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 To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
-----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 * * [[alternative HTML version deleted]]
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