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Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison

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- beets.RData
- budworm.RData
- coercion.Rnw
- KR-vcovAdj0.R
- KR-vcovAdj15.R
- KR-vcovAdj16.R
- pbkrtest.Rnw
- CITATION
- WORDLIST
- anovax.Rd
- anovax_list.Rd
- as.data.frame.PBmodcomp.Rd
- compare_column_space.Rd
- compute_auxiliary.Rd
- cov_matrix.Rd
- cov_par.Rd
- data-beets.Rd
- data-budworm.Rd
- devfun_vp.Rd
- fitted0.Rd
- get_covbeta.Rd
- get_ddf_Lb.Rd
- get_Fstat_ddf.Rd
- get_modcomp.Rd
- get_nested_model_info.Rd
- getLRT.Rd
- glance.gls.Rd
- internal-pbkrtest.Rd
- kr-vcovAdj.Rd
- kr__modcomp.Rd
- model-coerce.Rd
- pb-refdist.Rd
- pb2_modcomp.Rd
- pb__modcomp.Rd
- pb_refdist.Rd
- refit.Rd
- residuals0.Rd
- sat__modcomp.Rd
- simulate0.Rd
- summarize_pb.Rd
- tidy.gls.Rd
- x2__modcomp.Rd
- anovax.R
- DATA_pbkrtest.R
- get_info_functions.R
- init_modcomp.R
- KR_modcomp.R
- KR_Sigma_G2.R
- KR_utils.R
- KR_vcovAdj.R
- linear_algebra.R
- model_coerce.R
- NAMESPACE_pbkrtest.R
- nested_model_info.R
- nlme_lme4_extension.R
- nlme_lme4_extension.R~
- PB_modcomp.R
- PB_refdist.R
- pbkr_cov_matrix_cov_par.R
- pbkr_cov_matrix_cov_par.R~
- pbkr_extension.R
- pbkr_pb_modcomp.R
- pbkr_pb_modcomp.R~
- pbkr_refdist.R
- pbkr_refdist.R~
- pbkr_refit.R
- pbkr_simulate.R
- pbkr_utilities.R
- pbkr_utilities.R~
- SAT_modcomp.R
- tidy_gls.R
- X2_modcomp.R
- xx_modcomp_new.R
- - unnamed-chunk-2-1.png
  - unnamed-chunk-2-2.png
  - unnamed-chunk-2-3.png
- - pbkrunnamed-chunk-5-1.pdf
  - pbkrunnamed-chunk-6-1.pdf
- a01-pbkrtest.rmd
- a02-coercion.rmd
.gitignore
.Rbuildignore
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_pkgdown.yml
ChangeLog
cran-comments.md
CRAN-SUBMISSION
DESCRIPTION
LICENSE
NAMESPACE
NEWS
README.html
README.md
README.Rmd

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The `pbkrtest` package: Parametric Bootstrap, Kenward-Roger and
Satterthwaite Based Methods for Tests in Mixed Models
================

## What does `pbkrtest` do for you?

Hypothesis test of fixed effects in mixed models (also called random
effects models, hierarchical models etc) is most commonly based on large
sample asymptotics: When the amount of information becomes large, a test
can be based an a
![\\chi^2](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%5Cchi%5E2
"\\chi^2")-approximation. In small sample cases, this approximation can
be very unreliable. The `pbkrtest` provides alternatives to this
approximation. To be specific: For linear mixed models (as implemented
in the `lme4` package), `pbkrtest` implements the following tests for
fixed effects:

1.  a parametric bootstrap test,
2.  a Kenward-Roger-type F-test and
3.  a Satterthwaite-type F-test.

Moreover, for generalized linear mixed models (as implemented in `lme4`)
and for generalized linear models, `pbkrtest` also implements a
parametric bootstrap test

## Documentation

The facilities of the package are documented in the paper by \[Halekoh
and Højsgaard 2014)\]
(<https://www.jstatsoft.org/htaccess.php?volume=059&type=i&issue=09&filename=paper>)
Please see `citation("pbkrtest")` for information about citing the paper
and the package. If you use the package in your work, please do cite
this paper. Please notice: There are other packages that use `pbkrtest`
under the hood. If you use one of those packages, please do also cite
our paper.

We also refer to the [Webpage for the
package](https://people.math.aau.dk/~sorenh/software/pbkrtest/index.html)

## Online documentation

See <https://hojsgaard.github.io/pbkrtest/>.

## Installation

`pbkrtest` is available on CRAN and development versions can also be
found on Github:

## Install from CRAN:
    install.packages('pbkrtest')
    ## Install from Github: Use the remotes package:
    remotes::install_github("hojsgaard/pbkrtest", build_vignettes = TRUE)

## Development site

See <https://github.com/hojsgaard/pbkrtest>.

## Brief introduction

``` r
library(pbkrtest)
library(ggplot2)

## Sugar beets: Does suger content depend on harvest time?

beets |> ggplot(aes(x=sow, y=sugpct, group=harvest)) +
    geom_jitter(aes(color=harvest), width=0)
```

![](https://raw.githubusercontent.com/hojsgaard/pbkrtest/master/README_files/figure-gfm/unnamed-chunk-2-1.png)

``` r

fm0 <- lmer(sugpct ~ block + sow + harvest + (1|block:harvest), data=beets)
fm1 <- update(fm0, .~. -harvest)

## Is there an effect of harvest time?
an <- anova(fm0, fm1)
pb <- PBmodcomp(fm0, fm1)
kr <- KRmodcomp(fm0, fm1)
sa <- SATmodcomp(fm0, fm1)

tidy(an)
#> # A tibble: 2 × 9
#>   term   npar   AIC   BIC logLik deviance statistic    df   p.value
#>   <chr> <dbl> <dbl> <dbl>  <dbl>    <dbl>     <dbl> <dbl>     <dbl>
#> 1 fm1       9 -69.1 -56.5   43.5    -87.1      NA      NA NA       
#> 2 fm0      10 -80.0 -66.0   50.0   -100.       12.9     1  0.000326
tidy(pb)
#> # A tibble: 2 × 4
#>   type    stat    df  p.value
#>   <chr>  <dbl> <dbl>    <dbl>
#> 1 LRT     12.9     1 0.000326
#> 2 PBtest  12.9    NA 0.0300
tidy(kr)
#> # A tibble: 1 × 6
#>   type   stat   ndf   ddf F.scaling p.value
#>   <chr> <dbl> <int> <dbl>     <dbl>   <dbl>
#> 1 Ftest  15.2     1  2.00         1  0.0599
tidy(sa)
#> # A tibble: 1 × 5
#>   type  statistic   ndf   ddf p.value
#>   <chr>     <dbl> <int> <dbl>   <dbl>
#> 1 Ftest      15.2     1  2.00  0.0599
```

Please find more examples in the other vignettes available at
<https://hojsgaard.github.io/pbkrtest/>.

pbkrtest

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