R-packages – /branches/Matrix-for-R-2.3.x/R/lmer.R

Rev 3771 – Version 0.995-18 fixing problem with lmer(resp ~ 1|grp,

bates — Wed, 13 Sep 2006 19:50:14 +0000

bates – 3 file(s) modified
Version 0.995-18 fixing problem with lmer(resp ~ 1|grp,

~ /branches/Matrix-for-R-2.3.x/DESCRIPTION
~ /branches/Matrix-for-R-2.3.x/INDEX
~ /branches/Matrix-for-R-2.3.x/R/lmer.R

Rev 3543 – branching an "old-R" compatible version of Matrix

maechler — Sat, 02 Sep 2006 16:36:14 +0000

maechler – 1 file(s) modified
branching an "old-R" compatible version of Matrix

+ /branches/Matrix-for-R-2.3.x (copied from /trunk/Matrix@3542)

Rev 3524 – several smallish fixes

maechler — Wed, 30 Aug 2006 21:35:09 +0000

maechler – 19 file(s) modified
several smallish fixes

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/man/dsparseMatrix-class.Rd
~ /trunk/Matrix/man/LU-class.Rd
~ /trunk/Matrix/man/MatrixFactorization-class.Rd
~ /trunk/Matrix/man/sparseLU-class.Rd
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/Auxiliaries.R
~ /trunk/Matrix/R/dgCMatrix.R
~ /trunk/Matrix/R/dMatrix.R
~ /trunk/Matrix/R/dsparseMatrix.R
~ /trunk/Matrix/R/lgTMatrix.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/R/Matrix.R
~ /trunk/Matrix/R/sparseMatrix.R
~ /trunk/Matrix/tests/factorizing.R
~ /trunk/Matrix/tests/group-methods.R
~ /trunk/Matrix/tests/other-pkgs.R
~ /trunk/Matrix/tests/simple.R

Rev 3497 – Bug fix due to Emmanuel Tillard

bates — Fri, 25 Aug 2006 14:54:54 +0000

bates – 2 file(s) modified
Bug fix due to Emmanuel Tillard

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/R/lmer.R

Rev 3363 – + factorNames2char() utility for nicer warnings

maechler — Wed, 02 Aug 2006 20:43:52 +0000

maechler – 1 file(s) modified
+ factorNames2char() utility for nicer warnings

~ /trunk/Matrix/R/lmer.R

Rev 3361 – hatTrace and warnings about boundary convergence

bates — Tue, 01 Aug 2006 20:26:45 +0000

bates – 6 file(s) modified
hatTrace and warnings about boundary convergence

~ /trunk/Matrix/ChangeLog
+ /trunk/Matrix/inst/external/test3comp.rda
+ /trunk/Matrix/man/hatTrace.Rd
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/tests/lmer.R

Rev 3354 – Add hatTrace function

bates — Mon, 31 Jul 2006 23:05:04 +0000

bates – 3 file(s) modified
Add hatTrace function

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c

Rev 3350 – change unused class "correlation" to "corMatrix"

maechler — Mon, 31 Jul 2006 12:11:35 +0000

maechler – 6 file(s) modified
change unused class "correlation" to "corMatrix"

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/man/dpoMatrix-class.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/dpoMatrix.R
~ /trunk/Matrix/R/lmer.R

Rev 3340 – many method cleanups; notably some "dgC" -> "Csparse" generaliztations

maechler — Sat, 22 Jul 2006 17:59:53 +0000

maechler – 41 file(s) modified
many method cleanups; notably some "dgC" -> "Csparse" generaliztations

