[R] data for metaMDS (diagnostic tips) please help

From: stephen sefick <ssefick_at_gmail.com>
Date: Tue, 22 Apr 2008 20:42:05 -0400


I have a large data.frame rows=sites, column=species. Being a species matrix it is very sparse and I have found that there are no site rows that are = 0 and no species = 0 and I am getting and error that reads

x = read.table("shit.txt", sep="\t",header=T, row.names=1)

x.m <- as.matrix(x)
x.t <- t(x.m)
x.d <- as.data.frame(x.t)

metaMDS(x.d)
Error in if (autotransform && xam > 50) { :   missing value where TRUE/FALSE needed

I would gladly include data, but it is to large for the list >150k. Any help would be greatly appreciated.
Thanks

stephen

--

Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals.

-K. Mullis

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