tests/glmerWarn.R

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

    ## [glmer(*, gaussian) warns to rather use lmer()]
    m3 <- suppressWarnings(glmer(Reaction ~ Days + (Days|Subject), sleepstudy))
    m4 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
    m5 <- suppressWarnings(glmer(Reaction ~ Days + (Days|Subject), sleepstudy,
                                 family=gaussian))
    expect_equal(fixef(m3),fixef(m5))
    ## hack call -- comes out unimportantly different
    m4@call[[1]] <- quote(lme4::lmer)
    expect_equal(m3,m4)
    expect_equal(m3,m5)

    ## would like m3==m5 != m4 ??
    V4 <- VarCorr(m4)
    V5 <- VarCorr(m5)
    expect_equal(V4, V5, tolerance = 1e-14)
    th4 <- getME(m4,"theta")
    expect_equal(th4, getME(m5,"theta"), tolerance = 1e-14)

    ## glmer() - poly() + interaction
    if (requireNamespace("mlmRev")) {
        data(Contraception, package="mlmRev")
        ## ch := with child
        Contraception <- within(Contraception, ch <- livch != "0")
        ## gmC1 <- glmer(use ~ poly(age,2) + ch + age:ch + urban + (1|district),
        ##               Contraception, binomial)
### not a 'warning' per se {cannot suppressWarnings(.)}:
###    fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
### also printed with print(): labeled as  "fit warnings"

        ## ==> from ../R/modular.R  chkRank.drop.cols()
        ## --> Use   control = glmerControl(check.rankX = "ignore+drop.cols"))
        ## because further investigation shows "the problem" is really already
        ##     in model.matrix():
        set.seed(101)
        dd <- data.frame(ch = c("Y","N")[1+rbinom(12, 1, 0.7)], age = rlnorm(12, 16))
        colnames(mm1 <- model.matrix( ~ poly(age,2) + ch + age:ch, dd))
        ## "(Int.)" "poly(age, 2)1" "poly(age, 2)2" "chY" "chN:age" "chY:age"      
        ## If we make the poly() columns to regular variables, can interact:
        d2 <- within(dd, { p2 <- poly(age,2); ageL <- p2[,1]; ageQ <- p2[,2]; rm(p2)})
        ## then, we can easily get what want
        (mm2 <- model.matrix( ~ ageL+ageQ + ch + ageL:ch, d2))
        ## actually even more compactly now ("drawback": 'ageQ' at end):
        (mm2. <- model.matrix( ~ ageL*ch + ageQ, d2))
        cn2 <- colnames(mm2)
        stopifnot(identical(mm2[,cn2], mm2.[,cn2]))
    }
} ## skip on windows (for speed)

Try the lme4 package in your browser

Any scripts or data that you put into this service are public.

lme4 documentation built on June 22, 2021, 9:07 a.m.