[R] Problems with metaMDS from vegan

[Spencer Graves]

      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
>
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