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 <bps0...@auburn.edu>To: r-help@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.p...@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
______________________________________________> 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.> --View this message in context:
http://r.789695.n4.nabble.com/I-cannot-get-species-scores-to-plot-with-site-scores-in-MDS-when-I-use-a-distance-matrix-as-input-Pr-tp4103699p4104406.htmlSent
from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@r-project.org 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.
