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

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 3480 – Paring down dependencies

bates — Wed, 23 Aug 2006 22:13:34 +0000

bates – 1 file(s) modified
Paring down dependencies

~ /trunk/Matrix/src/lmer.h

Rev 3431 – using R_VERSION (useful more generally) - does not help

maechler — Fri, 18 Aug 2006 17:00:10 +0000

maechler – 2 file(s) modified
using R_VERSION (useful more generally) - does not help

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

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 3227 – Re-aligned deviance column in mcmcsamp output (and no longer use ...

bates — Sat, 10 Jun 2006 18:06:33 +0000

bates – 3 file(s) modified
Re-aligned deviance column in mcmcsamp output (and no longer use index of -1); added calculations of mer_hat_trace

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

Rev 3222 – Many changes in mcmcsample and other places

bates — Thu, 08 Jun 2006 16:06:02 +0000

bates – 2 file(s) modified
Many changes in mcmcsample and other places

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

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 3153 – Initial denom_df attempt

bates — Sat, 20 May 2006 11:34:18 +0000

bates – 4 file(s) modified
Initial denom_df attempt

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

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 2194 – Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

bates — Fri, 13 Jan 2006 23:47:38 +0000

bates – 10 file(s) modified
Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/src/chm_common.h
~ /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
~ /trunk/Matrix/tests/lmer.R

Rev 2174 – Switch to supernodal Cholesky representation of mer objects

bates — Thu, 12 Jan 2006 03:17:24 +0000

bates – 4 file(s) modified
Switch to supernodal Cholesky representation of mer objects

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

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

Rev 1560 – Release 0.95-11

bates — Sun, 29 May 2005 02:15:35 +0000

bates – 3 file(s) modified
Release 0.95-11

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

Rev 1540 – Fold bCrosstab.[ch] into lmer.[ch]

bates — Tue, 17 May 2005 17:45:24 +0000

bates – 4 file(s) modified
Fold bCrosstab.[ch] into lmer.[ch]

x /trunk/Matrix/src/bCrosstab.c
x /trunk/Matrix/src/bCrosstab.h
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1454 – changes related to Laplace approximation, including new function to compute ...

deepayan — Tue, 03 May 2005 16:08:26 +0000

deepayan – 4 file(s) modified
changes related to Laplace approximation, including new function to compute parts of the deviance in C code, which doesn't currently work

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

Rev 1448 – additions related to the Laplace approximation in glmm lmer models

deepayan — Fri, 29 Apr 2005 14:42:39 +0000

deepayan – 4 file(s) modified
additions related to the Laplace approximation in glmm lmer models

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

Rev 1217 – Added C function lmer_fitted

bates — Fri, 04 Mar 2005 03:49:53 +0000

bates – 3 file(s) modified
Added C function lmer_fitted

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

Rev 1054 – rearranging utility functions in the C code

bates — Thu, 10 Feb 2005 08:15:12 +0000

bates – 11 file(s) modified
rearranging utility functions in the C code

~ /trunk/Matrix/Done
~ /trunk/Matrix/R/dgBCMatrix.R
~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/dgBCMatrix.c
~ /trunk/Matrix/src/dgBCMatrix.h
~ /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
~ /trunk/Matrix/TODO

Rev 987 – renaming and rearranging classes

bates — Wed, 02 Feb 2005 19:11:51 +0000

bates – 28 file(s) modified
renaming and rearranging classes

~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/bCrosstab.h
+ /trunk/Matrix/src/dCholCMatrix.c (copied from /trunk/Matrix/src/sscChol.c@982)
+ /trunk/Matrix/src/dCholCMatrix.h (copied from /trunk/Matrix/src/sscChol.h@982)
~ /trunk/Matrix/src/DEPS.mkf
~ /trunk/Matrix/src/dgBCMatrix.c
~ /trunk/Matrix/src/dgBCMatrix.h
~ /trunk/Matrix/src/dgCMatrix.c
~ /trunk/Matrix/src/dgCMatrix.h
~ /trunk/Matrix/src/dgTMatrix.c
~ /trunk/Matrix/src/dgTMatrix.h
x /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.c
x /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.h
~ /trunk/Matrix/src/dpoMatrix.c
~ /trunk/Matrix/src/dpoMatrix.h
~ /trunk/Matrix/src/dsCMatrix.c
~ /trunk/Matrix/src/dsCMatrix.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/SOURCES_C.mkf
x /trunk/Matrix/src/sscChol.c
x /trunk/Matrix/src/sscChol.h
~ /trunk/Matrix/src/sscCrosstab.c
~ /trunk/Matrix/src/sscCrosstab.h
+ /trunk/Matrix/src/triplet_to_col.c (copied from /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.c@982)
+ /trunk/Matrix/src/triplet_to_col.h (copied from /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.h@982)

Rev 984 – renaming and rearranging classes

bates — Wed, 02 Feb 2005 17:20:55 +0000

bates – 8 file(s) modified
renaming and rearranging classes

~ /trunk/Matrix/src/bCrosstab.c
x /trunk/Matrix/src/cscBlocked.c
x /trunk/Matrix/src/cscBlocked.h
+ /trunk/Matrix/src/dgBCMatrix.c (copied from /trunk/Matrix/src/cscBlocked.c@982)
+ /trunk/Matrix/src/dgBCMatrix.h (copied from /trunk/Matrix/src/cscBlocked.h@982)
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h