Re: [R] using lme4 with three nested random effects

From: ONKELINX, Thierry <Thierry.ONKELINX_at_inbo.be>
Date: Fri, 29 Apr 2011 08:52:10 +0000

Dear Ben,

Are site, transect and plot factors? And do they have unique id's?

You could try this

rws30.UL$site <- factor(rws30.UL$site)
rws30.UL$transect <- interaction(rws30.UL$site, rws30.UL$transect, drop = TRUE)
rws30.UL$plot <- interaction(rws30.UL$site, rws30.UL$transect, rws30.UL$plot, drop = TRUE)
modelincrBS<-glmer(l.ru.ba.incr~shigo.av+pre.f.crwn.length+bak.thick.bh+Date+slope.pos.num+dens.T+dbh+leaf.area+can.pos.num +(1|site/transect/plot),  data=rws30.UL, family=gaussian, na.action=na.omit)

Or

modelincrBS<-glmer(l.ru.ba.incr~shigo.av+pre.f.crwn.length+bak.thick.bh+Date+slope.pos.num+dens.T+dbh+leaf.area+can.pos.num +(1|site) + (1|transect) + (1|plot),  data=rws30.UL, family=gaussian, na.action=na.omit)

Best regards,

Thierry



ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
Thierry.Onkelinx_at_inbo.be
www.inbo.be

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~ Roger Brinner

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> -----Oorspronkelijk bericht-----
> Van: r-help-bounces@r-project.org
> [mailto:r-help-bounces_at_r-project.org] Namens Benjamin Caldwell
> Verzonden: vrijdag 29 april 2011 0:37
> Aan: r-help
> Onderwerp: [R] using lme4 with three nested random effects
>
> Hi all,
> I'm trying to fit models for data with three levels of nested random
> effects: site/transect/plot. For example,
>
> modelincrBS<-glmer(l.ru.ba.incr~shigo.av+pre.f.crwn.length+bar
> k.thick.bh+Date+slope.pos.num+dens.T+dbh+leaf.area+can.pos.num
> +(1|site/transect/plot),
> data=rws30.UL, family=gaussian, na.action=na.omit)
>
> but I get the following error:
>
> Error: length(f1) == length(f2) is not TRUE In addition:
> Warning messages:
> 1: In plot:(transect:site) :
> numerical expression has 92 elements: only the first used
> 2: In plot:(transect:site) :
> numerical expression has 92 elements: only the first used
>
> The formulation works for two nested effects (e.g. 1|site/transect)
>
> I can get it to run in lme
> modelincrBS<-lme(l.ru.ba.incr~shigo.av+pre.f.crwn.length+bark.
> thick.bh+Date+slope.pos.num+dens.T+dbh+leaf.area+can.pos.num,
> data=rws30.UL, random=(~1| site/transect/plot),na.action=na.omit)
>
> but I can't specify a distribution family in that package.
>
> Any help much appreciated.
>
> Ben Caldwell
>
> *
> *
>
> [[alternative HTML version deleted]]
>
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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. Received on Fri 29 Apr 2011 - 10:00:55 GMT

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