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

1	as.picante(data, outfile = NULL)

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

This utility converts a community dataset (either from phylocom or spacodiR) into a format interpretable by picante (see picante-package). 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. The user has the option to save an output file, defined by outfile. SPACoDi format is similar to that for picante, where dataframes between these packages are transposed. SPACoDi format should have species as row names.

An array, formatted for use in picante

Jonathan Eastman

as.spacodi and as.phylocom for converting between phylocom and SPACoDi formats; see picante-package for an R-port of phylocom

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

# convert to phylocom
as.phylocom(data=spl, 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)

# run standardized effect size mean nearest taxon distances in picante
ses.mntd(as.picante(spl), cophenetic(phy))