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/Done
~ /trunk/Matrix/man/band.Rd
~ /trunk/Matrix/man/CsparseMatrix-class.Rd
~ /trunk/Matrix/man/ddenseMatrix-class.Rd
~ /trunk/Matrix/man/dgCMatrix-class.Rd
~ /trunk/Matrix/man/dgeMatrix-class.Rd
~ /trunk/Matrix/man/dgTMatrix-class.Rd
~ /trunk/Matrix/man/dMatrix-class.Rd
~ /trunk/Matrix/man/dsCMatrix-class.Rd
~ /trunk/Matrix/man/Matrix-class.Rd
~ /trunk/Matrix/man/pMatrix-class.Rd
+ /trunk/Matrix/man/replValue-class.Rd
~ /trunk/Matrix/man/Subassign-methods.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/Auxiliaries.R
~ /trunk/Matrix/R/Csparse.R
~ /trunk/Matrix/R/ddenseMatrix.R
~ /trunk/Matrix/R/denseMatrix.R
~ /trunk/Matrix/R/dgCMatrix.R
~ /trunk/Matrix/R/dgeMatrix.R
~ /trunk/Matrix/R/dgTMatrix.R
~ /trunk/Matrix/R/diagMatrix.R
~ /trunk/Matrix/R/dMatrix.R
~ /trunk/Matrix/R/dsCMatrix.R
~ /trunk/Matrix/R/dsparseMatrix.R
~ /trunk/Matrix/R/dtCMatrix.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/R/lsCMatrix.R
~ /trunk/Matrix/R/Matrix.R
~ /trunk/Matrix/R/pedigree.R
~ /trunk/Matrix/R/Tsparse.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/tests/bind.R
~ /trunk/Matrix/tests/bind.Rout.save
~ /trunk/Matrix/tests/indexing.R
~ /trunk/Matrix/tests/indexing.Rout.save
~ /trunk/Matrix/tests/matprod.R
~ /trunk/Matrix/tests/simple.R
~ /trunk/Matrix/TODO

Rev 3339 – pass verbose argument to (gl)mer_MCMCsamp() and use it in C ...

maechler — Fri, 21 Jul 2006 08:28:18 +0000

maechler – 6 file(s) modified
pass verbose argument to (gl)mer_MCMCsamp() and use it in C code

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/tests/lmer.R

Rev 3329 – Remove leading blanks in a string. They are being ...

bates — Mon, 17 Jul 2006 18:29:48 +0000

bates – 1 file(s) modified
Remove leading blanks in a string. They are being tabified and result in incorrect alignment

~ /trunk/Matrix/R/lmer.R

Rev 3327 – Added a "To Do" about always printing the log-likelihood and ...

bates — Mon, 17 Jul 2006 17:14:33 +0000

bates – 1 file(s) modified
Added a "To Do" about always printing the log-likelihood and the restricted-log-likelihood for an lmer object.

~ /trunk/Matrix/R/lmer.R

Rev 3288 – Establish new class glmer; modify validity check on pedigree to ...

bates — Thu, 06 Jul 2006 15:14:12 +0000

bates – 3 file(s) modified
Establish new class glmer; modify validity check on pedigree to account for nonparallel patterns of missingness in parents

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R

Rev 3253 – Correction in deviance method for mer objects; some cleanup

bates — Mon, 26 Jun 2006 14:33:16 +0000

bates – 1 file(s) modified
Correction in deviance method for mer objects; some cleanup

~ /trunk/Matrix/R/lmer.R

Rev 3246 – fix segfault from wrong formula

maechler — Mon, 19 Jun 2006 15:36:44 +0000

maechler – 2 file(s) modified
fix segfault from wrong formula

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/tests/lmer.R

Rev 3236 – Corrected naming of columns of an mcmcsamp object

bates — Mon, 12 Jun 2006 10:52:45 +0000

bates – 1 file(s) modified
Corrected naming of columns of an mcmcsamp object

~ /trunk/Matrix/R/lmer.R

Rev 3231 – mcmcsamp()[,"deviance"] was wrong column

maechler — Mon, 12 Jun 2006 08:06:21 +0000

maechler – 3 file(s) modified
mcmcsamp()[,"deviance"] was wrong column

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/man/mcmcsamp.Rd
~ /trunk/Matrix/R/lmer.R

