format interpretable by \pkg{picante} (see \code{\link[picante]{picante-package}}). \code{phylocom} format is also referred 
16to as \code{triplet}-formatting, where plots are within the first column, abundances in the second, and species names in the
17third column of the dataframe. The user has the option to save an output file, defined by \code{outfile}.  \code{SPACoDi} format is 
18similar to that for \pkg{picante}, where dataframes between these packages are transposed.  \code{SPACoDi} format should have species as row names.
19}
20
21\value{An array, formatted for use in \code{picante}}
22
23\author{Jonathan Eastman}
24
25\seealso{\code{\link{as.spacodi}} and \code{\link{as.phylocom}} for converting between \code{phylocom} 
26and \code{SPACoDi} formats; see \code{\link[picante]{picante-package}} 
27for an R-port of \code{phylocom}}
28
29\examples{
30# call example data from SPACoDi
31data(sp.example)
32attach(sp.example)
33sp.plot->d.spacodi  
34d.spacodi ## SPACoDi format
35
36# convert to phylocom
37as.phylocom(data=sp.plot, picante=FALSE)->d.phylocom
38d.phylocom ## phylocom format
39
40# convert dataset to picante
41as.picante(data=d.phylocom)->d.picante
42d.picante ## picante format
43
44# convert back to SPACoDi 
45as.spacodi(data=d.picante)
46
47}