PBmodcomp

0th

Percentile

Model comparison of mixed models using parametric bootstrap methods.

Model comparison of mixed models using parametric bootstrap methods.

Keywords
models, utilities, inference
Usage
PBmodcomp(largeModel, smallModel, nsim = 200, ref = NULL, cl = NULL, details = 0)
## S3 method for class 'mer':
PBmodcomp(largeModel, smallModel, nsim = 200, ref = NULL, cl = NULL, details = 0)
makePBcluster(n=2)
stopPBcluster()
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.
ref
Vector containing samples from the reference distribution. If NULL, this vector will be generated using PBrefdist().
cl
A vector identifying a cluster; used for calculating the reference distribution using several cores. See examples below.
n
Number of clusters to be used in computations; a typical choice of n would be the number of CPUs available.
details
The amount of output produced. Mainly relevant for debugging purposes.
Details

Under the fitted hypothesis (i.e. under the fitted small model) nsim samples of the likelihood ratio test statistic (LRT) are generetated. Then p-values are calculated as follows: LRT: Assuming that LRT has a chi-square distribution. PBtest: The fraction of simulated LRT-values that are larger or equal to the observed LRT value. Bartlett: A Bartlett correction is of LRT is calculated from the mean of the simulated LRT-values Gamma: The reference distribution of LRT is assumed to be a gamma distribution with mean and variance determined as the sample mean and sample variance of the simulated LRT-values.

Note

This functionality is not thoroughly tested and should be used with care. Please do report bugs etc.

See Also

KRmodcomp PBrefdist

Aliases
  • PBmodcomp
  • PBmodcomp.mer
  • makePBcluster
  • stopPBcluster
  • plot.XXmodcomp
Examples
data(beets)
head(beets)
beet0<-lmer(sugpct~block+sow+harvest+(1|block:harvest), data=beets, REML=FALSE)
beet_no.harv <- update(beet0, .~.-harvest)
PBmodcomp(beet0, beet_no.harv, nsim=20)

## Vanilla
PBmodcomp(beet0, beet_no.harv)
## Simulate reference distribution separately:
rr <- PBrefdist(beet0, beet_no.harv, nsim=20)
PBmodcomp(beet0, beet_no.harv, ref=rr)
Documentation reproduced from package pbkrtest, version 0.1.0, License: GPL (>= 2)

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