version 0.5.2

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: pbkrtest
-Version: 0.5.1
+Version: 0.5.2
 Title: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
         Methods for Test in Mixed Models
 Authors@R: c(
@@ -9,31 +9,28 @@ Authors@R: c(
         email = "sorenh@math.aau.dk", role = c("aut", "cre", "cph"))
   )
 Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
-Description: Test in mixed effects models. Attention is on mixed
-    effects models as implemented in the 'lme4' package. For linear
-    mixed models, this package implements (1) a parametric bootstrap
-    test, (2) a Kenward-Roger-typ modification of F-tests for linear
-    mixed effects models and (3) a Satterthwaite-type modification of
-    F-tests for linear mixed effects models. The package also
-    implements a parametric bootstrap test for generalized linear
-    mixed models.  The facilities of the package are documented in the
-    paper by Halehoh and Højsgaard, (2012,
-    <doi:10.18637/jss.v059.i09>).  Please see 'citation("pbkrtest")'
-    for citation details.
+Description: 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.
 URL: https://people.math.aau.dk/~sorenh/software/pbkrtest/
-Depends: R (>= 3.5.0), lme4 (>= 1.1.10)
-Imports: broom, dplyr, magrittr, MASS, Matrix (>= 1.2.3), methods,
-        numDeriv, parallel, knitr
+Depends: R (>= 4.1.0), lme4 (>= 1.1.31)
+Imports: broom, dplyr, MASS, Matrix (>= 1.2.3), methods, numDeriv,
+        parallel
+Suggests: knitr
 Encoding: UTF-8
-ZipData: no
+VignetteBuilder: knitr
 License: GPL (>= 2)
 ByteCompile: Yes
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 LazyData: true
-VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2021-03-09 07:41:11 UTC; sorenh
+Packaged: 2023-01-19 07:09:26 UTC; sorenh
 Author: Ulrich Halekoh [aut, cph],
   Søren Højsgaard [aut, cre, cph]
 Repository: CRAN
-Date/Publication: 2021-03-09 09:50:08 UTC
+Date/Publication: 2023-01-19 18:00:10 UTC

