Have you sent this question to the vegan maintainer, identified, e.g., with help(package="vegan")? I've added that name as a "cc" to this email.
Hope this helps. Spencer Graves Peter Roosen wrote: > Hello all, > > I recently used the Vegan library quite extensively (in the context of > text similarity assessment) on an Ubuntu 6.06 LTS system with R version > 2.2.1 (2005-12-20 r36812). The Vegan lib is version 1.6-10. > > I hit on a problem yesterday, though, when trying to install R and Vegan > on two further computers - one Windows XP and one further Ubuntu 6.06 > machine, taking either R version 2.4.0 on XP or 2.2.1 (as above) on > Ubuntu, and the newer Vegan version 1.8-3 on both machines. On the new > Ubuntu machine I even tried to regress to the Vegan 1.6-10, but to no > avail, as the error remains the same: > > As soon as a I try to process an R matrix (see below) to obtain the MDS > I am confronted with: > > > meta <- metaMDS(distab.dist, distance="bray", k, trymax=50) > Fehler in rowSums(x, na.rm = TRUE) : 'x' muss ein Array mit mindestens > zwei Dimensionen sein > Ausführung angehalten > > ( > translated: > error in rowSums(x, a.rm = TRUE) : 'x' must be an array of at least two > dimensions. > Execution stopped > ) > > This error is not appearing on identical data when using my older > installation. The only relevant googled mentioning of that error points > to a surplus (0,0) entry in the matrix to be processed, but this is > definitely not the case here. I crosschecked with *identical* data sets > on the mentioned systems. > > Following are my (rather small) processing program and a (small cut of > a) matrix that produces the error, but runs smoothly on the older > version mentioned: > > R batch script: > #### > library(vegan) > > simitab <- read.table("r.csv", header = TRUE, row.names = 1, sep = ";") > olimit <- max(simitab) > distab <- simitab / olimit > > distab.dist <- vegdist(distab) > > k <- 2 > meta <- metaMDS(distab.dist, distance="bray", k, trymax=50) > > postscript("metaMDS-CASE-DIMENd.ps", horizontal=TRUE) > > plot(meta$points, col="blue", xlab="Dim 1", ylab="Dim 2", > main=sprintf("metaMDS für Variante = \"CASE\", dim = %d, Stress = %.2f > %%", k, meta$stress)) > text(meta$points+xinch(0.09), labels=names(distab), cex=0.8) > ### > > Cut of data set: > ### > US-1020525;US-1027783;US-1032733 > US-1020525;1.00000000;0.00903941;0.93719674 > US-1027783;0.00903941;1.00000000;0.01013081 > US-1032733;0.93719674;0.01013081;1.00000000 > ### > (Remark: I did *not* test exactly the given small data set cut but took > the larger original one, being a 100*100 matrix + headers that I'd > rather not post in here.) > > > I'd appreciate any help in making the script functional again on our > newer installations! > > Regards, > > Peter > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.