R help - Nov 2011 - I cannot get species scores to plot with site scores in MDS when I use a distance matrix as input. Problems with NA's?

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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Sent from the R help mailing list archive at Nabble.com.

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.
> 

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Sent from the R help mailing list archive at Nabble.com.

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
______________________________________________> 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.

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.

HTH

G
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