as.spacodi: converting between data formats for community phylogenetics
In spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

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

as.spacodi converts from picante or phylocom data formats into spacodi format.

1	as.spacodi(data, outfile = NULL)

`data`	a community dataset in `phylocom` or `picante` format
`outfile`	an optional text file to which to write output

This utility converts a community dataset (either from phylocom or picante (see picante) into a format interpretable by either this R-package spacodiR or the external program SPACoDi, a Windows executable (available at http://ebe.ulb.ac.be/ebe/Software.html). Note also that the community-dataset format used here is also that called for by the package vegan; see vegandocs.

phylocom format is also referred to as triplet-formatting, where plots are within the first column, abundances in the second, and species names in the third column of the dataframe. picante format is simply the transpose of spacodiR-formatting of the community dataset: in spacodiR, species are expected as the row names of the dataframe, where plots are represented as the column names. The user has the option to save an output file, defined by outfile.

An array, formatted for use in spacodiR

Jonathan Eastman

as.phylocom; as.picante

# call example data from spacodiR
data(sp.example)
attach(sp.example)
spl->d.spacodi  
d.spacodi ## SPACoDi format

# convert to phylocom
as.phylocom(data=d.spacodi, picante=FALSE)->d.phylocom
d.phylocom ## phylocom format

# convert dataset to picante
as.picante(data=d.phylocom)->d.picante
d.picante ## picante format

# convert back to SPACoDi 
as.spacodi(data=d.picante)