[R-sig-eco] GAM parameters: Biomod 2

Hello, I am using Biomod 2 to modelling species distribution. I ran some algorithms like GAM, GLM, RF and CTA. I did not change the parameters. How can I known the quadratic terms of GAM? I used the variables with form linear (e.g. precipitation, altimetry, temperature) I did not use

[R-sig-eco] GAM (mgcv) model & variable importance

Dear R list, I’m trying to do a GAM model / variable importance using the mgcv R package. I’ve been googling around, and found posts stating that select=T is a good way to "penalized out” less important variables. m1

[R-sig-eco] GAM model

Hi all i have a question about GAM. Basically, i have a model with total litter mass as response variable and mother age, mother body mass, julian date, year, and sequence as independet variables. Sequence is a factors with 9 levels, basically is a combination of litter and sex (M, F, MM, FF, MF,

Re: [R-sig-eco] GAM - Cyclic splines

Perfect. That does exactly as needed. Thanks very much. And yes my days should run from 0 to 365, just a typo. Regarding predictions, yes I just found an error and one of my variables (X2) was also varying. I thought I had kept them all constant. Sorry about that. -- View this message in

[R-sig-eco] GAM - Cyclic splines

Hi, I am trying to use cyclic splines in gamm4 to model year day. I have data running from say day 6 to day 300 but I want to specify the outer limits of the data are at 0 and 366. I dont want to fix the inner position of the knots however (I allow for a total of 5 knots). Is there a way to do

Re: [R-sig-eco] GAM - Cyclic splines

To the best of my knowledge this works as per mgcv::gam and mgcv::gamm (as the only code in **gamm4** is that to fit the GAMM via **lme4** and nothing else, so leveraging existing code in **mgcv**). Whilst it would help to give more informative names than X1 and X2, and so on to your variables, I

[R-sig-eco] GAM GAMM course

We would like to announce the following statistics course: Beginner's Guide to MCMC, GAM and GAMM When: 10-14 March 2014 Where: Elche, Alicante, Spain For details, see: http://www.highstat.com/statscourse.htm Course flyer: http://www.highstat.com/Courses/Flyer2014_3ElcheV2.pdf Kind regards,

Re: [R-sig-eco] gam result

bericht- Van: r-sig-ecology-boun...@r-project.org [mailto:r-sig-ecology-boun...@r-project.org] Namens Mahnaz Rabbaniha Verzonden: maandag 21 mei 2012 18:33 Aan: r-sig-ecology Onderwerp: [R-sig-eco] gam result Dear all for finding the relation between this variable i use gam ( in base of non

[R-sig-eco] gam result

Dear all for finding the relation between this variable i use gam ( in base of non-normality) [1] temperature salinitydepth Clupeidae model-gam(Clupeidae~s(temperature)+s(salinity)+s(depth)) the result: Parametric coefficients: EstimateStd. Error

Re: [R-sig-eco] gam

On 05/17/2012 06:17 PM, Mahnaz Rabbaniha wrote: Dear all i have done GAM for data ( they are non- normal and i find regression between Sillaginidae with several hydrological factors),i done : [1] depthtemperature salinity Sillaginidae

Re: [R-sig-eco] gam variable selection

Hi All, Many thanks for your different perspectives on stepwise model building and the dredge function, you've helped me out as well as Marco and I shall read more thoroughly into all your points. All the best, Bex ___ R-sig-ecology mailing list

Re: [R-sig-eco] gam variable selection

(Gavin Simpson) -- Message: 1 Date: Tue, 27 Sep 2011 08:54:52 +0200 From: Marco Helbich marco.helb...@gmx.at To: r-sig-ecology@r-project.org Subject: [R-sig-eco] gam variable selection Message-ID: 4e81733c.8090...@gmx.at Content

Re: [R-sig-eco] gam variable selection

Hello Bex, thanks for the detailed answer. You mentioned a function called dredge, perhaps you still know the corresponding package? Again, thanks Gavin and Bex for you advices and patience! Marco ___ R-sig-ecology mailing list

Re: [R-sig-eco] gam variable selection

...@r-project.org] On Behalf Of Rebecca Ross Sent: 28 September 2011 10:45 To: r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] gam variable selection Hi Marco, Having recently been working with gams myself I would suggest a procedure whereby you build your model in a forward stepwise approach

Re: [R-sig-eco] gam variable selection

) -- Message: 1 Date: Tue, 27 Sep 2011 08:54:52 +0200 From: Marco Helbich marco.helb...@gmx.at To: r-sig-ecology@r-project.org Subject: [R-sig-eco] gam variable selection Message-ID: 4e81733c.8090...@gmx.at Content-Type: text/plain; charset=ISO-8859-15

[R-sig-eco] gam variable selection

Dear list, I am studying the influence of several environmental factors (numeric dummies) on species densities (= numeric) using the gam() function with a gaussian link function in the mgcv package. As stated in Wood (2006) there is no variable selection algorithm. Is it an appropriate

Re: [R-sig-eco] gam variable selection

On Tue, 2011-09-27 at 08:54 +0200, Marco Helbich wrote: Dear list, I am studying the influence of several environmental factors (numeric dummies) on species densities (= numeric) using the gam() function with a gaussian link function in the mgcv package. As stated in Wood (2006) there is

Re: [R-sig-eco] gam variable selection

Gavin, thank you for your reply, I appreciate it! After consulting the proposed paper, I have tried your suggestion setting select = T, which results again in another question: If the p-value is NA does this mean that the smoothing term is droped (or shrank to zero)? Independent of its high

Re: [R-sig-eco] gam variable selection

thank you for clarifying. so I can remove them all at once. best marco Am 27.09.2011 13:50, schrieb Gavin Simpson: On Tue, 2011-09-27 at 13:42 +0200, Marco Helbich wrote: Gavin, thank you for your reply, I appreciate it! After consulting the proposed paper, I have tried your suggestion

Re: [R-sig-eco] gam variable selection

On Tue, 2011-09-27 at 14:40 +0200, Marco Helbich wrote: thank you for clarifying. so I can remove them all at once. Given their effects are already removed you could just work with the model *as is*. If you refit, you might have to be careful to ensure that the same model (and smooth

[R-sig-eco] gam plotting (package: mgcv)

Dear r-sig-ecology list users, I have been using the mgcv package for fitting a GAM model to a large set of spatial/temporal data with several predictors. Each variable contains 1,000,000 values... I have been able to successfully fit a model using the bam() function for large data sets. It

Re: [R-sig-eco] gam plotting (package: mgcv)

On Mon, 2011-07-25 at 12:14 +0200, Marc Taylor wrote: Dear r-sig-ecology list users, I have been using the mgcv package for fitting a GAM model to a large set of spatial/temporal data with several predictors. Each variable contains 1,000,000 values... I have been able to successfully fit a

Re: [R-sig-eco] GAM with a Gamma error structure

On Sun, 2008-11-16 at 17:58 -0500, Sally Roman wrote: Hi- I'm try to run a GAM with a Gamma distribution, but am getting an error message that there are non positive values allowed for the gamma family. I do not have any negative values for my response or explanatory variables.