Rev 3228 – added simulestimate for lmer but hidden in NAMESPACE

bates — Sat, 10 Jun 2006 19:54:41 +0000

bates – 1 file(s) modified
added simulestimate for lmer but hidden in NAMESPACE

~ /trunk/Matrix/R/lmer.R

Rev 3221 – No longer create a generic for qqmath; add deviance to ...

bates — Thu, 08 Jun 2006 16:05:41 +0000

bates – 1 file(s) modified
No longer create a generic for qqmath; add deviance to mcmcsamp

~ /trunk/Matrix/R/lmer.R

Rev 3189 – add reference line and grid to qqmath method for ranef.lmer

bates — Thu, 01 Jun 2006 20:41:20 +0000

bates – 2 file(s) modified
add reference line and grid to qqmath method for ranef.lmer

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/R/lmer.R

Rev 3184 – Functions to allow nested grouping factors to be specified as ...

bates — Tue, 30 May 2006 16:00:35 +0000

bates – 1 file(s) modified
Functions to allow nested grouping factors to be specified as (1|foo/bar)

~ /trunk/Matrix/R/lmer.R

Rev 3181 – More careful checks in subbars and friends, code for calculating ...

bates — Sat, 27 May 2006 20:01:11 +0000

bates – 3 file(s) modified
More careful checks in subbars and friends, code for calculating inbreeding coefficients directly from the pedigree

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/pedigree.c

Rev 3180 – Add isNested and for an identity permutation for nested grouping ...

bates — Sat, 27 May 2006 19:51:01 +0000

bates – 7 file(s) modified
Add isNested and for an identity permutation for nested grouping factors

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 3172 – useDynlib(*, .registration=TRUE)

maechler — Tue, 23 May 2006 08:01:44 +0000

maechler – 33 file(s) modified
useDynlib(*, .registration=TRUE)

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/Auxiliaries.R
~ /trunk/Matrix/R/Csparse.R
~ /trunk/Matrix/R/denseMatrix.R
~ /trunk/Matrix/R/dgCMatrix.R
~ /trunk/Matrix/R/dgeMatrix.R
~ /trunk/Matrix/R/dgRMatrix.R
~ /trunk/Matrix/R/dgTMatrix.R
~ /trunk/Matrix/R/dpoMatrix.R
~ /trunk/Matrix/R/dppMatrix.R
~ /trunk/Matrix/R/dsCMatrix.R
~ /trunk/Matrix/R/dsparseMatrix.R
~ /trunk/Matrix/R/dspMatrix.R
~ /trunk/Matrix/R/dsTMatrix.R
~ /trunk/Matrix/R/dsyMatrix.R
~ /trunk/Matrix/R/dtCMatrix.R
~ /trunk/Matrix/R/dtpMatrix.R
~ /trunk/Matrix/R/dtrMatrix.R
~ /trunk/Matrix/R/dtTMatrix.R
~ /trunk/Matrix/R/eigen.R
~ /trunk/Matrix/R/lCholCMatrix.R
~ /trunk/Matrix/R/ldenseMatrix.R
~ /trunk/Matrix/R/lgCMatrix.R
~ /trunk/Matrix/R/lgTMatrix.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/R/lsCMatrix.R
~ /trunk/Matrix/R/ltCMatrix.R
~ /trunk/Matrix/R/ltTMatrix.R
~ /trunk/Matrix/R/LU.R
~ /trunk/Matrix/R/pedigree.R
~ /trunk/Matrix/R/Tsparse.R

Rev 3080 – Remove postVar generic and methods

bates — Wed, 19 Apr 2006 14:16:59 +0000

bates – 3 file(s) modified
Remove postVar generic and methods

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R

Rev 3054 – Added qqmath method for ranef.lmer and postVar for ranef methods

bates — Sun, 09 Apr 2006 00:02:26 +0000

bates – 9 file(s) modified
Added qqmath method for ranef.lmer and postVar for ranef methods

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/TODO

Rev 3042 – Added a qqmath method for the ranef.lmer class.

bates — Mon, 03 Apr 2006 20:51:37 +0000

bates – 1 file(s) modified
Added a qqmath method for the ranef.lmer class.

