lme4: drop1.merMod – R documentation

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drop1.merMod

Drop all possible single fixed-effect terms from a mixed effect model

Description

Drop allowable single terms from the model: see drop1 for details of how the appropriate scope for dropping terms is determined.

Usage

## S3 method for class 'merMod'
drop1(object, scope, scale = 0,
      test = c("none", "Chisq", "user"),
      k = 2, trace = FALSE, sumFun, ...)

Arguments

`object`	a fitted `merMod` object.
`scope`	a formula giving the terms to be considered for adding or dropping.
`scale`	Currently ignored (included for S3 method compatibility)
`test`	should the results include a test statistic relative to the original model? The Chisq test is a likelihood-ratio test, which is approximate due to finite-size effects.
`k`	the penalty constant in AIC
`trace`	print tracing information?
`sumFun`	a summary `function` to be used when `test=="user"`. It must allow arguments `scale` and `k`, but these may be ignored (e.g. swallowed by `...`, see the examples). The first two arguments must be `object`, the full model fit, and `objectDrop`, a reduced model. If `objectDrop` is missing, `sumFun(*)` should return a vector with the appropriate length and names (the actual contents are ignored).
`...`	other arguments (ignored)

Details

drop1 relies on being able to find the appropriate information within the environment of the formula of the original model. If the formula is created in an environment that does not contain the data, or other variables passed to the original model (for example, if a separate function is called to define the formula), then drop1 will fail. A workaround (see example below) is to manually specify an appropriate environment for the formula.

Value

An object of class anova summarizing the differences in fit between the models.

Examples

fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
## likelihood ratio tests
drop1(fm1,test="Chisq")
## use Kenward-Roger corrected F test, or parametric bootstrap,
## to test the significance of each dropped predictor
if (require(pbkrtest) && packageVersion("pbkrtest")>="0.3.8") {
   KRSumFun <- function(object, objectDrop, ...) {
      krnames <- c("ndf","ddf","Fstat","p.value","F.scaling")
      r <- if (missing(objectDrop)) {
          setNames(rep(NA,length(krnames)),krnames)
      } else {
         krtest <- KRmodcomp(object,objectDrop)
         unlist(krtest$stats[krnames])
      }
      attr(r,"method") <- c("Kenward-Roger via pbkrtest package")
      r
   }
   drop1(fm1, test="user", sumFun=KRSumFun)

   if(lme4:::testLevel() >= 3) { ## takes about 16 sec
     nsim <- 100
     PBSumFun <- function(object, objectDrop, ...) {
	pbnames <- c("stat","p.value")
	r <- if (missing(objectDrop)) {
	    setNames(rep(NA,length(pbnames)),pbnames)
	} else {
	   pbtest <- PBmodcomp(object,objectDrop,nsim=nsim)
	   unlist(pbtest$test[2,pbnames])
	}
	attr(r,"method") <- c("Parametric bootstrap via pbkrtest package")
	r
     }
     system.time(drop1(fm1, test="user", sumFun=PBSumFun))
   }
}
## workaround for creating a formula in a separate environment
createFormula <- function(resp, fixed, rand) {  
    f <- reformulate(c(fixed,rand),response=resp)
    ## use the parent (createModel) environment, not the
    ## environment of this function (which does not contain 'data')
    environment(f) <- parent.frame()
    f
}
createModel <- function(data) {
    mf.final <- createFormula("Reaction", "Days", "(Days|Subject)")
    lmer(mf.final, data=data)
}
drop1(createModel(data=sleepstudy))

lme4

Linear Mixed-Effects Models using 'Eigen' and S4

v1.1-26

GPL (>= 2)

Authors

Douglas Bates [aut] (<https://orcid.org/0000-0001-8316-9503>), Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>), Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), Steven Walker [aut] (<https://orcid.org/0000-0002-4394-9078>), Rune Haubo Bojesen Christensen [ctb] (<https://orcid.org/0000-0002-4494-3399>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Bin Dai [ctb], Fabian Scheipl [ctb] (<https://orcid.org/0000-0001-8172-3603>), Gabor Grothendieck [ctb], Peter Green [ctb] (<https://orcid.org/0000-0002-0238-9852>), John Fox [ctb], Alexander Bauer [ctb], Pavel N. Krivitsky [ctb, cph] (<https://orcid.org/0000-0002-9101-3362>, shared copyright on simulate.formula)

Initial release