[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]

On Thu, 2011-11-24 at 07:57 -0800, B77S wrote:
> Try the daisy() function from the package "cluster", it seems to be able to
> handle NAs and non-dummy coded character variables
> 
> metaMDS(daisy(df, metric="gower"))

That won't help the OP as the species scores (the species data, i.e. the
traits in this case) can not be computed from a site x site
dissimilarity matrix. This is has the same problem as the OPs existing
problem.

G

> 
> 
> 
> 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
> > 
> >  
> > Because the traits have different variable types, different measurement
> > scales, and also missing values for some species, I have calculated the
> > matrix of species distances using the Gower coefficient of similarity
> > available in Package “FD” (which allows missing values). 
> > My problem comes when I create a bi-plot of species and traits. As I have
> > used a distance matrix in function “metaMDS” there are no species scores
> > available. This is given as a warning in R: 
> >  
> > "> NMDSgowdis<- metaMDS(SpeciesGowdis)
> >> plot(NMDSgowdis, type = "t")
> > Warning message:In ordiplot(x, choices = choices, type = type, display =
> > display, :Species scores not available” 
> >  
> > I have read from internet resources that in principle I could obtain the
> > trait ("species") scores to plot them in the ordination but my attempts
> > have been unsuccessful. I have tried using the function “wascores” in
> > package vegan and “add.spec.scores” in package BiodiversityR. For this
> > purpuse I have created a new species x traits table where factor traits
> > were coded into dummy variables and all integer variables (including
> > binary) were coerced to numeric variables. Here are the codes used and the
> > error messages I have got: 
> >  
> > “> NMDSgowdis<- metaMDS(SpeciesGowdis)
> >> NMDSpoints<-postMDS(NMDSgowdis$points,SpeciesGowdis)
> >> NMDSwasc<-wascores(NMDSpoints,TraitsNMDSdummies)
> > Error in if (any(w < 0) || sum(w) == 0) stop("weights must be non-negative
> > and not all zero") : missing value where TRUE/FALSE needed” 
> >  
> > I imagine the problem is with the NA’s in the data. 
> > Alternatively, I have used the “add.spec.scores” function,
> > method=”cor.scores”, found in package BiodiversityR. This seemed to work,
> > as I got no error message, but the species scores were not returned. Here
> > the R code and results:
> > “>
> > A<-add.spec.scores(ordi=NMDSgowdis,comm=TraitsNMDSdummies,method="cor.scores",multi=1,
> > Rscale=F,scaling="1")
> >> plot(A)
> > Warning message:In ordiplot(x, choices = choices, type = type, display =
> > display, :Species scores not available“
> >  
> > Can anyone guide me to get the trait (“species”) scores to plot together
> > with my species (“site”) scores?
> > Thanks in advance,
> > Edwin
> > 
> >   		 	   		  
> > ______________________________________________
> > R-help@ 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.
> > 
> 
> 
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