[R-sig-ME] glmmTMB deviance enquiry
Rion Lerm
re@|erm @end|ng |rom @@eon@nr|@@c@z@
Mon Mar 13 08:08:16 CET 2023
Thanks Ben!
Regards/Groete,
*Rion Lerm*
SAEON Ndlovu
C: 076 913 8381
W: 013 735 3536
SAEON / Scientific Services, Kruger National Park Gate, Phalaborwa, South
Africa
South African Environmental Observation Network
Website <https://ndlovu.saeon.ac.za/> & Location of our offices
<https://www.google.co.za/maps/place/SAEON+Ndlovu+Node/@-23.9447244,31.164957,18z/data=!4m5!3m4!1s0x1ec36ec96261cfb7:0xb89a27144ba0ca2a!8m2!3d-23.9450103!4d31.1652626>
My research profiles:
*ResearchGate* <https://www.researchgate.net/profile/Rion-Lerm>
*ORCID <https://orcid.org/0000-0002-9992-2093>*
*Google Scholar
<https://scholar.google.com/citations?user=JV5d7E4AAAAJ&hl=en>*
On Fri, 10 Mar 2023 at 16:19, Ben Bolker <bbolker using gmail.com> wrote:
> I'm afraid this might be getting into more generic statistical
> territory, rather than anything specific to mixed models. If you're
> going to rank models without regard to nesting you should probably use
> AIC rather than deviance. Alain Zuur (Highland Statistics) has a whole
> series of books on ecological statistics that cover this topic ...
> maybe Symonds et al would be useful?
>
>
> Symonds, Matthew R. E., and Adnan Moussalli. 2011. “A Brief Guide to
> Model Selection, Multimodel Inference and Model Averaging in Behavioural
> Ecology Using Akaike’s Information Criterion.” Behavioral Ecology and
> Sociobiology 65 (1): 13–21. https://doi.org/10.1007/s00265-010-1037-6.
>
>
> On 2023-03-08 3:56 a.m., Rion Lerm wrote:
> > Thank you @bbolker using gmail.com <mailto:bbolker using gmail.com> for your
> > elaborate response.
> >
> > I am using the Deviance values in this manner to compare model fit.
> > Here, I selected for the model with second to smallest Deviance values.
> > May it be presented like this as I feel it is important to display how a
> > model was selected from various models (the reason for selecting the
> > second to smallest values aren't explained here as is the details of
> > this work):
> >
> > *Model predictor fixed effects*
> >
> >
> >
> > */SR.asymp/*
> >
> >
> >
> > */SES.FRic/*
> >
> >
> >
> > */SES.PD/*
> >
> > //
> >
> >
> >
> > Deviance
> >
> >
> >
> > //
> >
> > Tree + Shrub + Grass + Bare ground + Infrastructure + Seasonal water +
> > Permanent water
> >
> >
> >
> > 760.4 | 1,463.6
> >
> >
> >
> > 172.1 | 319.6
> >
> >
> >
> > 206.7 | 420.7
> >
> > Tree + Shrub + Bare ground + Infrastructure + Seasonal water + Permanent
> > water
> >
> >
> >
> > *766.3 | 1467.7*
> >
> >
> >
> > *179.0 | 325.2*
> >
> >
> >
> > *207.3 | 421.3*
> >
> > Tree + Shrub + Grass + Bare ground
> >
> >
> >
> > 777.1 | 1,520.3
> >
> >
> >
> > 179.4 | 368.7
> >
> >
> >
> > 229.3 | 441.5
> >
> > Tree + Shrub + Grass + Bare ground + Infrastructure
> >
> >
> >
> > 776.8 | 1,484.3
> >
> >
> >
> > 179.0 | 323.0
> >
> >
> >
> > 217.2 | 424.2
> >
> > Tree + Shrub + Grass + Bare ground + Seasonal water + Permanent water
> >
> >
> >
> > 760.5 | 1,498.4
> >
> >
> >
> > 172.3 | 363.2
> >
> >
> >
> > 216.8 | 439.9
> >
> >
> >
> >
> >
> >
> >
> >
> > Importantly, is there any literature I can cite on Deviance and its use?
> > If so, please supply a DOI.
