Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?

2013-03-06 Thread Sarah Loboda
Hi :D I finally had the chance to try your solutions. It was fast to modify the code of the function and it worked! I really appreciate your comments and your help. You are fast and clear ! I modified my code and I will never put white axes ever again ;) Thank you very much. 2013/2/26 Jari Oksanen

Re: [R-sig-eco] Should one remove highly correlated variables before doing PCA??

2013-03-06 Thread Baldwin, Jim -FS
Two additional issues might be considered: 1. Correlated variables are still correlated after PCA or after tossing one of the variables so teasing apart separate effects of the two variables is not resolved (nor can it necessarily be resolved with the particular dataset at hand). 2. The purp

[R-sig-eco] Course: Beginner's Guide to MCMC, GLM and GAM with R

2013-03-06 Thread Highland Statistics Ltd
There are a few places left on the following course: Beginner's Guide to MCMC, GLM and GAM with R When: 10 - 13 June 2013 Where: SAMS, Oban, Scotland Further information: http://www.highstat.com/statscourse.htm Flyer: http://www.highstat.com/Courses/Flyer2013June_SAMS.pdf Kind regards,

Re: [R-sig-eco] Should one remove highly correlated variables before doing PCA??

2013-03-06 Thread Chris Howden
With reference to jims point 2. One can use Partial Least Squares, which finds orthogonal PC's that best explain a set of responses. Chris Howden Founding Partner Tricky Solutions Tricky Solutions 4 Tricky Problems Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Ana

Re: [R-sig-eco] Projecting model to landscape

2013-03-06 Thread Robert J. Hijmans
Li, You can use the "predict" function in the 'raster' package. There are also examples with randomForest and other techniques in this vignette that comes with the 'dismo' package: http://cran.r-project.org/web/packages/dismo/vignettes/sdm.pdf Robert > Li Wen-2 wrote > > Dear list member > > >

Re: [R-sig-eco] Projecting model to landscape

2013-03-06 Thread Li Wen
Hi, Robert and all others Thanks for the suggestions and directions pointed out from the community. It seems there are two packages for the work: 1. Using predict function from package "raster". The function can project a fitted model of any class that has a 'predict' method (or supplying a s

[R-sig-eco] quantifying directed dependence of environmental factors

2013-03-06 Thread Jay Kerns
Hello, I'm posting to this list because I believe it's the best place to go. My question is R related only inasmuch as all the work I've done so far has been with R and I expect any answers I get from here will lead me to more R work. I'm consulting with an ecologist and an engineer on a project

[R-sig-eco] nMDS plot with points of different size

2013-03-06 Thread Stas Malavin
Dear list members, I want to plot an nMDS diagram with points' area proportional to the abundance of particular species. I could imagine just plotting with type = "n" and then using points() with different cex, but may be some special functions/packages exist for that which you can point me to? T