pb-refdist {pbkrtest}R Documentation

Calculate reference distribution using parametric bootstrap

Description

Calculate reference distribution of likelihood ratio statistic in mixed effects models using parametric bootstrap

Usage

PBrefdist(largeModel, smallModel, nsim = 1000, seed = NULL, cl = NULL,
  details = 0)

## S3 method for class 'lm'
PBrefdist(largeModel, smallModel, nsim = 1000, seed = NULL,
  cl = NULL, details = 0)

## S3 method for class 'merMod'
PBrefdist(largeModel, smallModel, nsim = 1000, seed = NULL,
  cl = NULL, details = 0)

## S3 method for class 'mer'
PBrefdist(largeModel, smallModel, nsim = 1000, seed = NULL,
  cl = NULL, details = 0)

Arguments

largeModel

A linear mixed effects model as fitted with the lmer() function in the lme4 package. This model muse be larger than smallModel (see below).

smallModel

A linear mixed effects model as fitted with the lmer() function in the lme4 package. This model muse be smaller than largeModel (see above).

nsim

The number of simulations to form the reference distribution.

seed

Seed for the random number generation.

cl

A vector identifying a cluster; used for calculating the reference distribution using several cores. See examples below.

details

The amount of output produced. Mainly relevant for debugging purposes.

Details

The model object must be fitted with maximum likelihood (i.e. with REML=FALSE). If the object is fitted with restricted maximum likelihood (i.e. with REML=TRUE) then the model is refitted with REML=FALSE before the p-values are calculated. Put differently, the user needs not worry about this issue.

Value

A numeric vector

Author(s)

Søren Højsgaard sorenh@math.aau.dk

References

Ulrich Halekoh, Søren Højsgaard (2014)., A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - The R Package pbkrtest., Journal of Statistical Software, 58(10), 1-30., http://www.jstatsoft.org/v59/i09/

See Also

PBmodcomp, KRmodcomp

Examples


data(beets)
head(beets)
beet0 <- lmer(sugpct ~ block + sow + harvest + (1|block : harvest), data=beets, REML=FALSE)
beet_no.harv <- update(beet0, .~.-harvest)
rr <- PBrefdist(beet0, beet_no.harv, nsim=20)
rr

## Note: Many more simulations must be made in practice.

## Computations can be made in parallel using several processors:
## Not run: 
cl <- makeSOCKcluster(rep("localhost", 4))
clusterEvalQ(cl, library(lme4))
clusterSetupSPRNG(cl)
rr <- PBrefdist(beet0, beet_no.harv, nsim=20)
stopCluster(cl)

## End(Not run)
## Above, 4 cpu's are used and 5 simulations are made on each cpu.
[Package pbkrtest version 0.4-7 Index]