R-packages – /branches/gappy-lmer/src/init.c

Rev 4767 – Cleanup, add new functions for .Call

bates — Tue, 11 Sep 2007 22:17:21 +0000

bates – 3 file(s) modified
Cleanup, add new functions for .Call

~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4728 – changes for glmer (not yet complete), code cleanup

bates — Sun, 12 Aug 2007 13:21:10 +0000

bates – 5 file(s) modified
changes for glmer (not yet complete), code cleanup

~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/Syms.h

Rev 4715 – Update nlmer and clean up

bates — Tue, 07 Aug 2007 01:17:27 +0000

bates – 8 file(s) modified
Update nlmer and clean up

~ /branches/gappy-lmer/inst/doc/Implementation.Rnw
~ /branches/gappy-lmer/man/lmer-class.Rd
~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h
~ /branches/gappy-lmer/ToDo

Rev 4709 – Got nlmer working

bates — Sat, 04 Aug 2007 23:44:27 +0000

bates – 7 file(s) modified
Got nlmer working

~ /branches/gappy-lmer/man/lmer.Rd
~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h
~ /branches/gappy-lmer/src/Syms.h

Rev 4707 – Update Matrix API, amalgamate source files, include R.h before other ...

bates — Fri, 03 Aug 2007 19:31:23 +0000

bates – 7 file(s) modified
Update Matrix API, amalgamate source files, include R.h before other R headers

~ /branches/gappy-lmer/DESCRIPTION
~ /branches/gappy-lmer/src/init.c
x /branches/gappy-lmer/src/lme4_utils.h
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h
x /branches/gappy-lmer/src/pedigree.c
x /branches/gappy-lmer/src/pedigree.h

Rev 4664 – work on glmer, nlmer, and lmer_postVar

bates — Tue, 24 Jul 2007 21:24:15 +0000

bates – 9 file(s) modified
work on glmer, nlmer, and lmer_postVar

~ /branches/gappy-lmer/inst/doc/Implementation.Rnw
~ /branches/gappy-lmer/inst/doc/Theory.Rnw
~ /branches/gappy-lmer/man/cbpp.Rd
~ /branches/gappy-lmer/man/lmer-class.Rd
~ /branches/gappy-lmer/man/lmer.Rd
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4658 – More work on nlmer

bates — Mon, 23 Jul 2007 13:26:47 +0000

bates – 4 file(s) modified
More work on nlmer

~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4654 – Got nlmer running for simple models but still problems with ...

bates — Fri, 20 Jul 2007 20:41:16 +0000

bates – 4 file(s) modified
Got nlmer running for simple models but still problems with multiple random effects per level

~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4646 – More work on nlmer. Consistency of classes.

bates — Thu, 19 Jul 2007 21:28:40 +0000

bates – 6 file(s) modified
More work on nlmer. Consistency of classes.

Rev 4640 – More work on nlmer and glmer

bates — Thu, 19 Jul 2007 12:41:14 +0000

bates – 5 file(s) modified
More work on nlmer and glmer

~ /branches/gappy-lmer/R/AllGeneric.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4635 – Working on glmer_condDev

bates — Tue, 17 Jul 2007 22:12:30 +0000

bates – 5 file(s) modified
Working on glmer_condDev

~ /branches/gappy-lmer/man/cbpp.Rd
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4620 – Preparing for a beta release

bates — Mon, 16 Jul 2007 14:18:24 +0000

bates – 7 file(s) modified
Preparing for a beta release

~ /branches/gappy-lmer/man/lmer.Rd
~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/AllGeneric.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4604 – Correct ordering of operations in PSTp_dense_mult; allow external access to ...

bates — Wed, 11 Jul 2007 20:33:27 +0000

bates – 3 file(s) modified
Correct ordering of operations in PSTp_dense_mult; allow external access to mer_update_VtL

~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4592 – Clean up the code.

bates — Tue, 10 Jul 2007 16:36:56 +0000

bates – 4 file(s) modified
Clean up the code.

