R version 4.4.0 beta (2024-04-14 r86421 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 + }) > > proc.time() user system elapsed 1.06 0.10 1.10