[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?

[Edwin Lebrija Trejos]

Hi,
I have used the daisy() function from the package "cluster" as suggested. Indeed it can handle Na's but this is not different from the gowdis() function in Package "FD". My problem is not calculating the similarity matrix for its use with the metaMDS() function. My problem is that because I am using a similarity matrix as input for the metaMDS() function, then there are no "species scores" (in my case plant traits) available to plot together with the "site scores" (in my case species). Using the daisy() function does not solve the problem (see warning message):
 
> NMDSdaysi<-metaMDS(daisy(TraitsNMDS, metric="gower",type = list(ordratio = 8:9,asymm = 7)))
> plot(NMDSdaysi)
Warning message:
In ordiplot(x, choices = choices, type = type, display = display,  :
  Species scores not available
 
In my original post I explain that I have tried obtaining species scores using the functions wascores() and add.spec.scores() of the packages vegan and BiodiversityR but wascores returns an error:
 
> TraitsNMDSdummies<-dummy.data.frame(TraitsNMDS, c("leaf.type","dispersal.rank"))
> 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
 
And function add.spec.scores() does not solves the problem as the warning message shows:
> A<-add.spec.scores(ordi=NMDSdaysi,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
 
I still don' know why I get an error in wascores() or how can I get species scores to use in a biplot. 



 
 
------------------------------ Message: 47Date: Thu, 24 Nov 2011 07:57:57 -0800 (PST)
From: B77S <bps0002 at auburn.edu>To: r-help at r-project.orgSubject: Re: [R] I cannot get species scores to plot with site scoresin MDS when I use a distance matrix as input. Problems with NA's?Message-ID: <1322150277396-4104406.post at n4.nabble.com>Content-Type: 
 
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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