[R] Vegan: Anova.CCA accessing original data using option by="margin"

[Steve Pawson]

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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