On Thu, 2010-11-11 at 18:14 +1100, Nevil Amos wrote:> I am having a problem with NA handling in capscale function.
>
> as I understand it from the help capscale should permit NA values when
> na.action=na.mit or na.exclude,
>
> however I am getting the error
>
> Error in X[nas, , drop = FALSE] : incorrect number of dimensions
>
> trivial example is pasted below.
>
> library(vegan)
> mydist<- matrix(1:25, 5, 5)
> mydata<-matrix(rnorm(1:25),5,5)
> mydata[3,1]<-NA
> mydata<-data.frame(mydata)
>
> capscale(mydist~X1+X2+Condition(X3),data=mydata,na.action = na.omit)
>
>
> Thanks
>
> Nevil Amos
It is failing within the formula parsing code because ordiParseFormula
thinks the response is a matrix but it was getting a dissimilarity
matrix in class "dist" form.
I think Jari has just fixed this in the R-Forge svn sources, but that
revision has not yet been built on the R-Forge build system. Check back
here later:
https://r-forge.r-project.org/R/?group_id=68
Thanks for the report.
G
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
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