R-packages – /branches/Matrix-mer2/src/lmer.h

Rev 2101 – Changes to glmer_PQL and glmer_devLaplace but still not working properly

bates — Thu, 29 Dec 2005 20:18:08 +0000

bates – 4 file(s) modified
Changes to glmer_PQL and glmer_devLaplace but still not working properly

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 2073 – Still messing around with glmer_devLaplace

bates — Tue, 13 Dec 2005 22:12:58 +0000

bates – 4 file(s) modified
Still messing around with glmer_devLaplace

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 2071 – Messing with the Laplace approximation

bates — Tue, 13 Dec 2005 00:26:11 +0000

bates – 4 file(s) modified
Messing with the Laplace approximation

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 2021 – Use defaults for useScale and REML

bates — Tue, 22 Nov 2005 23:27:42 +0000

bates – 4 file(s) modified
Use defaults for useScale and REML

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 2011 – Add slots to mer object, change to automatic factor and ...

bates — Sun, 13 Nov 2005 20:58:55 +0000

bates – 7 file(s) modified
Add slots to mer object, change to automatic factor and mer_secondary

~ /branches/Matrix-mer2/R/AllClass.R
~ /branches/Matrix-mer2/R/dMatrix.R
~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h
~ /branches/Matrix-mer2/src/Syms.h

Rev 2010 – Fold mer2 representation into lmer. Remove dgBCMatrix, pdmatrix, etc.

bates — Sun, 13 Nov 2005 14:00:15 +0000

bates – 26 file(s) modified
Fold mer2 representation into lmer. Remove dgBCMatrix, pdmatrix, etc.

~ /branches/Matrix-mer2/INDEX
~ /branches/Matrix-mer2/inst/doc/Comparisons.Rnw
~ /branches/Matrix-mer2/inst/doc/Introduction.Rnw
x /branches/Matrix-mer2/man/bCrosstab.Rd
x /branches/Matrix-mer2/man/dgBCMatrix-class.Rd
~ /branches/Matrix-mer2/man/dpoMatrix-class.Rd
~ /branches/Matrix-mer2/man/lmer-class.Rd
~ /branches/Matrix-mer2/man/mcmcsamp.Rd
x /branches/Matrix-mer2/man/pdmatrix-class.Rd
~ /branches/Matrix-mer2/man/ranef.Rd
~ /branches/Matrix-mer2/man/VarCorr.Rd
~ /branches/Matrix-mer2/NAMESPACE
~ /branches/Matrix-mer2/R/AllClass.R
x /branches/Matrix-mer2/R/bCrosstab.R
x /branches/Matrix-mer2/R/dgBCMatrix.R
~ /branches/Matrix-mer2/R/dgCMatrix.R
~ /branches/Matrix-mer2/R/lmer.R
x /branches/Matrix-mer2/R/pdmatrix.R
~ /branches/Matrix-mer2/src/DEPS.mkf
x /branches/Matrix-mer2/src/dgBCMatrix.c
x /branches/Matrix-mer2/src/dgBCMatrix.h
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h
~ /branches/Matrix-mer2/src/SOURCES_C.mkf
~ /branches/Matrix-mer2/tests/Class+Meth.R

Rev 2003 – mer2_simulate

bates — Sat, 12 Nov 2005 00:27:23 +0000

bates – 4 file(s) modified
mer2_simulate

~ /branches/Matrix-mer2/src/dpoMatrix.c
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1996 – mer2_gradComp enhancements

bates — Thu, 10 Nov 2005 23:37:09 +0000

bates – 3 file(s) modified
mer2_gradComp enhancements

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1993 – gradient components for mer2 objects

bates — Thu, 10 Nov 2005 16:03:36 +0000

bates – 3 file(s) modified
gradient components for mer2 objects

~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1967 – Add call and family to the mer2 object

bates — Mon, 07 Nov 2005 23:21:17 +0000

bates – 4 file(s) modified
Add call and family to the mer2 object

~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h
~ /branches/Matrix-mer2/src/Syms.h

Rev 1966 – Separate creation of Zt from creation of the mer2 object

bates — Mon, 07 Nov 2005 14:00:00 +0000

bates – 3 file(s) modified
Separate creation of Zt from creation of the mer2 object

~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1958 – Unsuccessful attempt to add IPLS iterations

bates — Wed, 02 Nov 2005 21:30:27 +0000

bates – 4 file(s) modified
Unsuccessful attempt to add IPLS iterations

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1957 – Added mer2_dtCMatrix_inv

bates — Tue, 01 Nov 2005 13:27:14 +0000

bates – 3 file(s) modified
Added mer2_dtCMatrix_inv

~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1954 – Modify calling sequence for mer2_create

bates — Mon, 31 Oct 2005 13:20:52 +0000

bates – 4 file(s) modified
Modify calling sequence for mer2_create

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1953 – Added mer2_fitted

bates — Sun, 30 Oct 2005 14:53:52 +0000

bates – 3 file(s) modified
Added mer2_fitted

~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1949 – mcmcsamp for mer2

bates — Sat, 29 Oct 2005 01:00:14 +0000

bates – 4 file(s) modified
mcmcsamp for mer2

~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1941 – Updates on mer2

bates — Thu, 27 Oct 2005 12:34:09 +0000

bates – 4 file(s) modified
Updates on mer2

~ /branches/Matrix-mer2/DESCRIPTION
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1937 – Added fixef and ranef methods for mer2 objects

bates — Wed, 26 Oct 2005 01:51:46 +0000

bates – 5 file(s) modified
Added fixef and ranef methods for mer2 objects

~ /branches/Matrix-mer2/ChangeLog
~ /branches/Matrix-mer2/R/lmer.R
~ /branches/Matrix-mer2/src/init.c
~ /branches/Matrix-mer2/src/lmer.c
~ /branches/Matrix-mer2/src/lmer.h