MD5

@@ -1,50 +1,53 @@
 3279c01f6caf536d363ded574523fef7 *ChangeLog
-76bdb6ee388fe2d650941eb138b76263 *DESCRIPTION
-6c9c5588ac5473db103c8de04338c904 *NAMESPACE
-573e765dbaf9b92e72c2167fb561d8a2 *NEWS
-015d4f88f384871659053b52d378b962 *R/KR-Sigma-G2.R
+553b180594e4725165bb4fbc3e30e87e *DESCRIPTION
+1f40bf9b45d5cf74f3d04c008bf37575 *NAMESPACE
+be5fdb17f326d444ad4592b54916c6ce *NEWS
+0b7b5f834a5bda641fe0b55a08356513 *R/KR-Sigma-G2.R
 7f17aca2b6550f68b23c2faff800c3f8 *R/KR-across-versions.R
-4babf9bf83a39ae02f42fb49d9f3c0dc *R/KR-modcomp.R
-e7f296cc5ecdbcbf583f9cea74b6245a *R/KR-utils.R
-9cf9db472f6f3a5799e67439b3808d0e *R/KR-vcovAdj.R
-2811cf1b83de66252b5ef6411c6f8b42 *R/NAMESPACE.R
-5fb3a6458ff6279a9e32dc6909d3cf58 *R/PB-modcomp.R
-896258c23ba2fdd6d7dcda164747dbea *R/PB-refdist.R
-0b7feed23b7c977e4066547c0fe92d6b *R/PB-utils.R
-9c1bac981405d1bf18a48f1c3218e8b5 *R/SAT-modcomp.R
-be8744773b3d0dbb9ebc4957921a54bf *R/data-beets.R
-94d64fd2f1ca6c7cb800ed79522fed60 *R/data-budworm.R
-1af8640e29be21efe84e65dccd908134 *R/getKR.R
-5d1e277317ad81d659e16d37dd15ef89 *R/get_ddf_Lb.R
-4776f35d0573157ce483bc44521e21d0 *R/init-modcomp.R
-96415b1894fcad7a94222fadf028244a *R/internal-pbkrtest.R
-9cbb49cf272cab01cddea35fdad9a313 *R/model-coerce.R
-8863ab7f8803aaabe3ffe28b6cfbf82a *README.md
-3e926d66211ab80c66456fdc8612e731 *build/vignette.rds
+c58b3a21b870530b98120a397f41f38d *R/KR-modcomp.R
+e565cf3384e961ab98e7199a838d9ee2 *R/KR-utils.R
+02e6835edcd6aa83d4b081ee64eb1227 *R/KR-vcovAdj.R
+9584efc058023d75073d368d2ed2654d *R/NAMESPACE-pbkrtest.R
+8c8c56e9abdccddf66f9ecbd15989fe9 *R/PB-modcomp.R
+7742d6df36bb2dacdf3b141f02baf4a4 *R/PB-refdist.R
+1b0a0f99a44f16836946114c331aa5ee *R/PB-utils.R
+a3be8c961d464993ebd0dcec664ab397 *R/SAT-modcomp.R
+83cfd1cc047607ed669f1036b8e810de *R/data-beets.R
+135c5f9c4d4e4fd499cd6cee3e23ea2d *R/data-budworm.R
+7cc46f7e57400bbb3e292a4768871848 *R/getKR.R
+1b5009adf3cc565ea38af7ecab9a7e8d *R/get_ddf_Lb.R
+fc2da0cd568fe69204e50cb09f84d711 *R/init-modcomp.R
+ae9dbf94511ebae28835be23a2b59b29 *R/internal-pbkrtest.R
+20fa5a92bd482fb9a4c5307e92569695 *R/model-coerce.R
+460a524ca9a754631a9c491599d0311b *R/utilities.R
+7fda9e53a0c4fd1d49bef84982f2b1d7 *README.md
+22b613238a9499bad714ffcfabdfb77c *build/vignette.rds
 25a3a55d27aa15aa5472e6fc4d10310d *data/beets.RData
 0bf3e5202394edbc9390961036629ad1 *data/budworm.RData
 2f0435596b9735ee0852c2d135281569 *inst/CITATION
-a1f073d2a8539678ee0ee0f79184178d *inst/doc/coercion.R
-46fc1f3ccebd87ff0988272385282ca2 *inst/doc/coercion.Rnw
-efb4ffd229ff9963390e1031d2007f25 *inst/doc/coercion.pdf
