[R-sig-ME] Question on random effect

Tue Jul 11 14:53:21 CEST 2017

Thankyou very much Steven! this is great help.
Cheers,
Joaquín.

2017-07-11 9:47 GMT-03:00 Steven J. Pierce <pierces1 at msu.edu>:

> Joaquín,
>
> There are a very large number of R2 formulas for mixed models, but they
> are not all doing the same thing and do not always agree. Be prepared to
> defend any choice you make. Here are some references.
>
> Edwards, L. J., Muller, K. E., Wolfinger, R. D., Qaqish, B. F., &
> Schabenberger, O. (2008). An R2 statistic for fixed effects in the linear
> mixed model. Statistics in Medicine, 27(29), 6137-6157. doi:10.1002/sim.3429
>
> Jaeger, B. C., Edwards, L. J., Das, K., & Sen, P. K. (2017). An R2
> statistic for fixed effects in the generalized linear mixed model. Journal
> of Applied Statistics, 44(6), 1086-1105. doi:10.1080/02664763.02662016.
> 01193725
>
> Johnson, P. C. D. (2014). Extension of Nakagawa & Schielzeth's R2 GLMM to
> random slopes models. Methods in Ecology and Evolution, 5(9), 944-946.
> doi:10.1111/2041-210X.12225
>
> Kramer, M. (2005). R2 statistics for mixed models. Proceedings of the
> Conference on Applied Statistics in Agriculture, 17, 148-160. Retrieved
> from https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ars.
> usda.gov_sp2UserFiles_ad-5Fhoc_12000000SpatialWorkshop_
> 19KramerSupplRsq.pdf&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=oWPX5qlfffXiVV_
> GUw6XfiFzgvZaW1Z21RgAeOJfW1A&m=Uc04YW3KXsYZCbVsPoWqHdWzhNglmq
> 0ndvtDjCKLF9I&s=6qqs7Vr-WbE2YW1X6OE7_35mJ09siJR077ygMnE2hr0&e=
>
> LaHuis, D. M., Hartman, M. J., Hakoyama, S., & Clark, P. C. (2014).
> Explained variance measures for multilevel models. Organizational Research
> Methods, 17(4), 433-451. doi:10.1177/1094428114541701
>
> Liu, H., Zheng, Y., & Shen, J. (2008). Goodness-of-fit measures of R2 for
> repeated measures mixed effect models. Journal of Applied Statistics, 35,
> 1081–1092.
>
> Nakagawa, S., & Schielzeth, H. (2013). A general and simple method for
> obtaining R2 from generalized linear mixed-effects models. Methods in
> Ecology and Evolution, 4(2), 133-142. doi:10.1111/j.2041-210x.2012.00261.x
>
> Nakagawa, S., & Schielzeth, H. (2016). Extending R2 and intra-class
> correlation coefficient from generalized linear mixed-effects models:
> capturing and characterizing biological variation. bioRxiv.
> doi:10.1101/095851
>
> Orelien, J. G., & Edwards, L. J. (2008). Fixed-effect variable selection
> in linear mixed models using R2 statistics. Computational Statistics & Data
> Analysis, 52(4), 1896-1907. doi:10.1016/j.csda.2007.06.006
>
> Roberts, J. K., Monaco, J. P., Stovall, H., & Foster, V. (2011). Explained
> variance in multilevel models. In J. J. Hox & J. K. Roberts (Eds.),
> Handbook of advanced multilevel analysis (pp. 219-230). New York, NY:
> Routledge.
>
> Snijders, T. A. B., & Bosker, R. J. (2012). Multilevel analysis: An
> introduction to basic and advanced multilevel modeling (2nd ed.). London,
> UK: Sage.
>
> Xu, R. (2003). Measuring explained variation in linear mixed effects
> models. Statistics in Medicine, 22(22), 3527-3541. doi:10.1002/sim.1572
>
> Steven J. Pierce
> E-mail: pierces1 at msu.edu
>
>
>
>
> -----Original Message-----
> From: Joaquín Aldabe [mailto:joaquin.aldabe at gmail.com]
> Sent: Tuesday, July 11, 2017 7:28 AM
> To: Ben Bolker <bbolker at gmail.com>
> Cc: r-sig-mixed-models <r-sig-mixed-models at r-project.org>
> Subject: Re: [R-sig-ME] Question on random effect
>
> Thank you Ben. Another question: is there any kind of R2 in mixed models
> that allow me to estimate the explanatory power of the model?
> Thanks again. Joaquin
>
> 2017-07-11 8:22 GMT-03:00 Ben Bolker <bbolker at gmail.com>:
>
> > Yes, the assumption is that the random effects are (conditionally)
> > independent.  It can help to specify covariates  (such as
> > latitude/longitude or eastings/northings, or environmental conditions
> > [temperature, elevation, etc.]) for sites to mop up some of the
> > independence. It is theoretically possible, although I don't know of
> > an easy off-the-shelf way to do it, to impose (e.g.) spatial
> > correlation structures at the level of the random effects ...  or you
> > could examine the spatial dependence of the conditional modes/random
> > effects and try to convince yourself it was weak ...
> >
> > On Tue, Jul 11, 2017 at 7:14 AM, Joaquín Aldabe
> > <joaquin.aldabe at gmail.com> wrote:
> > > Hi all, when working with mixed models, do the levels of the random
> > effect
> > > have to be independent? For example, if my random effect is the
> identity
> > of
> > > sites and it is associated to the intercept, do sites have to be
> > > independent?
> > >
> > > I appreciate comments and bibliographic references.
> > >
> > > Thank you very much in advanced,
> > >
> > > Joaquin
> > >
> > > --
> > > *Joaquín Aldabe*
> > >
> > > *Grupo Biodiversidad, Ambiente y Sociedad*
> > > Centro Universitario de la Región Este, Universidad de la República
> > > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> > >
> > > *Departamento de Conservación*
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> > > BirdLife International
> > > Canelones 1164, Montevideo
> > >
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> 0JOu7EX0JXpv1RAD47-Ko&e=>
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> > >
> > >
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>
>
> --
> *Joaquín Aldabe*
>
> *Grupo Biodiversidad, Ambiente y Sociedad*
> Centro Universitario de la Región Este, Universidad de la República
> Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
>
> *Departamento de Conservación*
> Aves Uruguay
> BirdLife International
> Canelones 1164, Montevideo
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.
> google.com_site_joaquin.aldabe&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=
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>         [[alternative HTML version deleted]]
>
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>
>

-- 
*Joaquín Aldabe*

*Grupo Biodiversidad, Ambiente y Sociedad*
Centro Universitario de la Región Este, Universidad de la República
Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha

*Departamento de Conservación*
Aves Uruguay
BirdLife International
Canelones 1164, Montevideo

https://sites.google.com/site/joaquin.aldabe
<https://sites.google.com/site/perfilprofesionaljoaquinaldabe>

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