using lme4 with three nested random effects

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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~ Sir Ronald Aylmer Fisher

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~ Roger Brinner

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-----Oorspronkelijk bericht-----
Van: r-help-bounces at 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

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