-763cbfbf07cc25c593f104b1b5cb4b41 *inst/doc/pbkrtest.R
-56750b6576c3a6c4fe8484b5aedbfeff *inst/doc/pbkrtest.Rnw
-9c9620cef64f7aa61f3a67f550a1db7f *inst/doc/pbkrtest.pdf
-cd74378c3f739073feea6d88dc38fc18 *man/compute_auxillary.Rd
-3f2dd16922eff9acf1da8c0cb05b0c2b *man/data-beets.Rd
-1b5ad0a8036bad4511136fcb5120ed0d *man/data-budworm.Rd
-6cbc3b21441a255670e66e0190ee92b2 *man/devfun_vp.Rd
-10c50cfe579d9ea6bf4d0011ce7ed371 *man/get_Fstat_ddf.Rd
-5d0b2785821736471c7ffdae8227bb6b *man/get_covbeta.Rd
-a47be8efd68bf4d303ba0ded6cea4ecd *man/get_ddf_Lb.Rd
-7b89f7ee32cd21f0c1cf5563f319e34e *man/getkr.Rd
-b46405368093f698931e9b0ea81ff962 *man/internal-pbkrtest.Rd
-e8186025e845c03cf0879ab080e18d1f *man/internal.Rd
-2345791082137beb3bc5ec8d481e6190 *man/kr-modcomp.Rd
-1dc8efe9da169af8d16a7dd9a08e38e1 *man/kr-vcov.Rd
-ab4d97d8dfb5b26297e8a5806f49c28c *man/model-coerce.Rd
-0a72ac8927ba191825054400b62b3095 *man/pb-modcomp.Rd
-34496b88e1b3786b5cd8eb0d83a669fa *man/pb-refdist.Rd
-5168806858a1173f871871d3b119830e *man/sat-modcomp.Rd
-46fc1f3ccebd87ff0988272385282ca2 *vignettes/coercion.Rnw
-56750b6576c3a6c4fe8484b5aedbfeff *vignettes/pbkrtest.Rnw
+e09c85aa411e04badc0a6c9a7279e8b2 *inst/WORDLIST
+e7dff7723ccf47ded812bfcdaa07f78e *inst/doc/a01-pbkrtest.R
+aecbeb724049cf311bd21a17815143cb *inst/doc/a01-pbkrtest.html
+3622cceae54af2d0fa6a6f2214c3ca67 *inst/doc/a01-pbkrtest.rmd
+ca7dd9e98be995bea8b29d4e3556a908 *inst/doc/a02-coercion.R
+062425d1bb44f2db0075f3bc47b44514 *inst/doc/a02-coercion.html
+ba7121c845079e0be2bf49a6560d7de4 *inst/doc/a02-coercion.rmd
+739c8d108bc9661ac1a37592252d5be8 *man/compare_column_space.Rd
+faf456dd438f7e96fe3b27ee1dd62795 *man/compute_auxiliary.Rd
+cb6e5969cf66ced75c9ea006dafa3139 *man/data-beets.Rd
+344038481b6ba6cec17fa88b1a8eba0a *man/data-budworm.Rd
+4bfd983c89bfc167cc9cc75402d8e0ea *man/devfun_vp.Rd
+195d81b5540da86be88a9e6c9b0e7776 *man/get_Fstat_ddf.Rd
+792124d0b42f0bbb1268ebf26ed97453 *man/get_covbeta.Rd
+366d0b5abd29fc829e0c9b4cf315ef23 *man/get_ddf_Lb.Rd
+a6a52280f51827e74a134de830503797 *man/get_modcomp.Rd
+7d06f8c38cb2c10d98542c40c04ff3a9 *man/internal-pbkrtest.Rd
+7e9bb07603f61359b04fe87509bf1abc *man/internal.Rd
+eb94c9f1cd6acfdc8a3044802bcc6e5a *man/kr-modcomp.Rd
+80e47e5ae135404d1f3940a54dc00a0a *man/kr-vcovAdj.Rd
+e5a7a07032e69307fd55d16cc0c9899a *man/model-coerce.Rd
+2ed5bf6edf2f76b0cb1c2e4bc6fb02d1 *man/pb-modcomp.Rd
+0487620876b059ea8e057bed5fc09383 *man/pb-refdist.Rd
+32bc75ff6d555e129e073f069fa8ee33 *man/sat-modcomp.Rd
+3622cceae54af2d0fa6a6f2214c3ca67 *vignettes/a01-pbkrtest.rmd
+ba7121c845079e0be2bf49a6560d7de4 *vignettes/a02-coercion.rmd

