[R] GAM quasipoisson in MuMIn
Hi, I have a GAM quasipoisson that I'd like to run through MuMIn package - dredge - gettop.models - model.avg However, I'm having no luck with script from an example in MuMIn help file. In MuMIn help they advise include only models with smooth OR linear term (but not both) for each variable. Their example is: # Example with gam models (based on example(gam)) require(mgcv) dat - gamSim(1, n = 500, dist=poisson, scale=0.1) gam1 - gam(y ~ s(x0) + s(x1) + s(x2) + s(x3) + (x1+x2+x3)^2, family = poisson, data = dat, method = REML) cat(dQuote(getAllTerms(gam1)), \n) # include only models with smooth OR linear term (but not both) for each variable: dd - dredge(gam1, subset=(!`s(x1)` | !x1) (!`s(x2)` | !x2) (!`s(x3)` | !x3)) But I'm not sure at all how to apply these instructions to my data My formula is GAM-gam(Species richness (count) ~ Categorical + Continous + Continous + * s*(Continous ) + Continous : Continous + Continous : Continous, family=quasipoisson, data =) Thanks for any advice on script Karen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GAM quasipoisson in MuMIn
On Fri, 2011-02-04 at 12:31 +, Karen Moore wrote: Hi, snip / My formula is GAM-gam(Species richness (count) ~ Categorical + Continous + Continous + * s*(Continous ) + Continous : Continous + Continous : Continous, family=quasipoisson, data =) Ok, I'm reasonably certain that that is *not* your gam() call. Why not post the *actual* code you would enter for your GAM model? dd - dredge(GAM) should evaluate all possible models from the global model you specified. The example you quote is for a global model with both smooth and linear terms for the same variables, hence in dredge() they need to select models that include only the smooth for a particular variable or the linear term for that variable, but not both. By the looks of it, you don't have this problem. G Thanks for any advice on script Karen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GAM quasipoisson in MuMIn
Thanks for that Gavin - yeah you're right that was not my actual model, which is: GAMV2c-gam(VASCSR~ROTATION+ CANCOV +LAreaoldwood+ + s(SOILPH) + CANCOV:LAreaoldwood + CANCOV:SOILPH,family=quasipoisson, data =HIGHBRYOSR) For MMI the script I use, and have used successfully with *exactly* same GAM with a poisson distribution, is: - ddGAMV2c-dredge(GAMV2c) - ddGAMV2c The above 2 steps run fine - top.models4_GAMV2c-get.models(ddGAMV2c, subset = delta = 4, method=REML) So after request for top.models I get error * Error in update.formula(formula(object), formula.) : formula expected* And this is were I'm stumbling. I also tried - bestGAMV2c - get.models(ddGAMV2c, cumsum(weight) = .95) *Error in update.formula(formula(object), formula.) : formula expected* Again any help with this would be much appreciated as out of the 4 models I'm running through MMI for my data this is only one giving me problems (again all of the above script works fine with *exactly* same GAM model with a poisson distribution!) Regards, Karen On 4 February 2011 12:47, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Fri, 2011-02-04 at 12:31 +, Karen Moore wrote: Hi, snip / My formula is GAM-gam(Species richness (count) ~ Categorical + Continous + Continous + * s*(Continous ) + Continous : Continous + Continous : Continous, family=quasipoisson, data =) Ok, I'm reasonably certain that that is *not* your gam() call. Why not post the *actual* code you would enter for your GAM model? dd - dredge(GAM) should evaluate all possible models from the global model you specified. The example you quote is for a global model with both smooth and linear terms for the same variables, hence in dredge() they need to select models that include only the smooth for a particular variable or the linear term for that variable, but not both. By the looks of it, you don't have this problem. G Thanks for any advice on script Karen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/http://www.ucl.ac.uk/%7Eucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% -- Karen Moore PhD Researcher, FORESTBIO, Department of Botany, Trinity College Dublin Ireland Ph: 00 353 (0)87 9422 502 http://www.ucc.ie/en/planforbio [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GAM quasipoisson in MuMIn - SOLVED
Hi, Got my issues sorted. Error message solved: I heard from the guy who developed MuMIn and his suggestion worked. As for the error you get, it seems you are running an old version of MuMIn. Please update the package first. I did (I was only 1 version behind in both R and in MuMIn) and error disappeared! Running quasipoisson GAM in MuMIn: As for my questions on GAM and to include only models with smooth OR linear term (but not both) for each variable, as Gavin said, this refers only to global models with both smooth and linear terms for the *same*variableswhich I didn't have. Regards, Karen On 4 February 2011 12:31, Karen Moore kmo...@tcd.ie wrote: Hi, I have a GAM quasipoisson that I'd like to run through MuMIn package - dredge - gettop.models - model.avg However, I'm having no luck with script from an example in MuMIn help file. In MuMIn help they advise include only models with smooth OR linear term (but not both) for each variable. Their example is: # Example with gam models (based on example(gam)) require(mgcv) dat - gamSim(1, n = 500, dist=poisson, scale=0.1) gam1 - gam(y ~ s(x0) + s(x1) + s(x2) + s(x3) + (x1+x2+x3)^2, family = poisson, data = dat, method = REML) cat(dQuote(getAllTerms(gam1)), \n) # include only models with smooth OR linear term (but not both) for each variable: dd - dredge(gam1, subset=(!`s(x1)` | !x1) (!`s(x2)` | !x2) (!`s(x3)` | !x3)) But I'm not sure at all how to apply these instructions to my data My formula is GAM-gam(Species richness (count) ~ Categorical + Continous + Continous + *s*(Continous ) + Continous : Continous + Continous : Continous, family=quasipoisson, data =) Thanks for any advice on script Karen -- Karen Moore PhD Researcher, FORESTBIO, Department of Botany, Trinity College Dublin Ireland Ph: 00 353 (0)87 9422 502 http://www.ucc.ie/en/planforbio [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
