Barry Cooke
2001-Feb-17 15:28 UTC
Krebs for R (was Re: [R] canonical correspondence analysis)
R-ecologists: Anyone wanting to create a Krebs package for R can do so using the C-source code avalaible at: ftp://gause.biology.ualberta.ca/pub/jbrzusto/krebs/source.zip Barry J. Cooke Current mailing address: Ph.D. Candidate 3971 NW 23 Circle Environmental Biology and Ecology Gainesville, Florida, USA Department of Biological Sciences 32605 University of Alberta Edmonton, AB, T6G 2E9 http://www.ualberta.ca/~bcooke bcooke at ualberta.ca ---------- Forwarded message ---------- Date: Sat, 17 Feb 2001 11:18 +0000 (GMT) From: Graham Smith <myotis at cix.compulink.co.uk> To: R-help at stat.math.ethz.ch Cc: myotis at cix.compulink.co.uk Subject: Re: [R] canonical correspondence 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 reciprocal averaging form of correspondence analysis. However, at each cycle of the averaging process, a multiple regression is performed of the sample scores on the environmental variables. New site scores are calculated based on this regression, and then the process is repeated , continuing until the scores stabilise. The result is that the axes of the final ordination, rather than simply reflecting dimensions of the greatest variability in the species data, are restricted to the linear combinations of the environmental variables and the species data. In this way these two sets of data are then directly related." Ref 1: ter Braak, CJF (1986) Canonical correspondence analysis: A new eigenfactor technique for multivariate direct gradient analysis. Ecology, 67:1167-1179 Ref 2: ter Braak, CJF (1987) The analysis of vegetation-environment relationships by canonical correspondence analysis. Vegetatio, 64:69-77 More general references are: Jongman, RHG., Ter Braak, CJF., and, van Tongeren, OFR. (1995) Data analysis in community and landscape ecology. CUP. Kent, M. & Coker, P. (1992) Vegetation description and analysis: A practical approach. Wiley. As far as I am aware, only MVSP and Canoco carry out CCA. I hope this is of some interest and it does raise the general point that programming literate ecologists don't seem to have yet fully embraced S-Plus or R. Having only recently found S-Plus and R myself I had rather hoped that some of the common ecological statistical tools such as CCA, Twinspan and Decorana, plus the miscellaneous tools described in Krebs (1989) might have found there way into an R package. Krebs, CJ (1989) Ecological Methodology, Harper & Row. Now as a 2nd edition 1995?) Cheers, Graham S -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._