NAMESPACE

@@ -10,39 +10,47 @@ S3method(as.data.frame,KRmodcomp)
 S3method(as.data.frame,PBmodcomp)
 S3method(as.data.frame,SATmodcomp)
 S3method(as.data.frame,XXmodcomp)
+S3method(getLRT,glmerMod)
+S3method(getLRT,lm)
+S3method(getLRT,lmerMod)
 S3method(get_Lb_ddf,lmerMod)
 S3method(get_SigmaG,lmerMod)
-S3method(model2remat,default)
-S3method(model2remat,lm)
-S3method(model2remat,merMod)
+S3method(model2restriction_matrix,default)
+S3method(model2restriction_matrix,lm)
+S3method(model2restriction_matrix,merMod)
 S3method(plot,PBmodcomp)
 S3method(print,KRmodcomp)
 S3method(print,PBmodcomp)
 S3method(print,SATmodcomp)
-S3method(print,summaryPB)
-S3method(remat2model,default)
-S3method(remat2model,lm)
-S3method(remat2model,merMod)
+S3method(print,summary_PBmodcomp)
+S3method(restriction_matrix2model,default)
+S3method(restriction_matrix2model,glmerMod)
+S3method(restriction_matrix2model,lm)
+S3method(restriction_matrix2model,lmerMod)
 S3method(summary,KRmodcomp)
 S3method(summary,PBmodcomp)
 S3method(tidy,KRmodcomp)
 S3method(tidy,PBmodcomp)
 S3method(tidy,SATmodcomp)
+S3method(tidy,summary_KRmodcomp)
+S3method(tidy,summary_PBmodcomp)
 S3method(vcovAdj,lmerMod)
-export("%>%")
 export(KRmodcomp)
 export(Lb_ddf)
 export(PBmodcomp)
 export(PBrefdist)
 export(SATmodcomp)
+export(compare_column_space)
 export(ddf_Lb)
 export(getKR)
+export(getLRT)
+export(getSAT)
 export(get_Lb_ddf)
 export(get_SigmaG)
-export(make_modelmat)
-export(make_remat)
-export(model2remat)
-export(remat2model)
+export(make_model_matrix)
+export(make_restriction_matrix)
+export(model2restriction_matrix)
+export(restriction_matrix2model)
 export(tidy)
 export(vcovAdj)
 export(vcovAdj.lmerMod)
@@ -58,7 +66,6 @@ importFrom(graphics,abline)
 importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,plot)
-importFrom(magrittr,"%>%")
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(parallel,clusterCall)

NEWS

@@ -1,11 +1,24 @@
-pbkrtest v0.5.1 (Release date: 2021-03-09)
+pbkrtest 0.5.2 (Release date: 2023-01-19)
+============================================
+
+Changes
+
+* remat changed to restriction_matrix for increased readability
+* WORDLIST file added
+* Changes in reference to JSS paper
+* Various changes in documentation
+* Satterthwaite approximation now illustrated in vignette
+* Fixed bug in computation of LRTstatistic. Thanks to Helle Sorensen for pointing it out.
+
+
+pbkrtest 0.5.1 (Release date: 2021-03-09)
 ============================================
 
 Changes
 
 * Improved documentation
 
-pbkrtest v0.5-0.0 (Release date: 2020-08-04)
+pbkrtest 0.5-0.0 (Release date: 2020-08-04)
 ============================================
 
 Changes
@@ -19,7 +32,7 @@ Changes
 * doi added to DESCRIPTION file
 
 
-pbkrtest v0.4-8.6 (Release date: 2020-02-20)
+pbkrtest 0.4-8.6 (Release date: 2020-02-20)
 ============================================
 
 Bug fixes:
@@ -32,7 +45,7 @@ Bug fixes:
   to make emmeans used generic function vcovAdj.
 
