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

2013-03-07 Thread Sarah Goslee
That sounds like a job for path analysis or for structural equation modeling, depending on the level of sophistication desired and the hypotheses to be tested. There are plenty of good resources for both, in and out of R. Sarah On Wednesday, March 6, 2013, Jay Kerns wrote: Hello, I'm

[R-sig-eco] ordipointlabel for triplots

2013-03-07 Thread carolina monmany
Hi all, I would like to use ordipointlabel() to plot a RDA but the function only displays species and sites. How can I include environmental variables as vectors? Thanks! -- --- A. CAROLINA MONMANY Universidad de Puerto Rico Departamento de Biologia - CN 235 POBOX

[R-sig-eco] GLM

2013-03-07 Thread Mahnaz Rabbaniha
Dear all I want to find regression between fish larva abundance and some abiotic factor ,i used this code: glm(formula = mychto ~ po4 + No3 + Si + Tn) result: Deviance Residuals: Min 1Q Median 3Q Max -26.586 -18.262 -12.296 -2.949 226.229 Coefficients:

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

2013-03-07 Thread Mark Fulton
There's probably something off the shelf, but I use a little function written in R: #A function for doing an xyz bubbleplot. bubbleplot - function(x, y, z, bmax=4, bmin=.5) { plot(x,y, type=n) z - z-min(z); z - z/max(z) for (i in 1:length(x)) {

Re: [R-sig-eco] GLM

2013-03-07 Thread Bob O'Hara
On 03/07/2013 04:24 PM, Mahnaz Rabbaniha wrote: Dear all I want to find regression between fish larva abundance and some abiotic factor ,i used this code: glm(formula = mychto ~ po4 + No3 + Si + Tn) result: Deviance Residuals: Min 1Q Median 3Q Max -26.586 -18.262

[R-sig-eco] R: GLM

2013-03-07 Thread Enrico Caprio
Hi Mahnaz, First of all check whether you're using the right family error distribution according to tour respinse varia le. If you use team abundancea from counts you need to specify family = poisson in your model. Then AIC is used to select the best from a set of candidate models, it is not

Re: [R-sig-eco] ordipointlabel for triplots

2013-03-07 Thread Gavin Simpson
On Thu, 2013-03-07 at 10:48 -0400, carolina monmany wrote: Hi all, I would like to use ordipointlabel() to plot a RDA but the function only displays species and sites. How can I include environmental variables as vectors? Thanks! You can use text(ord, display = bp) (where `ord` is

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

2013-03-07 Thread Gavin Simpson
On Thu, 2013-03-07 at 15:37 +, Mark Fulton wrote: There's probably something off the shelf, but I use a little function written in R: #A function for doing an xyz bubbleplot. bubbleplot - function(x, y, z, bmax=4, bmin=.5) { plot(x,y, type=n) z - z-min(z); z - z/max(z) for (i in

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

2013-03-07 Thread Philippi, Tom
Jay-- I'm not sure how one would combine SEM / graphical models with compositional dissimilarity as a response. You might be able to fit a series of models in adonis() or capscale(), comparing just direct factors to direct + intermediate, etc.. I don't have any good ideas on how you might test

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

2013-03-07 Thread Sarah Goslee
Hi, I'm not sure how one would combine SEM / graphical models with compositional dissimilarity as a response. You might be able to fit a series of models in adonis() or capscale(), comparing just direct factors to direct + intermediate, etc.. I don't have any good ideas on how you might