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 -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ 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.