 
-pbkrtest v0.4-8 (Release date: 2020-02-20)
+pbkrtest 0.4-8 (Release date: 2020-02-20)
 ==========================================
 
 Bug fixes:

R/KR-Sigma-G2.R

@@ -112,43 +112,43 @@ get_SigmaG.lmerMod  <- function(object, details=0) {
 ## Modular implementation
 ##
 
-.get_GI_parms <- function( object ){
-  GGamma <- VarCorr(object)
-  parmList <- lapply(GGamma, function(Lii){  Lii[ lower.tri( Lii, diag=TRUE ) ] })
-  parmList <- c( parmList, sigma( object )^2 )
-  parmList
-}
-
-.get_GI_matrices <- function( object ){
-
-  SS     <- .shgetME( object )
-  Zt <- getME( object, "Zt" )
-
-  G  <- NULL
-  G  <- vector("list", SS$n.RT+1)
+## .get_GI_parms <- function( object ){
+  ## GGamma <- VarCorr(object)
+  ## parmList <- lapply(GGamma, function(Lii){  Lii[ lower.tri( Lii, diag=TRUE ) ] })
+  ## parmList <- c( parmList, sigma( object )^2 )
+  ## parmList
+## }
 
-  for (ss in 1:SS$n.RT) {
-    ZZ    <- .shget_Zt_group( ss, Zt, SS$Gp )
-    n.lev <- SS$n.lev.by.RT2[ ss ] ## ; cat(sprintf("n.lev=%i\n", n.lev))
-    Ig    <- sparseMatrix(1:n.lev, 1:n.lev, x=1)
-    UU <- vector("list", SS$n.parm.by.RT)
-    for (rr in 1:SS$n.parm.by.RT[ ss ]) {
-      ii.jj <- .index2UpperTriEntry( rr, SS$n.comp.by.RT[ ss ] )
-      ii.jj <- unique(ii.jj)
-      if (length(ii.jj)==1){
-        EE <- sparseMatrix(ii.jj, ii.jj, x=1, dims=rep(SS$n.comp.by.RT[ ss ], 2))
-      } else {
-        EE <- sparseMatrix(ii.jj, ii.jj[2:1], dims=rep(SS$n.comp.by.RT[ ss ], 2))
-      }
-      EE <- Ig %x% EE  ## Kronecker product
-      UU[[ rr ]] <- t(ZZ) %*% EE %*% ZZ
-    }
-    G[[ ss ]] <- UU
-  }
-  n.obs <- nrow(getME(object,'X'))
-  G[[ length( G ) ]] <- sparseMatrix(1:n.obs, 1:n.obs, x=1 )
-  G
-}
+## .get_GI_matrices <- function( object ){
+
+  ## SS     <- .shgetME( object )
+  ## Zt <- getME( object, "Zt" )
+
+  ## G  <- NULL
+  ## G  <- vector("list", SS$n.RT+1)
+
+  ## for (ss in 1:SS$n.RT) {
+    ## ZZ    <- .shget_Zt_group( ss, Zt, SS$Gp )
+    ## n.lev <- SS$n.lev.by.RT2[ ss ] ## ; cat(sprintf("n.lev=%i\n", n.lev))
+    ## Ig    <- sparseMatrix(1:n.lev, 1:n.lev, x=1)
+    ## UU <- vector("list", SS$n.parm.by.RT)
+    ## for (rr in 1:SS$n.parm.by.RT[ ss ]) {
+      ## ii.jj <- .index2UpperTriEntry( rr, SS$n.comp.by.RT[ ss ] )
+      ## ii.jj <- unique(ii.jj)
+      ## if (length(ii.jj)==1){
+        ## EE <- sparseMatrix(ii.jj, ii.jj, x=1, dims=rep(SS$n.comp.by.RT[ ss ], 2))
+      ## } else {
+        ## EE <- sparseMatrix(ii.jj, ii.jj[2:1], dims=rep(SS$n.comp.by.RT[ ss ], 2))
+      ## }
+      ## EE <- Ig %x% EE  ## Kronecker product
+      ## UU[[ rr ]] <- t(ZZ) %*% EE %*% ZZ
+    ## }
+    ## G[[ ss ]] <- UU
+  ## }
+  ## n.obs <- nrow(getME(object,'X'))
+  ## G[[ length( G ) ]] <- sparseMatrix(1:n.obs, 1:n.obs, x=1 )
+  ## G
+## }