Re: [R-sig-eco] Retrieving canonical coefficients and correlation coefficients according to ter Braak using vegan package cca() function
Hi Jari, Thank you very much for your quick answer. I was aware of that difference already though, so I did scale the environmental variables before using them, and used the square root on the species counts as described in the paper of ter Braak. I believe I have the correct transformation, as the coefficients and correlation on the first axis are pretty much comparable. Cheers Joris On Thu, Jun 14, 2012 at 9:09 PM, Jari Oksanen jari.oksa...@oulu.fi wrote: Joris, On 14/06/2012, at 17:39 PM, Joris Meys wrote: Hi all, I get results that differ from the table given by ter Braak. I can explain the differences in sign (that's normal, as the solution of cca is defined up to the sign), and I can believe there would be small differences as we're talking different ways of estimation, but the canonical coefficients for the second axis differ substantially. My question : - Did I use the correct methods to extract what ter Braak calls canonical coefficients and correlation coefficients? - is there a logical explanation for the big difference in some results ? I haven't checked that paper, and can't do that for several days. However, one essential difference in canonical coefficients between Canoco and vegan::cca is that Canoco standardizes all constraining variables to unit variance whereas vegan uses unstandardized variables. Does it help if you use Model - cca(hs.spec ~ ., data = scale(hs.ev)) ? Cheers, Jari Oksanen -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa -- Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Mathematical Modelling, Statistics and Bio-Informatics tel : +32 9 264 59 87 joris.m...@ugent.be --- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] option --enable-R-shlib
On Fri, Jun 15, 2012 at 7:05 AM, Michel Rapinski mrapi...@uottawa.ca wrote: Hello, How can I check if my the R program that I've installed is compiled with the option --enable-R-shlib? Michel, You can check this by using the command ldd /usr/lib/R/bin/exec/R. If libR.so (the shared R library) appears in the resulting list, then you have R built with --enable-R-shlib. And, if need be, how do I enable that option? If needed, you can enable this option during the build process by passing the option, e.g. ./config --enable-R-shlib, just before make. Hope this helps, Ivailo -- UBUNTU: a person is a person through other persons. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] option --enable-R-shlib
Hi Ivailo, Do I run this command in R? Or in terminal? Maybe I should have added that I have a mac, I don't know if that makes a difference. Thank you very much for the help. Michel On Fri, Jun 15, 2012 at 7:05 AM, Michel Rapinski mrapi...@uottawa.ca wrote: Hello, How can I check if my the R program that I've installed is compiled with the option --enable-R-shlib? Michel, You can check this by using the command ldd /usr/lib/R/bin/exec/R. If libR.so (the shared R library) appears in the resulting list, then you have R built with --enable-R-shlib. And, if need be, how do I enable that option? If needed, you can enable this option during the build process by passing the option, e.g. ./config --enable-R-shlib, just before make. Hope this helps, Ivailo -- UBUNTU: a person is a person through other persons. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] option --enable-R-shlib
On Fri, Jun 15, 2012 at 6:20 PM, Michel Rapinski mrapi...@uottawa.ca wrote: Hi Ivailo, Do I run this command in R? Or in terminal? Maybe I should have added that I have a mac, I don't know if that makes a difference. Sorry, Michel, I missed to mention that ldd needs to be run in the terminal, and don't forget to provide the correct path to the R executable. You can check http://v.gd/ZPswag for further details on how to build R under Mac OS X. Good luck, Ivailo -- UBUNTU: a person is a person through other persons. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
