I'm having trouble with the ordisurf function in the vegan package. I have created an ordination plot (cmdscale) of 60 samples based on Bray-Curtis dissimilarities, and would like to overlay various soil edaphic characteristics as possible clues to the clustering I observe in my plot. However, I find that ordisurf creates a surface on the plot that is a perfect, even gradient - and doesn't match my data. An example of this output is attached (as .ps file), while these are the data for the environmental variable of interest:
> edaphic$K
[1] 28 61 48 29 28 26 45 28 34 33 55 62 44 51 60 68 51 31 54 32 58 50 37 35
35 34 52 29 53 24 37 50 62 51
[35] 28 39 47 41 49 83 33 50 55 71 59 50 57 47 46 49 43 30 56 23 49 35 31 27
38 52
The contour lines suggest that there are only two values below 32, when in
fact there are 11.
Any ideas? Thanks!
>>>
> bc <- read.table("braycurtis_noheader.dist",header=F)
> sample.mds <- cmdscale(bc)
> edaphic <- read.table("edaphic.txt", header=T)
> library(vegan)
This is vegan 1.17-2
> ordisurf(sample.mds, edaphic$K, xlab="PC 1", ylab="PC 2", main="K")
Loading required package: mgcv
This is mgcv 1.6-1. For overview type `help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
Estimated degrees of freedom:
2 total = 3
GCV score: 140.9051
--
Matthew Bakker
Ph.D. Candidate
Department of Plant Pathology
University of Minnesota
495 Borlaug Hall
1991 Upper Buford Circle
Saint Paul, MN 55108 USA
612-624-2253
matt.g.bak...@gmail.com
http://plpa.cfans.umn.edu/Matt_Bakker.html
ordisurf_output.ps
Description: PostScript document
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