[R] I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?

Gavin Simpson gavin.simpson at ucl.ac.uk
Tue Nov 29 22:44:54 CET 2011

On Thu, 2011-11-24 at 12:16 +0000, Edwin Lebrija Trejos wrote:
> Hi, First I should note I am relatively new to R so I would appreciate
> answers that take this into account.
> I am trying to perform an MDS ordination using the function “metaMDS”
> of the “vegan” package. I want to ordinate species according to a set
> of functional traits. “Species” here refers to “sites” in traditional
> vegetation analyses while “traits” here correspond to “species” in
> such analyses.  
> My data looks like this:
>          Trait1   Trait2 Trait3  Trait4  Trait5  Trait…  
> Species1 228.44   16.56   1.66   13.22     1     short 
> Species2 150.55   28.07   0.41   0.60      1     mid
> Species3     NA   25.89     NA   0.55      0     large
> Species4 147.70   17.65   0.42   1.12     NA     large
> Species… 132.68      NA   1.28   2.75      0     short
<snip />

> Can anyone guide me to get the trait (“species”) scores to plot
> together with my species (“site”) scores?
> Thanks in advance,
> Edwin

I think you should pass metaMDS the species trait matrix and then get it
to use FD to compute the dissimilarities. Note from ?metaMDS there is a
distfun argument for metaMDSdit. metaMDS passes the community data to
metaMDSdist to compute the dissimilarities.

The only snag is that gowdis doesn't accept a `method` argument so we
need a wrapper:

wrapper <- function(x, method, ...) {
    gowdis(x, ...)

then do

metaMDS(SpeciesGowdis, distfun = wrapper, XXXXX)

where XXXX represents any other arguments you want to pass to gowdis via
our wrapper. Essentially the wrapper ignores the method argument, we
just need it as metaMDSdist wants to call the dissimilarity function
with a method argument.

This is not tested as there wasn't reproducible code, but hopefully
you'll be able to work it out from the above.


 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
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