~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4576 – Change name famType to ftyp and Nested to nest in ...

bates — Mon, 09 Jul 2007 18:54:29 +0000

bates – 4 file(s) modified
Change name famType to ftyp and Nested to nest in the dims vector (output form is easier to read)

~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4557 – First cut at the docs and some methods including printing

bates — Thu, 05 Jul 2007 23:05:13 +0000

bates – 17 file(s) modified
First cut at the docs and some methods including printing

~ /branches/gappy-lmer/man/fixef.Rd
~ /branches/gappy-lmer/man/hatTrace.Rd
~ /branches/gappy-lmer/man/lmer-class.Rd
~ /branches/gappy-lmer/man/lmer.Rd
~ /branches/gappy-lmer/man/mcmcsamp.Rd
x /branches/gappy-lmer/man/nlmer-class.Rd
x /branches/gappy-lmer/man/nlmer.Rd
~ /branches/gappy-lmer/man/ranef.Rd
~ /branches/gappy-lmer/man/VarCorr.Rd
~ /branches/gappy-lmer/NAMESPACE
~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/carryOver.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/R/mlirt.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4546 – Replaced the C functions glmer_create and nlmer_create by R code

bates — Wed, 04 Jul 2007 18:38:25 +0000

bates – 5 file(s) modified
Replaced the C functions glmer_create and nlmer_create by R code

~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h

Rev 4537 – Got a version that runs a simple model fit! ...

bates — Mon, 02 Jul 2007 22:38:33 +0000

bates – 7 file(s) modified
Got a version that runs a simple model fit! Hooray!

~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer.c
~ /branches/gappy-lmer/src/lmer.h
~ /branches/gappy-lmer/src/Syms.h
~ /branches/gappy-lmer/ToDo

Rev 4516 – rationalizing the symbols

bates — Fri, 29 Jun 2007 03:41:43 +0000

bates – 3 file(s) modified
rationalizing the symbols

~ /branches/gappy-lmer/src/init.c
~ /branches/gappy-lmer/src/lmer2.c
~ /branches/gappy-lmer/src/Syms.h

Rev 4514 – Switch lmer2 to lmer, glmer and nlmer

bates — Thu, 28 Jun 2007 21:00:19 +0000

bates – 21 file(s) modified
Switch lmer2 to lmer, glmer and nlmer

~ /branches/gappy-lmer/ChangeLog
~ /branches/gappy-lmer/DESCRIPTION
~ /branches/gappy-lmer/inst/doc/Theory.Rnw
~ /branches/gappy-lmer/man/gsummary.Rd
~ /branches/gappy-lmer/man/lmList.Rd
~ /branches/gappy-lmer/NAMESPACE
~ /branches/gappy-lmer/R/AllClass.R
~ /branches/gappy-lmer/R/lmer.R
x /branches/gappy-lmer/src/glmer.c
x /branches/gappy-lmer/src/glmer.h
~ /branches/gappy-lmer/src/init.c
x /branches/gappy-lmer/src/lme4_utils.c
x /branches/gappy-lmer/src/lme4_utils.h
x /branches/gappy-lmer/src/lmer.c
x /branches/gappy-lmer/src/lmer.h
~ /branches/gappy-lmer/src/lmer2.c
~ /branches/gappy-lmer/src/lmer2.h
~ /branches/gappy-lmer/src/pedigree.h
~ /branches/gappy-lmer/src/Syms.h
x /branches/gappy-lmer/src/Wishart.c
x /branches/gappy-lmer/src/Wishart.h

Rev 4475 – lmer based on vertical concatenation of indicators

bates — Mon, 18 Jun 2007 16:34:38 +0000

bates – 1 file(s) modified
lmer based on vertical concatenation of indicators

+ /branches/gappy-lmer (copied from /trunk/lme4@4474)

Rev 4446 – A working nlmer - hooray!

bates — Thu, 07 Jun 2007 21:15:01 +0000

bates – 10 file(s) modified
A working nlmer - hooray!

~ /trunk/lme4/DESCRIPTION
+ /trunk/lme4/man/nlmer-class.Rd
+ /trunk/lme4/man/nlmer.Rd
~ /trunk/lme4/man/VarCorr.Rd
~ /trunk/lme4/NAMESPACE
~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4436 – Finally got nlmer_bhat running - hooray!

bates — Tue, 05 Jun 2007 21:13:54 +0000

bates – 3 file(s) modified
Finally got nlmer_bhat running - hooray!

