Vegan: Anova.CCA accessing original data using option by="margin"
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.simpson at ucl.ac.uk]
Sent: Wednesday, 12 October 2011 1:31 a.m.
To: Steve Pawson
Cc: r-help at 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.
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