~ /trunk/Matrix/R/lmer.R

Rev 3040 – Add warning about ignored arguments to coef method for lmer

bates — Sun, 02 Apr 2006 23:45:47 +0000

bates – 1 file(s) modified
Add warning about ignored arguments to coef method for lmer

~ /trunk/Matrix/R/lmer.R

Rev 3027 – Propagate DimNames in dsyMatrix_as_dspMatrix

bates — Thu, 23 Mar 2006 15:16:17 +0000

bates – 5 file(s) modified
Propagate DimNames in dsyMatrix_as_dspMatrix

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/dsyMatrix.c
~ /trunk/Matrix/tests/lmer.R
~ /trunk/Matrix/TODO

Rev 3024 – Change name of lmer.ranef class to ranef.lmer, add coef.lmer and ...

bates — Tue, 21 Mar 2006 12:33:28 +0000

bates – 4 file(s) modified
Change name of lmer.ranef class to ranef.lmer, add coef.lmer and update plot methods for these classes

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R

Rev 3022 – modifying return value of ranef method and adding residuals method

bates — Tue, 21 Mar 2006 11:07:55 +0000

bates – 4 file(s) modified
modifying return value of ranef method and adding residuals method

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R

Rev 2347 – lmer(): non-trivial summary() method -> summary.*mer classes

maechler — Tue, 07 Mar 2006 11:05:08 +0000

maechler – 7 file(s) modified
lmer(): non-trivial summary() method -> summary.*mer classes

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/man/lmer-class.Rd
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/tests/lmer.R

Rev 2277 – Fix case of cbind(successes, failures) for lmer fitting a GLMM ...

bates — Tue, 07 Feb 2006 23:44:07 +0000

bates – 5 file(s) modified
Fix case of cbind(successes, failures) for lmer fitting a GLMM (see Changelog)

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c

Rev 2235 – fix mcmcsamp(*, saveb=TRUE)

maechler — Fri, 20 Jan 2006 18:12:04 +0000

maechler – 2 file(s) modified
fix mcmcsamp(*, saveb=TRUE)

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/tests/lmer.R

Rev 2224 – Over to Martin for release 0.995-2

bates — Thu, 19 Jan 2006 00:43:37 +0000

bates – 4 file(s) modified
Over to Martin for release 0.995-2

~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/tests/lmer.R

Rev 2218 – Modifications to lmer.R - still not working

bates — Wed, 18 Jan 2006 15:38:12 +0000

bates – 1 file(s) modified
Modifications to lmer.R - still not working

~ /trunk/Matrix/R/lmer.R

Rev 2212 – Munging the data frame

bates — Tue, 17 Jan 2006 23:41:36 +0000

bates – 6 file(s) modified
Munging the data frame

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c

Rev 2204 – Extract the slot contents from S4 objects, not the component

bates — Mon, 16 Jan 2006 16:59:46 +0000

bates – 1 file(s) modified
Extract the slot contents from S4 objects, not the component

~ /trunk/Matrix/R/lmer.R

Rev 2203 – Throw an error for mcmcsamp on a GLMM, at least ...

bates — Mon, 16 Jan 2006 16:38:00 +0000

bates – 1 file(s) modified
Throw an error for mcmcsamp on a GLMM, at least until it is implemented

~ /trunk/Matrix/R/lmer.R

Rev 2201 – Modifications to propagate column names from an mer object to ...

bates — Mon, 16 Jan 2006 14:40:39 +0000

bates – 3 file(s) modified
Modifications to propagate column names from an mer object to a VarCorr summary

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/dpoMatrix.R
~ /trunk/Matrix/R/lmer.R