tests/lme4_nlme.R

In lme4: Linear Mixed-Effects Models using 'Eigen' and S4

if (lme4:::testLevel() > 1 || .Platform$OS.type != "windows") withAutoprint({

    ## testing whether lme4 and nlme play nicely.  Only known issue
    ## is lmList-masking ...
    library("lme4")
    library("nlme")
    fm1_lmer <- lmer(Reaction ~ Days   +       (Days|Subject), sleepstudy)
    fm1_lme  <- lme (Reaction ~ Days, random = ~Days|Subject,  sleepstudy)
    ## variance-covariance matrices: annoyingly different structures
    vc_lmer <- VarCorr(fm1_lmer)
    vc_lme  <- VarCorr(fm1_lme, rdig = 8)
    suppressWarnings(storage.mode(vc_lme) <- "numeric")# 2 NAs
    vc_lmerx <- c(diag(vc_lmer[[1]]), attr(vc_lmer[[1]],"correlation")[1,2])
    vc_lmex  <- c( vc_lme[1:2,1],     vc_lme[2,3])
    stopifnot(
        all.equal(vc_lmex, vc_lmerx, tolerance= 4e-4) # had 3e-5, now see 0.000296
      , ## fixed effects (much easier) :
        all.equal(fixef(fm1_lmer), fixef(fm1_lme)) # 3.6e-15
       ,
        all.equal(unname(unlist(unclass(ranef(fm1_lmer)))),
                  unname(unlist(unclass(ranef(fm1_lme)))),
                  tolerance = 2e-4) # had 2e-5, now see 8.41e-5
    )

    fm1L_lme  <- nlme::lmList(distance ~ age | Subject, Orthodont)
    fm1L_lmer <- lme4::lmList(distance ~ age | Subject, Orthodont)
    stopifnot(all.equal(fixef(fm1L_lmer),
                        fixef(fm1L_lme)))
    sm1L_e  <- summary(fm1L_lme)
    sm1L_er <- summary(fm1L_lmer)
    stopifnot(
        all.equal(coef(sm1L_e),
                  coef(sm1L_er), tol=1e-12)# even tol=0 works on some Lnx 64b
    )

    ## FIXME: test opposite order
})