I don't think the %in% works at all. It's non-standard and I think an incorrect model specification. Here is an example where we can see that the transpose of the model matrix for the random effects is different when we compare what would be the same model if it "worked".
I don't think there is an extractor function so I pull out the slot directly. There is some "danger" in this because extractor functions should be used rather than directly accessing the slots, but I think it works OK. library(lme4) data(egsingle, package='mlmRev') fm1 <- lmer(math ~ 1 + (1|schoolid/childid), egsingle, control = list(grad = 0, nit = 0, msV = 1)) fm2 <- lmer(math ~ 1 + (1|childid%in%schoolid), egsingle, control = list(grad = 0, nit = 0, msV = 1)) z1 <- [EMAIL PROTECTED] z2 <- [EMAIL PROTECTED] identical(z1,z2) [1] FALSE fm1 is the correct specification as it properly denotes that children are nested in schools. When we compare the model matrices, we can see that they are not identical; hence the model specification is not the same. I have no clue what %in% does and am not sure it even works with lmer, but could be wrong. Note in this case fm3 <- lmer(math ~ 1 + (1|schoolid) + (1|childid), egsingle, control = list(grad = 0, nit = 0, msV = 1)) z3 <- [EMAIL PROTECTED] identical(z1,z3) [1] TRUE Is exactly the same as fm1 because the IDs are always nested. Harold > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Mark Difford > Sent: Saturday, August 09, 2008 8:32 AM > To: r-help@r-project.org > Subject: Re: [R] [lme4]Coef output with binomial lmer > > > Hi Tom, > > >> 1|ass%in%pop%in%fam > > This is "non-standard," but as you have found, it works. The > correct translation is in fact > > 1|fam/pop/ass > > and not 1|ass/pop/fam as suggested by Harold Doran. Dropping > %, ass%in%pop%in%fam reads [means] as: nest ass in pop [= > pop/ass], and then nest this in fam == fam/pop/ass > > HTH, Mark. > > > T.C. Cameron wrote: > > > > Dear R users > > > > I have built the following model > > > > m1<-lmer(y~harn+foodn+(1|ass%in%pop%in%fam),family = > "quasibinomial") > > > > where y<-cbind(alive,dead) > > > > where harn and foodn are categorical factors and the random > effect is > > a nested term to represent experimental structure e.g. > > Day/Block/Replicate ass= 5 level factor, pop= 2 populations per > > treatment factor in each assay, 7 reps per population > > > > The model can be family = quasibinomial or binomial > > > > My complete lack of understanding is in retrieving the coefficients > > for the fixed effects to back-transform the effects of my > factors on > > proportional survival > > > > I get the following output: > >> coef(m1) > > $`ass %in% pop %in% fam` > > (Intercept) harn1 harn2 foodn2 > > FALSE 1.0322375 -0.1939521 0.0310434 0.810084 > > TRUE 0.5997679 -0.1939521 0.0310434 0.810084 > > > > Where FALSE and TRUE refer to some attribute of the random effect > > > > My hunch is that it refers to the Coefficients with (=TRUE) and > > without > > (=FALSE) the random effects? > > > > Any help appreciated > > > > > > > .............................................................. > .......... > > ............ > > Dr Tom C Cameron > > Genetics, Ecology and Evolution > > IICB, University of Leeds > > Leeds, UK > > Office: +44 (0)113 343 2837 > > Lab: +44 (0)113 343 2854 > > Fax: +44 (0)113 343 2835 > > > > > > Email: [EMAIL PROTECTED] > > Webpage: click here > > <http://www.fbs.leeds.ac.uk/staff/profile.php?tag=Cameron_TC> > > > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > 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. > > > > > > -- > View this message in context: > http://www.nabble.com/-lme4-Coef-output-with-binomial-lmer-tp1 > 8894407p18904468.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help@r-project.org mailing list > 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. > ______________________________________________ R-help@r-project.org mailing list 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.
