[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?

B77S bps0002 at auburn.edu
Thu Nov 24 16:57:57 CET 2011

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"))

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
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