[R] unknown decorana error returned (vegan package)

[Jari Oksanen]

Dear Jeremy,

`vegan' is a little known add-on package for a special group of users.
Contacting its author directly might be more useful than broadcasting the whole
R mailing list.

Then to the problem: This is an error that occurs (at least) when you have 
all-zero rows or columns in your data set: 

> decorana(rbind(varespec, rep(0, ncol(varespec))))
Error in decorana(rbind(varespec, rep(0, ncol(varespec)))) : 
	NA/NaN/Inf in foreign function call (arg 1)

So check your data for column and row sums, and remove the empty columns and 
rows (arguably decorana should check this and fail more informatively than now).

Decorana implements a peculiar variant of Correspondence Analysis. CA can
handle only non-negative matrix values and all marginal totals must be above
zero. The name you use for your matrix (covN) sounds like you might have a
covariance matrix which cannot be handled by correspondence analysis at all.
With the information you posted, I cannot give any better guesses.

cheers, jari oksanen
-- 
Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland
Ph. +358 8 5531526, cell +358 40 5136529, fax +358 8 5531061
email jari.oksanen at oulu.fi, homepage http://cc.oulu.fi/~jarioksa/