[R-sig-eco] data structures for ecological data

[Law, Jason]

Hello all,

This is a general question about data structures for what I'll call generically 'organism occurrence data'. Most of the packages for dealing with ecology/phylogenetic data in R deal with some combination of occurrence data (sample unit x taxa), site/sample data (data about the sampling units), trait data (data about the taxa), and taxonomic (some kind of tree, taxonomic or phylogenetic). I started to look around and see if there was a package that provided data structures and some generic functionality for manipulating this kind of data in R; I think I'm looking for the "organism occurrence" equivalent of the "sp" package for spatial data. The mefa package does some of this, but the idea of 'segments' appears to introduce some limitations. And it doesn't have things like accessors that I would expect for data structures (coords for SpatialDataFrames). The phylobase package does this for phylogenetic data, but I'm looking for something that would include occurrence data.

Is there currently a package that provides data structures (other than mefa) for this type of data. If not, has anyone ever talked about trying to put something like this together?

Jason Law
Statistician, City of Portland
Water Pollution Control Laboratory
6543 N Burlington Ave,
Portland, OR

503-823-1038
jason.law at portlandoregon.gov


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