------------------------------ Message: 4 Date: Wed, 29 Aug 2018 17:38:44 +0000 From: dani <orchidn at live.com> To: Ben Bolker <bbolker at gmail.com>, "r-sig-mixed-models at r-project.org" <r-sig-mixed-models at r-project.org> Subject: Re: [R-sig-ME] question about a GAM model Message-ID: <BYAPR06MB38321CD8470AE34E57716661D6090 at BYAPR06MB3832.namprd06.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Thank you very much Udita and Dr. Bolker for your responses. It is still not clear to me how should I proceed. Would anyone else be able help with this issue,? Dani, GAMs are useful if you use them with care, but confusing if you just apply them because someone else is doing it as well. Perhaps you should first ask yourself the question why you are applying a GAM. Then focus on the question whether the output makes sense. Based on your output it seems that nothing is important (not even as parametric terms). But I am not familiar with your data; things like collinearity can mess up the shape of smoothers. And you don't mention the size of your data set neither. I suggest that you have a go at Wood (2017), or if I may be bold enough to self-cite....try our Beginner's Guide to GAM (2012). Kind regards, Alain Zuur ?Best regards, Dani Sent from Outlook<http://aka.ms/weboutlook>
From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on behalf of Ben Bolker <bbolker at gmail.com>
Sent: Tuesday, August 28, 2018 6:19 AM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] question about a GAM model
Sent: Tuesday, August 28, 2018 6:19 AM
To: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] question about a GAM model
Don't forget to run k.check() on your model to see if you specified a large enough basis dimension to start with ... On 2018-08-28 05:51 AM, Bansal, Udita wrote: > Hi Dani, > > I don?t know much about GAM but I know you can look at the plots for fitted model results to check if there is any curvature. You can use the following code: > > par(mfrow = c(1,3)) > plot(GAMmodel) > > Bests > Udita > > On 28/08/18, 1:58 AM, "R-sig-mixed-models on behalf of dani" <r-sig-mixed-models-bounces at r-project.org on behalf of orchidn at live.com> wrote: > > Hi everyone, > > > I have a question about a GAM model where I included three non-parametric terms. I obtained the results below. can I conclude that the associations were in fact linear and run a final GLM model without including splines? To me it seems unnecessary to include splines in the final model. How should I report these results? > > > # Approximate significance of smooth terms: > # edf Ref.df Chi.sq p-value > # s(x1) 1.61 2.01 1.17 0.550 > # s(x2) 1.00 1.00 0.00 0.955 > # s(x3) 1.00 1.00 4.61 0.032 * > > Thank you very much, > Dani > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-mixed-models at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > > > _______________________________________________ > R-sig-mixed-models at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models [[alternative HTML version deleted]] ------------------------------ Subject: Digest Footer _______________________________________________ R-sig-mixed-models mailing list R-sig-mixed-models at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models ------------------------------ End of R-sig-mixed-models Digest, Vol 140, Issue 34 ***************************************************
Dr. Alain F. Zuur Highland Statistics Ltd. 9 St Clair Wynd AB41 6DZ Newburgh, UK Email: highstat at highstat.com URL: www.highstat.com And: NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands Author of: 1. Beginner's Guide to Spatial, Temporal and Spatial-Temporal Ecological Data Analysis with R-INLA. (2017). 2. Beginner's Guide to Zero-Inflated Models with R (2016). 3. Beginner's Guide to Data Exploration and Visualisation with R (2015). 4. Beginner's Guide to GAMM with R (2014). 5. Beginner's Guide to GLM and GLMM with R (2013). 6. Beginner's Guide to GAM with R (2012). 7. Zero Inflated Models and GLMM with R (2012). 8. A Beginner's Guide to R (2009). 9. Mixed effects models and extensions in ecology with R (2009). 10. Analysing Ecological Data (2007).