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I think i mentioned this in private communication a while back, but in case anyone else cares: I have a version of canonical correspondence analysis (CCA) coded up in R. I based it on Ter Braak and Prentice (1988) Adv. Ecol. Res. 18:271-317, Ter Braak (1986) Ecol. 67(5):1167-1179, and Ter Braak (1995) Section 5.9 in Jongman, Ter Braak, and van Tongeren "Data Analysis in Community and Landscape Ecology". Actually, there are two versions: one which follows Ter...

...dence analysis In-Reply-To: <Pine.GSO.4.31.0102170733280.13118-100000 at auk.stats> Brian, As an ecologist, this is something I am also interested in. However, as I am more an ecologist than a statistician, I quote from the MVSP manual: "Canonical Correspondence Analysis(CCA; ter Braak, 1986,1987) is a multivariate direct gradient analysis method that has become widely used in ecology. As the name suggests, this method is derived from correspondence analysis, but has been modified to allow environmental data to be incorporated into the analysis. It is calculated using recip...

Is there an R function that does canonical correspondence analysis. Can it be done using the VR function corresp()? If not, how hard it be to write R code to do it? I am a population biologist with long but patchy programming experience in C, Smalltalk, Java and other languages. Thanks, Patrick Foley patfoley at csus.edu

Full_Name: cajo ter Braak Version: 2.1.1 OS: Windows Submission from: (NULL) (137.224.10.105) # I would like to attach the matrix C in the Rdata file; it is 50x50 and comes from a geostatistical problem (spherical covariogram) > rm(list=ls(all=TRUE)) > load(file= "test.eigen.Rdata") > ls() [1] "C&...

Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch X-Spam-Level: **** X-Spam-Status: No, hits=4.2 required=5.0 tests=MSGID_FROM_MTA_HEADER,RCVD_IN_BL_SPAMCOP_NET autolearn=no version=2.63 Dear r-help list, my question is about ordination technics:

Hi, I want to include a vector representing the sites - environmental data correlation in a PCA. I currently use prcomp (no scaling) to perform the PCA, and envfit to retrieve the coordinates of the environmental data vector. However, the vector length is different from the one obtained in CAnoco when performing a species - environmental biplot (scaling -2). How can I scale the vector in order to

I would presume this is another manifestation of what I reported (reproduced below) on 2003-12-01. cajo.terbraak at wur.nl wrote: >Full_Name: cajo ter Braak >Version: 2.1.1 >OS: Windows >Submission from: (NULL) (137.224.10.105) > > ># I would like to attach the matrix C in the Rdata file; it is 50x50 and comes >from a geostatistical problem (spherical covariogram) > > > &gt...

I'm getting lots of grief from reviewers about figures generated with the envfit function in the Vegan package. Has anyone else struggled to effectively explain this analysis? If so, can you share any helpful tips? The most recent comment I've gotten back: "What this shows is which NMDS axis separates the communities, not the relationship between the edaphic factor and the

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

Hi, from what I understand about the canonical correlation function 'cancor', it looks for correlations in two sets of variables, each represented in matrix form. Right? Sounds exactly like what I need. I have tried the following but I am not sure how to interpret the results. AudioPCs <- c(ArTHarF0PCA$x[,2], ArTHarF1PCA$x[,2], ArTHarF2PCA$x[,2], ArTHarF3PCA$x[,2],