Package: pbkrtest 0.5.6

pbkrtest: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models

Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see 'citation("pbkrtest")' for citation details.

Authors:Ulrich Halekoh [aut, cph], Søren Højsgaard [aut, cre, cph]

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pbkrtest.pdf |pbkrtest.html✨
pbkrtest/json (API)
NEWS

# Install 'pbkrtest' in R:
install.packages('pbkrtest', repos = c('https://hojsgaard.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hojsgaard/pbkrtest/issues

Datasets:

On CRAN:

Conda:

14.92 score 7 stars 1.0k packages 736 scripts 309k downloads 102 mentions 32 exports 73 dependencies

Last updated from:bb7c4f9a91. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTotal timeArtifact
linux-devel-x86_64ERROR174
source / vignettesOK263
linux-release-x86_64ERROR200
macos-devel-arm64ERROR111
macos-release-arm64ERROR127
windows-develERROR111
windows-releaseERROR129
windows-oldrelERROR130
wasm-releaseOK155

Exports:anovaxanovax_listcompare_column_spacecov_matrixcov_parddf_Lbfitted0get_Lb_ddfget_nested_model_infoget_SigmaGgetKRgetLRTgetSATglance.glsKRmodcompLb_ddfmake_model_matrixmake_restriction_matrixmodel2restriction_matrixpb_refdistpb_refdist_sequentialpb2_modcompPBmodcompPBrefdistresiduals0restriction_matrix2modelSATmodcompsimulate0summarize_pbvcovAdjvcovAdj.lmerModX2modcomp

Dependencies:backportsbootbroomclicodetoolscolorspacecowplotcpp11curlDerivdigestdoBydplyrfarverforecastfracdifffurrrfuturegenericsggplot2globalsgluegtableisobandjsonlitelabelinglatticelifecyclelistenvlme4lmtestmagrittrMASSMatrixmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivparallellypillarpkgconfigpurrrquadprogquantmodR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS7scalesstringistringrtibbletidyrtidyselecttimeDatetseriesTTRurcautf8vctrsviridisLitewithrxtszoo

01 - Introduction to 'pbkrtest'

Søren Højsgaard and Ulrich Halekoh

Rendered froma01-pbkrtest.rmdusingknitr::knitron Jan 31 2026.

Last update: 2025-07-28
Started: 2025-07-28

02 - Coercion between model objects and restriction matrices in 'pbkrtest'

Søren Højsgaard and Ulrich Halekoh

Rendered froma02-coercion.rmdusingknitr::knitron Jan 31 2026.

Last update: 2025-07-28
Started: 2025-07-28

Readme and manuals

Help Manual

Help pageTopics
anova like functionanovax anovax.default anovax.lmerMod print.anovax
Various different tests for model comparisonanovax_list
Coerce PBmodcomp objects to data framesas.data.frame.PBmodcomp as.data.frame.summary_PBmodcomp
Compare column spacescompare_column_space
Compute Marginal Covariance Matrix of the Responsecov_matrix cov_matrix.gls cov_matrix.lm cov_matrix.lme cov_matrix.lmerMod
Extract Variance and Correlation Parameters from Fitted Modelscov_par cov_par.gls cov_par.lm cov_par.lme cov_par.lmerMod
Sugar beets databeets data-beets
Budworm databudworm data-budworm
Return fitted valuesfitted0
Adjusted denominator degrees of freedom for linear estimate for linear mixed model.ddf_Lb get_ddf_Lb get_ddf_Lb.lmerMod get_Lb_ddf get_Lb_ddf.lmerMod Lb_ddf
Extract (or "get") components from a 'KRmodcomp' or 'SATmodcomp' object.getKR getSAT get_modcomp
Resolve Nested Model Representationget_nested_model_info
Likelihood Ratio Test Between Nested ModelsgetLRT
Glance method for nlme::gls objectsglance.gls
pbkrtest internalinternal-pbkrtest
F-test and degrees of freedom based on Kenward-Roger approximationKRmodcomp KRmodcomp.lmerMod KRmodcomp.mer KRmodcomp_internal kr__modcomp
Adjusted covariance matrix for linear mixed models according to Kenward and Rogerget_SigmaG get_SigmaG.lmerMod get_SigmaG.mer kr-vcovAdj LMM_Sigma_G vcovAdj vcovAdj.lmerMod vcovAdj.mer vcovAdj0 vcovAdj2 vcovAdj_internal
Conversion between a model object and a restriction matrixmake_model_matrix make_restriction_matrix model-coerce model2restriction_matrix restriction_matrix2model
Model comparison using parametric bootstrap methods.getLRT.mer PBmodcomp PBmodcomp.gls PBmodcomp.lm PBmodcomp.mer PBmodcomp.merMod pb__modcomp plot.XXmodcomp seqPBmodcomp
Parametric Bootstrap Reference Distributionpb_refdist pb_refdist_sequential
Calculate reference distribution using parametric bootstrappb-refdist PBrefdist PBrefdist.gls PBrefdist.lm PBrefdist.merMod
Parametric Bootstrap Model Comparisonpb2_modcomp
Refit nlme model with New Responserefit.gls refit.lm refit.lme
Residuals ignoring random effects (population-level residuals)residuals0
F-test and degrees of freedom based on Satterthwaite approximationSATmodcomp SATmodcomp.lmerMod sat__modcomp
Simulate Response Vectors from a Fitted Mixed Modelsimulate0
Summarize parametric bootstrap results for LRTsummarize_pb
Tidy method for nlme::gls objectstidy.gls
Chisq testX2modcomp X2modcomp.default x2__modcomp
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