Thank you so much for your response! This clarifies the issue I was having.
Cheers,
Matt


On Fri, Mar 29, 2013 at 2:43 AM, Jari Oksanen [via R] <
ml-node+s789695n4662809h42@n4.nabble.com> wrote:

> MWilson <mjw029 <at> bucknell.edu> writes:
>
> >
> > Hi All,
> > I am using canonical correspondence analysis to compare a community
> > composition matrix to a matrix of sample spatial relationships and
> > environmental variables. In order to parse out how much variance is
> > explained purely by space (S/E) or the environment (E/S) I am using a
> > conditional (partial) CCA.  I want to test significance via Monte Carlo
> but
> > I can not find a way to do this with a conditional CCA.  I have been
> using
> > vegan for the CCA and attempting to use ade4 to run a Monte Carlo.
> However,
> > these two packages conflict when it comes to CCA.  If I use vegan I can
> run
> > a conditional CCA, and if I use ade4 I can do a Monte Carlo - but I
> can't
> > figure out how to do a conditional CCA with ade4 OR a Monte Carlo with
> > vegan.  If anyone has experience with this I would be truly grateful for
> > your help!  I am fairly new to R, and I have quickly found myself in a
> place
> > where "Google-ing" has no longer proven useful.  Below are my scripts
> and
> > error messages.
>
> > --
> > View this message in context:
> http://r.789695.n4.nabble.com/Conditional-CCA-and-Monte-Carlo-
> Help-tp4662572.html
> > Sent from the R help mailing list archive at Nabble.com.
> >
> >
> randtest() is an ade4 function that only works with ade4 result
> objects. That you found the hard way.  In vegan we have permutest: see
> ?permutest.cca. Some other similar functions are described together
> with permutest.cca, but permutest() is similar to randtest.
>
> ade4::randtest.cca and vegan:::permutest.cca work similarly and are
> comparable with basic models, but there are following differences:
>
> 1) vegan uses ter Braak's pseudo-F statistic, whereas ade4 returns the
> proportion constrained/all eigenvalues. These are similar to a
> constant multiplier in non-conditional models and with "direct" or
> "reduced" permutation models in vegan, but differ otherwise. The ade4
> alternative is not good for partial models (but that does not matter
> since ade4 has no partial models). The vegan:::permutest.cca function
> returns items num and den (numerator and denominator) that can be used
> to get the proportion of ade4.
>
> 2) vegan permutes response (community) data whereas ade4 permutes
> constraints (environmental data).  This makes only difference in
> partial (conditional) models or with some non-default permutation
> strategies in vegan. However, because of this, ade4 and vegan results
> are not identical with the same random number seed (with little
> trickery this can be fixed, but that is hardly for
> beginners). Permutation of community data is needed in analysis of
> conditional (partial) models, and in some permutation strategies.
>
> 3) We do not call it Monte Carlo, but permutation. (Monte Carlo is too
> expensive for me -- I prefer Menton). That may explain why Google did
> not find it to you.
>
> In general, you should not expect methods functions (such as
> ade4::randtest.cca) to work across packages. In sometimes they do, but
> in those cases the package authors have taken special care to make
> their functions to work with alien objects. Not in this case. It
> neither makes sense for ade4::randtest be able to handle vegan object
> because randtest does not know what to do with contional (partial)
> models.
>
> Cheers, Jari Oksanen
>
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