tests/modFormula.R

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

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

    .get.checkingOpts <- lme4:::.get.checkingOpts
    stopifnot(identical(
        .get.checkingOpts(
            c("CheckMe", "check.foo", "check.conv.1", "check.rankZ", "check.rankX"))
      , c("check.foo", "check.rankZ")))

    lmod <- lFormula(Reaction ~ Days + (Days|Subject), sleepstudy)
    devfun <- do.call(mkLmerDevfun, lmod)
    opt <- optimizeLmer(devfun)
    cc <- lme4:::checkConv(attr(opt,"derivs"), opt$par, ctrl = lmerControl()$checkConv,
                           lbound=environment(devfun)$lower)
    fm1 <- mkMerMod(environment(devfun), opt, lmod$reTrms, fr = lmod$fr,
                    lme4conv=cc)
    fm2 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)

    ## basic equivalence
    fm1C <- fm1
    fm1C@call <- fm2@call
    expect_equal(fm2,fm1C)
    expect_equal(range(residuals(fm1)), c(-101.18, 132.547), tolerance = 1e-5) # these are "outliers"!
    expect_is(model.frame(fm1),"data.frame")
    ## formulae
    mfm1 <- model.frame(fm1)
    expect_equal(formula(fm1),         Reaction ~ Days + (Days | Subject))
    expect_equal(formula(terms(mfm1)), Reaction ~ Days + (Days + Subject))
    new_form_modframe <- (getRversion() >= "3.6.0" &&
                          as.numeric(version[["svn rev"]]) >= 75891)
    expect_equal(formula(mfm1),
                 if(new_form_modframe) {
                     Reaction ~ Days + (Days + Subject)
                 } else
                     Reaction ~ Days + Subject
                 )
    ## predictions
    expect_equal(predict(fm1,newdata=sleepstudy[1:10,],re.form=NULL),
                 predict(fm2,newdata=sleepstudy[1:10,],re.form=NULL))
    expect_equal(predict(fm1,newdata=sleepstudy),
                 predict(fm1))

    lmodOff <- lFormula(Reaction ~ Days + (Days|Subject) + offset(0.5*Days),
                        sleepstudy)
    devfunOff <- do.call(mkLmerDevfun, lmodOff)
    opt <- optimizeLmer(devfunOff)
    fm1Off <- mkMerMod(environment(devfunOff), opt, lmodOff$reTrms, fr = lmodOff$fr)
    fm2Off <- lmer(Reaction ~ Days + (Days|Subject) + offset(0.5*Days), sleepstudy)
    expect_equal(predict(fm1Off,newdata=sleepstudy[1:10,],re.form=NULL),
                 predict(fm2Off,newdata=sleepstudy[1:10,],re.form=NULL))

    ## FIXME: need more torture tests with offset specified, in different environments ...

    ## FIXME: drop1(.) doesn't work with modular objects ... hard to see how it
    ##  could, though ...
    ## drop1(fm1Off)
    drop1(fm2Off)

} ## skip on windows (for speed)