R-packages – /trunk/Matrix/src/lmer.c

Rev 1897 – Added a factorization in mer2_create so the permutation could be ...

bates — Fri, 07 Oct 2005 14:20:23 +0000

bates – 1 file(s) modified
Added a factorization in mer2_create so the permutation could be applied to Z'X and Z'y

~ /trunk/Matrix/src/lmer.c

Rev 1896 – Permutation of Z'X and Z'y in mer2_factor

bates — Thu, 06 Oct 2005 23:34:20 +0000

bates – 1 file(s) modified
Permutation of Z'X and Z'y in mer2_factor

~ /trunk/Matrix/src/lmer.c

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 1798 – Remove unnecessary declaration

bates — Wed, 07 Sep 2005 20:43:18 +0000

bates – 1 file(s) modified
Remove unnecessary declaration

~ /trunk/Matrix/src/lmer.c

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 1769 – Add simulate method for lmer

bates — Sun, 28 Aug 2005 13:57:39 +0000

bates – 4 file(s) modified
Add simulate method for lmer

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

Rev 1735 – Coercion method for graphNEL to sparseMatrix class

bates — Thu, 18 Aug 2005 21:31:07 +0000

bates – 9 file(s) modified
Coercion method for graphNEL to sparseMatrix class

~ /trunk/Matrix/R/dsTMatrix.R
~ /trunk/Matrix/R/sparseMatrix.R
~ /trunk/Matrix/src/dgTMatrix.c
~ /trunk/Matrix/src/dgTMatrix.h
~ /trunk/Matrix/src/dsTMatrix.c
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.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 1679 – Version 0.98-1

bates — Wed, 27 Jul 2005 23:07:04 +0000

bates – 12 file(s) modified
Version 0.98-1

~ /trunk/Matrix/ChangeLog
+ /trunk/Matrix/data/sleepstudy.rda
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer.Rd
+ /trunk/Matrix/man/mcmcsamp.Rd
+ /trunk/Matrix/man/sleepstudy.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/tests/lmer.R

Rev 1677 – updates on lmer_MCMCsamp

bates — Tue, 26 Jul 2005 22:46:14 +0000

bates – 2 file(s) modified
updates on lmer_MCMCsamp

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

Rev 1675 – Working version of lmer_MCMCsamp - may have chisq in wrong ...

bates — Tue, 26 Jul 2005 12:36:10 +0000

bates – 1 file(s) modified
Working version of lmer_MCMCsamp - may have chisq in wrong place when sampling sigmasqr

~ /trunk/Matrix/src/lmer.c

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 1670 – Working version of the glmmMCMC producing an mcmc object

bates — Thu, 21 Jul 2005 23:05:52 +0000

bates – 2 file(s) modified
Working version of the glmmMCMC producing an mcmc object

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

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 1646 – Release 0.97-3

bates — Mon, 11 Jul 2005 15:05:40 +0000

bates – 1 file(s) modified
Release 0.97-3

~ /trunk/Matrix/src/lmer.c

Rev 1644 – Preliminary version of glmmMCMC

bates — Fri, 08 Jul 2005 15:38:43 +0000

bates – 3 file(s) modified
Preliminary version of glmmMCMC

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

Rev 1643 – More work on glmer_ranef_update - still not complete

bates — Fri, 08 Jul 2005 03:47:35 +0000

bates – 1 file(s) modified
More work on glmer_ranef_update - still not complete

~ /trunk/Matrix/src/lmer.c

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 1639 – got glmer_fixed_update working

bates — Wed, 06 Jul 2005 23:55:39 +0000

bates – 2 file(s) modified
got glmer_fixed_update working

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

Rev 1638 – Updates for release 0.97-2

bates — Wed, 06 Jul 2005 16:24:33 +0000

bates – 4 file(s) modified
Updates for release 0.97-2

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

Rev 1635 – Clean up

bates — Tue, 05 Jul 2005 00:38:09 +0000

bates – 1 file(s) modified
Clean up

~ /trunk/Matrix/src/lmer.c

Rev 1630 – Added AGQ for glmer class

bates — Mon, 04 Jul 2005 14:56:57 +0000

bates – 1 file(s) modified
Added AGQ for glmer class

~ /trunk/Matrix/src/lmer.c

Rev 1617 – Still modifying glmer_devAGQ

bates — Thu, 30 Jun 2005 16:59:12 +0000

bates – 2 file(s) modified
Still modifying glmer_devAGQ

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

Rev 1615 – Developing AGQ but still not right

bates — Tue, 28 Jun 2005 13:58:41 +0000

bates – 1 file(s) modified
Developing AGQ but still not right

~ /trunk/Matrix/src/lmer.c

Rev 1613 – Conditional modes now ok for MCMC - still need sampling ...

bates — Sun, 26 Jun 2005 16:22:56 +0000

bates – 1 file(s) modified
Conditional modes now ok for MCMC - still need sampling methods

~ /trunk/Matrix/src/lmer.c

Rev 1612 – More work on MCMC (still incomplete)

bates — Sun, 26 Jun 2005 03:42:21 +0000

bates – 3 file(s) modified
More work on MCMC (still incomplete)

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

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 1596 – Adding AGQ (but not yet correct)

bates — Wed, 15 Jun 2005 15:52:19 +0000

bates – 2 file(s) modified
Adding AGQ (but not yet correct)

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

Rev 1595 – Non-working version - needs adjustment of deviance by multiplicative factor

bates — Tue, 14 Jun 2005 04:05:54 +0000

bates – 1 file(s) modified
Non-working version - needs adjustment of deviance by multiplicative factor

~ /trunk/Matrix/src/lmer.c

Rev 1594 – release 0.96-2

bates — Tue, 14 Jun 2005 04:02:57 +0000

bates – 3 file(s) modified
release 0.96-2

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

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 1588 – Adding flag to skip fixed-effects terms (for use with generalized ...

bates — Thu, 09 Jun 2005 18:30:33 +0000

bates – 1 file(s) modified
Adding flag to skip fixed-effects terms (for use with generalized linear or nonlinear models)

~ /trunk/Matrix/src/lmer.c