> >
> > Regards/Groete,
> >
> > *Rion Lerm*
> >
> > SAEON Ndlovu
> >
> > C: 076 913 8381
> >
> > W: 013 735 3536
> >
> > SAEON / Scientific Services, Kruger National Park Gate, Phalaborwa,
> > South Africa
> >
> > South African Environmental Observation Network
> >
> > Website <https://ndlovu.saeon.ac.za/>& Location of our offices
> > <
> https://www.google.co.za/maps/place/SAEON+Ndlovu+Node/@-23.9447244,31.164957,18z/data=!4m5!3m4!1s0x1ec36ec96261cfb7:0xb89a27144ba0ca2a!8m2!3d-23.9450103!4d31.1652626
> >
> >
> >
> >
> > My research profiles:
> > *ResearchGate* <https://www.researchgate.net/profile/Rion-Lerm>
> > *ORCID <https://orcid.org/0000-0002-9992-2093>
> > *
> > *Google Scholar
> > <https://scholar.google.com/citations?user=JV5d7E4AAAAJ&hl=en>*
> >
> >
> > On Tue, 7 Mar 2023 at 16:32, Ben Bolker <bbolker using gmail.com
> > <mailto:bbolker using gmail.com>> wrote:
> >
> > The deviance is twice the negative log-likelihood; if the
> deviance
> > is D for a model with p parameters, then AIC = D + 2*p. The
> > deviance is
> > an *unpenalized* measure of goodness of fit (badness of fit actually
> -
> > lower deviance means better fit).
> >
> > There's no need to report deviance in a paper if it's not
> > useful to
> > you or your readers. The deviance for a model alone is not
> particularly
> > useful; you can use the deviances for several nested models to
> compute
> > likelihood ratio rests (via anova()), or you can use deviance as the
> > basis for computing AIC or BIC.
> >
> > Hope that helps.
> >
> > Ben Bolker
> >
> > On 2023-03-07 9:08 a.m., Rion Lerm via R-sig-mixed-models wrote:
> > > I reported, in a paper, on the *Deviance* value for model fit as
> > produced
> > > by the *glmmTMB* function.
> > >
> > > Please explain how this value is computed, and what are the
> > pros/cons of
> > > this compared to e.g., AIC. I need to comprehend its use and
> > explain the
> > > how and why? to a reviewer and possibly the paper's readers.
> > >
> > > Regards and thanks in advance,
> > >
> > > *Rion Lerm*
> > >
> > > SAEON Ndlovu
> > >
> > > C: 076 913 8381
> > >
> > > W: 013 735 3536
> > >
> > > SAEON / Scientific Services, Kruger National Park Gate,
> > Phalaborwa, South
> > > Africa
> > >
> > > South African Environmental Observation Network
> > >
> > > Website <https://ndlovu.saeon.ac.za/
> > <https://ndlovu.saeon.ac.za/>> & Location of our offices
> > >
> > <
> https://www.google.co.za/maps/place/SAEON+Ndlovu+Node/@-23.9447244,31.164957,18z/data=!4m5!3m4!1s0x1ec36ec96261cfb7:0xb89a27144ba0ca2a!8m2!3d-23.9450103!4d31.1652626
> <
> https://www.google.co.za/maps/place/SAEON+Ndlovu+Node/@-23.9447244,31.164957,18z/data=!4m5!3m4!1s0x1ec36ec96261cfb7:0xb89a27144ba0ca2a!8m2!3d-23.9450103!4d31.1652626
> >>
> > >
> > >
> > >
> > > My research profiles:
> > > *ResearchGate* <https://www.researchgate.net/profile/Rion-Lerm
> > <https://www.researchgate.net/profile/Rion-Lerm>>
> > >
> > > *ORCID <https://orcid.org/0000-0002-9992-2093
> > <https://orcid.org/0000-0002-9992-2093>>*
> > > *Google Scholar
> > > <https://scholar.google.com/citations?user=JV5d7E4AAAAJ&hl=en
> > <https://scholar.google.com/citations?user=JV5d7E4AAAAJ&hl=en>>*
> > >
> >
> > --
> > Dr. Benjamin Bolker
> > Professor, Mathematics & Statistics and Biology, McMaster University
> > Director, School of Computational Science and Engineering
> > (Acting) Graduate chair, Mathematics & Statistics
> > > E-mail is sent at my convenience; I don't expect replies outside
> of
> > working hours.
> >
> > _______________________________________________
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> >
> >
> > http://www.nrf.ac.za/email-legal-notice.php
> > <http://www.nrf.ac.za/email-legal-notice.php>
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> (Acting) Graduate chair, Mathematics & Statistics
> > E-mail is sent at my convenience; I don't expect replies outside of
> working hours.
>
--
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