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.