Rev 1929 – Incorporating CHOLMOD-based lmer

bates — Fri, 21 Oct 2005 19:33:37 +0000

bates – 1 file(s) modified
Incorporating CHOLMOD-based lmer

+ /branches/Matrix-mer2 (copied from /trunk/Matrix@1928)

Rev 1917 – More mer2 modifications

bates — Mon, 10 Oct 2005 13:54:09 +0000

bates – 4 file(s) modified
More mer2 modifications

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

Rev 1916 – mer2_initial

bates — Fri, 07 Oct 2005 22:14:47 +0000

bates – 4 file(s) modified
mer2_initial

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1894 – More updates on lmer - still not quite correct

bates — Thu, 06 Oct 2005 03:07:23 +0000

bates – 6 file(s) modified
More updates on lmer - still not quite correct

~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Makefile
~ /trunk/Matrix/src/Syms.h

Rev 1876 – Modifications to mer2

bates — Mon, 03 Oct 2005 01:44:56 +0000

bates – 9 file(s) modified
Modifications to mer2

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h

Rev 1851 – Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

bates — Tue, 27 Sep 2005 00:50:35 +0000

bates – 8 file(s) modified
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
x /trunk/Matrix/src/AMD/Source/Makefile.bak
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/SOURCES_C.mkf

Rev 1840 – Updated DEPS.mkf and some include files

bates — Mon, 19 Sep 2005 23:04:52 +0000

bates – 4 file(s) modified
Updated DEPS.mkf and some include files

~ /trunk/Matrix/src/dense.h
~ /trunk/Matrix/src/DEPS.mkf
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Makefile.win

Rev 1792 – Add "start" argument to lmer

bates — Tue, 06 Sep 2005 01:26:11 +0000

bates – 7 file(s) modified
Add "start" argument to lmer

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer.Rd
~ /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 1779 – New simulate method for lmer objects

bates — Thu, 01 Sep 2005 13:46:21 +0000

bates – 7 file(s) modified
New simulate method for lmer objects

~ /trunk/Matrix/man/simulate.Rd
~ /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

Rev 1770 – Added simulate generic and method

bates — Tue, 30 Aug 2005 14:35:05 +0000

bates – 6 file(s) modified
Added simulate generic and method

+ /trunk/Matrix/man/simulate.Rd
~ /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 1694 – Allow mcmcsamp on transformed parameters

bates — Sat, 06 Aug 2005 20:01:51 +0000

bates – 6 file(s) modified
Allow mcmcsamp on transformed parameters

~ /trunk/Matrix/data/sleepstudy.rda
~ /trunk/Matrix/man/mcmcsamp.Rd
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1672 – Added lmer_MCMCsamp to the C sources

bates — Sun, 24 Jul 2005 23:53:40 +0000

bates – 3 file(s) modified
Added lmer_MCMCsamp to the C sources

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1668 – New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

bates — Thu, 21 Jul 2005 16:41:42 +0000

bates – 4 file(s) modified
New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

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

Rev 1667 – Added an rWishart function, which should later be moved to ...

bates — Thu, 21 Jul 2005 14:59:04 +0000

bates – 4 file(s) modified
Added an rWishart function, which should later be moved to the stats package

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

Rev 1642 – Preparing for glmmMCMC

bates — Thu, 07 Jul 2005 20:05:47 +0000

bates – 4 file(s) modified
Preparing for glmmMCMC

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

Rev 1610 – Adding MCMC capability (currently incomplete)

bates — Fri, 24 Jun 2005 23:06:33 +0000

bates – 5 file(s) modified
Adding MCMC capability (currently incomplete)

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

Rev 1609 – Further development on AGQ and MCMC for glmm models

bates — Fri, 24 Jun 2005 15:38:43 +0000

bates – 5 file(s) modified
Further development on AGQ and MCMC for glmm models

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

Rev 1593 – Setting up for AGQ

bates — Mon, 13 Jun 2005 19:45:04 +0000

bates – 4 file(s) modified
Setting up for AGQ

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

Rev 1592 – Factoring C code in preparation for AGQ

bates — Mon, 13 Jun 2005 01:22:28 +0000

bates – 5 file(s) modified
Factoring C code in preparation for AGQ

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h

Rev 1591 – Moving devLaplace calculations to C code

bates — Fri, 10 Jun 2005 18:40:54 +0000

bates – 5 file(s) modified
Moving devLaplace calculations to C code

~ /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 1577 – Isolating and cleaning up the mer, lmer, and glmer functions

bates — Tue, 07 Jun 2005 23:03:34 +0000

bates – 5 file(s) modified
Isolating and cleaning up the mer, lmer, and glmer functions

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h

Rev 1571 – Use mer objects; Replace REML slot by method slot

bates — Mon, 06 Jun 2005 15:51:24 +0000

bates – 4 file(s) modified
Use mer objects; Replace REML slot by method slot

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h