Package: pbkrtest 0.5.3
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:
pbkrtest_0.5.3.tar.gz
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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
Last updated 3 days agofrom:c3dab6ff2c. Checks:1 OK, 7 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 29 2025 |
| R-4.5-win | WARNING | Jan 29 2025 |
| R-4.5-mac | WARNING | Jan 29 2025 |
| R-4.5-linux | WARNING | Jan 29 2025 |
| R-4.4-win | WARNING | Jan 29 2025 |
| R-4.4-mac | WARNING | Jan 29 2025 |
| R-4.3-win | WARNING | Jan 29 2025 |
| R-4.3-mac | WARNING | Jan 29 2025 |
Exports:compare_column_spaceddf_Lbfanovafmodcompget_Lb_ddfget_SigmaGget_varygetLRTgls_cov_matrixgls_varcorrKRmodcompLb_ddfmake_model_matrixmake_restriction_matrixmodel2restriction_matrixPBFmodcompPBmodcompPBrefdistrefit_glsrestriction_matrix2modelSATmodcompseqPBmodcomptidyvcovAdjvcovAdj.lmerModX2modcomp
Dependencies:backportsbootbroomclicolorspacecowplotcpp11DerivdoBydplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnumDerivpillarpkgconfigpurrrR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
01 - Introduction to 'pbkrtest'
Rendered froma01-pbkrtest.rmdusingknitr::knitron Jan 29 2025.Last update: 2024-12-12
Started: 2022-11-28
02 - Coercion between model objects and restriction matrices in 'pbkrtest'
Rendered froma02-coercion.rmdusingknitr::knitron Jan 29 2025.Last update: 2024-11-25
Started: 2022-11-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare column spaces | compare_column_space |
| Sugar beets data | beets data-beets |
| Budworm data | budworm data-budworm |
| anova like function | fanova fanova.gls fanova.lm fanova.lmerMod print.fanova |
| Model comparison | fmodcomp fmodcomp.gls fmodcomp.lm fmodcomp.lmerMod |
| 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 |
| Get variance covariance matrix for lmerMod and gls | get_vary |
| Returns covariance matrix for gls model | gls_cov_matrix |
| Variance and correlation parameters from gls object | gls_varcorr |
| Internal functions for the pbkrtest package | as.data.frame.XXmodcomp internal KRmodcomp_init KRmodcomp_init.lmerMod KRmodcomp_init.mer plot.PBmodcomp print.KRmodcomp print.PBmodcomp print.summary_PBmodcomp summary.KRmodcomp summary.PBmodcomp tidy |
| pbkrtest internal | internal-pbkrtest |
| F-test and degrees of freedom based on Kenward-Roger approximation | KRmodcomp KRmodcomp.gls KRmodcomp.lmerMod KRmodcomp.mer KRmodcomp_internal kr_modcomp |
| Adjusted covariance matrix for linear mixed models according to Kenward and Roger | get_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 matrix | make_model_matrix make_restriction_matrix model-coerce model2restriction_matrix restriction_matrix2model |
| Model comparison using parametric bootstrap methods. | getLRT getLRT.lm getLRT.mer getLRT.merMod PBFmodcomp PBmodcomp PBmodcomp.gls PBmodcomp.lm PBmodcomp.mer PBmodcomp.merMod pb_modcomp plot.XXmodcomp seqPBmodcomp |
| Calculate reference distribution using parametric bootstrap | pb-refdist PBrefdist PBrefdist.gls PBrefdist.lm PBrefdist.lme PBrefdist.merMod |
| Refit a gls object to new response variable | refit_gls |
| F-test and degrees of freedom based on Satterthwaite approximation | SATmodcomp SATmodcomp.gls SATmodcomp.lmerMod sat_modcomp |
| Simulate data for 'gls' object | simulate.gls |
| Chisq test | KRmodcomp KRmodcomp.lmerMod KRmodcomp.mer KRmodcomp_internal X2modcomp X2modcomp.gls X2modcomp.lmerMod x2_modcomp |