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4414 – More modifications to nlmer

bates — Sun, 03 Jun 2007 19:16:42 +0000

bates – 5 file(s) modified
More modifications to nlmer

~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4410 – more work on nlmer

bates — Sat, 02 Jun 2007 16:15:35 +0000

bates – 5 file(s) modified
more work on nlmer

~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4387 – Adding more nlmer capabilities

bates — Fri, 25 May 2007 18:17:40 +0000

bates – 7 file(s) modified
Adding more nlmer capabilities

~ /trunk/lme4/ChangeLog
~ /trunk/lme4/NAMESPACE
~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4348 – Beginning an nlmer class and constructor

bates — Tue, 15 May 2007 13:47:30 +0000

bates – 3 file(s) modified
Beginning an nlmer class and constructor

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4236 – More on lmer2 version of glmm models

bates — Mon, 02 Apr 2007 21:30:16 +0000

bates – 4 file(s) modified
More on lmer2 version of glmm models

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h
~ /trunk/lme4/src/Syms.h

Rev 4234 – glmm under lmer2 improvements

bates — Mon, 02 Apr 2007 14:38:36 +0000

bates – 4 file(s) modified
glmm under lmer2 improvements

~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4217 – Add lmer2_update_y

bates — Thu, 29 Mar 2007 00:10:43 +0000

bates – 3 file(s) modified
Add lmer2_update_y

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4200 – Modified and simplified lmer2

bates — Sun, 25 Mar 2007 19:35:56 +0000

bates – 7 file(s) modified
Modified and simplified lmer2

~ /trunk/lme4/INDEX
~ /trunk/lme4/NAMESPACE
~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4188 – Begin moving glmm fitting to mer2 representation

bates — Tue, 20 Mar 2007 22:45:52 +0000

bates – 5 file(s) modified
Begin moving glmm fitting to mer2 representation

~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h

Rev 4185 – Use renamed header and stubs files; Use lmer2_create

bates — Fri, 16 Mar 2007 22:16:41 +0000

bates – 8 file(s) modified
Use renamed header and stubs files; Use lmer2_create

~ /trunk/lme4/INDEX
~ /trunk/lme4/NAMESPACE
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h
~ /trunk/lme4/src/local_stubs.c
~ /trunk/lme4/src/Makevars

Rev 4177 – Call port optimization code from with the C code.

bates — Mon, 12 Mar 2007 13:29:16 +0000

bates – 8 file(s) modified
Call port optimization code from with the C code.

~ /trunk/lme4/DESCRIPTION
~ /trunk/lme4/INDEX
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer2.c
~ /trunk/lme4/src/lmer2.h
~ /trunk/lme4/src/local_stubs.c
~ /trunk/lme4/src/Makevars

Rev 4155 – Split lmer.c into lmer.c and lmer2.c

bates — Fri, 16 Feb 2007 22:36:41 +0000

bates – 5 file(s) modified
Split lmer.c into lmer.c and lmer2.c

~ /trunk/lme4/INDEX
~ /trunk/lme4/man/ranef.Rd
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer.c
~ /trunk/lme4/src/lmer.h

Rev 4145 – Clean up representation, add internal_update_A, add validity check

bates — Mon, 12 Feb 2007 01:38:05 +0000

bates – 7 file(s) modified
Clean up representation, add internal_update_A, add validity check

~ /trunk/lme4/INDEX
~ /trunk/lme4/R/AllClass.R
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer.c
~ /trunk/lme4/src/lmer.h
~ /trunk/lme4/src/Syms.h

Rev 4144 – Change to enum from defines - fix some -Wall warnings

bates — Sun, 11 Feb 2007 00:41:18 +0000

bates – 4 file(s) modified
Change to enum from defines - fix some -Wall warnings

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lme4_utils.h
~ /trunk/lme4/src/lmer.c
~ /trunk/lme4/src/lmer.h

Rev 4139 – Preparing for mer2_MCMCsamp

bates — Thu, 08 Feb 2007 23:46:07 +0000

bates – 3 file(s) modified
Preparing for mer2_MCMCsamp

~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer.c
~ /trunk/lme4/src/lmer.h

Rev 4127 – Added ranef for mer2 representation (including posterior variances)

bates — Sun, 04 Feb 2007 19:40:11 +0000

bates – 5 file(s) modified
Added ranef for mer2 representation (including posterior variances)

~ /trunk/lme4/DESCRIPTION
~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/init.c
~ /trunk/lme4/src/lmer.c
~ /trunk/lme4/src/lmer.h

Rev 4100 – Incorporate "deviance" argument in mcmcsamp method for glmer objects

bates — Thu, 25 Jan 2007 20:19:13 +0000

bates – 4 file(s) modified
Incorporate "deviance" argument in mcmcsamp method for glmer objects

~ /trunk/lme4/R/lmer.R
~ /trunk/lme4/src/glmer.c
~ /trunk/lme4/src/glmer.h
~ /trunk/lme4/src/init.c