Dear Gavin, My apologies for the delay in responding to your request for further information I have been travelling for work since you replied and have only just returned to email contact.
The output from the traceback is as follows # This is the capscale model that I called > beetlecap <-capscale(log(beetles+1) ~ size + Clearfell + Absolute.Distance+ > Distance_from_edge+ clearfell.harvest_area + Canopy.Cover + X500mnative + > Litter3 + X500mexotic + X5000exotic + Condition(AdjLong + AdjLat + AdjLat.2 + > AdjLat.2.long + AdjLong.3), environ, distance = "bray") This is the ANOVA by margin option with the error > anova(beetlecap, by="margin") Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Corresponding traceback > traceback() 9: `colnames<-`(`*tmp*`, value = c("CAP1", "CAP0")) 8: capscale(formula = log(beetles + 1) ~ size + Clearfell + Absolute.Distance + Distance_from_edge + clearfell.harvest_area + Canopy.Cover + X500mnative + Litter3 + X500mexotic + X5000exotic + Condition(AdjLong + AdjLat + AdjLat.2 + AdjLat.2.long + AdjLong.3) + Condition(size + Clearfell + Absolute.Distance + Distance_from_edge + clearfell.harvest_area + Canopy.Cover + Litter3 + X500mexotic + X5000exotic + AdjLong + AdjLat + AdjLat.2 + AdjLat.2.long + AdjLong.3), data = environ, distance = "bray") 7: eval(expr, envir, enclos) 6: eval(call, parent.frame()) 5: update.default(object, fla) 4: update(object, fla) 3: anova.ccabymargin(object, alpha = alpha, beta = beta, step = step, perm.max = perm.max, by = NULL, ...) 2: anova.cca(beetlecap, by = "margin") 1: anova(beetlecap, by = "margin") I note that in the traceback point 8 it appears that my original model statement has been modified to include all my environmental predictors as conditions as well as all the original conditional variables that I wished to partial out. Any help on finding the cause of this error greatly appreciated, if it helps I can provide you with data files in a personal email. Kind regards Steve Pawson -----Original Message----- From: Gavin Simpson [mailto:gavin.simp...@ucl.ac.uk] Sent: Wednesday, 12 October 2011 1:31 a.m. To: Steve Pawson Cc: r-help@r-project.org Subject: Re: [R] Vegan: Anova.CCA accessing original data using option by="margin" On Mon, 2011-10-10 at 23:51 -0700, Steve Pawson wrote: > Hello, > > I am attempting to use the ANOVA.CCA function with the by="margin" option. > The process works fine using the by="terms" option and I note in the Vegan > manual that Jari suggests that an error may occur if the anova does not have > access to the data on the original constraints. > > This is the error that I get: > > Error in dimnames(x) <- dn : > length of 'dimnames' [2] not equal to array extent > > My question is, does anyone know if this error relates to what Jari is > referring to (or is it a different problem), and if it is, how do I link the > anova to the original constraints? It is almost impossible to answer that without a lot more information. For starters, what does traceback() say when run immediately *after* you get the error? G > Many thanks for any help provided. > > Regards > > Steve > > -- > View this message in context: > http://r.789695.n4.nabble.com/Vegan-Anova-CCA-accessing-original-data-using-option-by-margin-tp3893005p3893005.html > Sent 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it. Scion does not accept responsibility for anything in this e-mail which is not provided in the course of Scion’s usual business or for any computer virus, data corruption, interference or delay arising from this e-mail. ______________________________________________ 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.