tests/HSAURtrees.R

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

if (.Platform$OS.type != "windows") withAutoprint({
    library("lme4")

    ## example from HSAUR2 package; data from 'multcomp'; see ../inst/testdata/trees513.R
    load(system.file("testdata","trees513.RData",package="lme4"))

    ## model formula:
    modForm <- damage ~ species - 1 + (1 | lattice / plot)

    dfun <- glmer(modForm, data = trees513B, family = binomial,
                  devFunOnly = TRUE)
    ls.str(environment(dfun))# "for your information"

    .not.call <- function(x) x[names(x) != "call"]

    if(lme4:::testLevel() < 2) q("no")
    ## else  (testLevel >= 2) : --------------------------------------------------

    ## Generate oldres:
    ## ----------------
    ## library(lme4.0)
    ## system.time(mmod0 <- glmer(damage ~ species - 1 + (1 | lattice / plot),
    ##               data = trees513, family = binomial()))
    ## ## 4 seconds
    ## oldres <- c(fixef(mmod0),getME(mmod0,"theta"))
    ## detach("package:lme4.0")
    ## dput(oldres)
    oldres <- structure(c(5.23645064474105, 4.73568475545248, 2.65289926317093,
                          1.29043984816924, 1.59329381563025,
                          0.532663142106669, 1.16703186884403
                          ), .Names = c("speciesspruce", "speciespine",
                                        "speciesbeech",
                                        "speciesoak", "specieshardwood",
                                        "plot:lattice.(Intercept)",
                                        "lattice.(Intercept)"))
    system.time(mmodA <- glmer(modForm, data = trees513A, family = binomial()))
    ## 7 seconds
    newres <- c(fixef(mmodA), getME(mmodA,"theta"))
    stopifnot(all.equal(oldres, newres, tolerance=1.5e-3))
    system.time(mmodB <- glmer(modForm, data = trees513B, family = binomial()))
    ## 10.4 seconds
    ##
    if(FALSE) { ## defuncted in 2019-05 [been deprecated since 2013-06]
        ## lmer( + family) -> diverts to glmer() with a warning [TODO: use assertWarning(.) eventually]
        system.time(lmodB <-
                        lmer(modForm, data = trees513B, family = binomial()))
        stopifnot(all.equal(.not.call(summary(mmodB)),
                            .not.call(summary(lmodB))))
        newresB <- c(fixef(mmodB),getME(mmodB,"theta"))
        stopifnot(length(newresB) == length(oldres) + 1)# extra: species[ash/maple/elm/lime]
    }


}) ## skip on windows (for speed)