How to modify slots lme4 >1.0

Question

I have been using the code below to successfully modify the \'Zt\', \'L\', and \'A\' slots of models fit using lme4 versions <1.0. I just updated to lme4 1.0-4 today and foun

Answer 1

Does this do what you want? (This follows ?modular pretty closely ...)

Create the Zl and ZZ matrices:

Zl <- lapply(c("pop1","pop2"),
         function(nm) Matrix:::fac2sparse(dat[[nm]], "d", drop=FALSE)) 
ZZ <- Reduce("+", Zl[-1], Zl[[1]]) 

Construct the random-effects data structures:

lf <- lFormula(Y ~ X + (1|pop1), data=dat)

Modify them:

lf$reTrms$Zt <- ZZ

Proceed through the remaining model-construction and fitting steps:

dfun <- do.call(mkLmerDevfun,lf)   ## create dev fun from modified lf
opt <- optimizeLmer(dfun)          ## fit the model
## make the results into a 'merMod' object
fit <- mkMerMod(environment(dfun), opt, lf$reTrms,
         fr = lf$fr)