[R-sig-ME] question about a GAM model (dani)

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Wed Aug 29 21:30:59 CEST 2018


Message: 4
Date: Wed, 29 Aug 2018 17:38:44 +0000
From: dani <orchidn using live.com>
To: Ben Bolker <bbolker using gmail.com>, "r-sig-mixed-models using r-project.org"
	<r-sig-mixed-models using r-project.org>
Subject: Re: [R-sig-ME] question about a GAM model
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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,?


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,


Sent from Outlook<http://aka.ms/weboutlook>

From: R-sig-mixed-models <r-sig-mixed-models-bounces using r-project.org> on behalf of Ben Bolker <bbolker using gmail.com>
Sent: Tuesday, August 28, 2018 6:19 AM
To: r-sig-mixed-models using 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 using r-project.org on behalf of orchidn using 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
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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 using highstat.com
URL:   www.highstat.com

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).

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