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+s789695n4662809...@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 > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4662809&i=0>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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Conditional-CCA-and-Monte-Carlo-Help-tp4662572p4662809.html > To unsubscribe from Conditional CCA and Monte Carlo - Help!, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4662572&code=bWp3MDI5QGJ1Y2tuZWxsLmVkdXw0NjYyNTcyfC0xMjYyOTcxMTM3> > . > NAML<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://r.789695.n4.nabble.com/Conditional-CCA-and-Monte-Carlo-Help-tp4662572p4662832.html Sent from the R help mailing list archive at Nabble.com. 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