2007-11-09 18:33 Douglas Bates <bates@stat.wisc.edu> * [r4845] R/AllGeneric.R,lmer.R, NAMESPACE: new functions lmer2, for back-compatibility, and devvals * [r4847] DESCRIPTION: standardized LICENSE information * [r4848] src/lmer.c: Minor clean-up * [r4849] inst/doc/Implementation.Rnw: Switch location of datasets to MEMSS package 2007-10-06 18:06 Douglas Bates <bates@stat.wisc.edu> * [r4816] DESCRIPTION, R/lmer.R: Update fitted and resid methods; new version of R 2007-10-04 20:33 Douglas Bates <bates@stat.wisc.edu> * [r4809] src/lmer.c: remove alloc3DArray (part of R from 2.6.0) 2007-09-26 17:32 Douglas Bates <bates@stat.wisc.edu> * [r4787] R/lmer.R: Reinstitute the names of variance components from formatVC 2007-09-25 15:08 Douglas Bates <bates@stat.wisc.edu> * [r4782] src/lmer.h: Provide definition of alloca for Solaris 10 2007-09-11 22:17 Douglas Bates <bates@stat.wisc.edu> * [r4767] src/init.c, src/lmer.c, src/lmer.h: Cleanup, add new functions for .Call 2007-08-31 10:50 Douglas Bates <bates@stat.wisc.edu> * [r4750] man/lmer-class.Rd, man/ranef.Rd: Update documentation * [r4751] Done, ToDo: Update * [r4752] R/AllClass.R: Incorporate mu and resid slots in mer class * [r4753] R/lmer.R: Incorporate mu and resid slots in mer class 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu> * [r4731] src/lmer.h: declare alloca * [r4732] src/lmer.c: unused variable 2007-08-12 13:21 Douglas Bates <bates@stat.wisc.edu> * [r4728] R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c, src/lmer.c: changes for glmer (not yet complete), code cleanup 2007-08-04 23:44 Douglas Bates <bates@stat.wisc.edu> * [r4709] R/AllClass.R, R/lmer.R, man/lmer.Rd, src/Syms.h, src/init.c, src/lmer.c, src/lmer.h: Got nlmer working 2007-08-03 19:19 Douglas Bates <bates@stat.wisc.edu> * [r4705] NAMESPACE, R/AllClass.R, man/lmer-class.Rd, man/ranef.Rd: Change name of ranef.mer class * [r4706] R/lmList.R, R/lmer.R, R/pedigree.R: Use seq_along * [r4707] DESCRIPTION, src/init.c, src/lme4_utils.h, src/lmer.c, src/lmer.h, src/pedigree.c, src/pedigree.h: Update Matrix API, amalgamate source files, include R.h before other R headers 2007-08-01 16:29 Douglas Bates <bates@stat.wisc.edu> * [r4688] src/lme4_utils.h: Preparing to remove this file * [r4689] src/pedigree.h: Preparing to remove this file 2007-07-26 14:28 Douglas Bates <bates@stat.wisc.edu> * [r4664] R/lmer.R, inst/doc/Implementation.Rnw, inst/doc/Theory.Rnw, man/cbpp.Rd, man/lmer-class.Rd, man/lmer.Rd, src/init.c, src/lmer.c, src/lmer.h: work on glmer, nlmer, and lmer_postVar * [r4678] src/lmer.c: Conditional compilation of alloc3DArray 2007-07-23 13:26 Douglas Bates <bates@stat.wisc.edu> * [r4658] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: More work on nlmer 2007-07-20 20:41 Douglas Bates <bates@stat.wisc.edu> * [r4654] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Got nlmer running for simple models but still problems with multiple random effects per level 2007-07-19 21:28 Douglas Bates <bates@stat.wisc.edu> * [r4640] R/AllGeneric.R, R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: More work on nlmer and glmer * [r4645] Done, ToDo: Tracking * [r4646] R/AllClass.R, R/lmer.R, man/lmer.Rd, src/init.c, src/lmer.c, src/lmer.h: More work on nlmer. Consistency of classes. 2007-07-17 22:12 Douglas Bates <bates@stat.wisc.edu> * [r4715] R/AllClass.R, R/lmer.R, ToDo, inst/doc/Implementation.Rnw, man/lmer-class.Rd, src/init.c, src/lmer.c, src/lmer.h: Update nlmer and clean up * [r4717] src/lmer.c: Work on glmer * [r4635] R/lmer.R, man/cbpp.Rd, src/init.c, src/lmer.c, src/lmer.h: Working on glmer_condDev 2007-07-16 23:02 Douglas Bates <bates@stat.wisc.edu> * [r4620] R/AllClass.R, R/AllGeneric.R, R/lmer.R, man/lmer.Rd, src/init.c, src/lmer.c, src/lmer.h: Preparing for a beta release * [r4621] man/lmer-class.Rd, man/mcmcsamp.Rd, man/ranef.Rd, tests/lmer.R: Adjust tests and examples for unimplemented or broken functions and methods * [r4622] src/lmer.c: documentation infelicity * [r4623] R/AllClass.R, R/lmer.R: Rationalize summary class structure * [r4624] R/mlirt.R: Remove references to defunct C functions * [r4627] src/lmer.c: New version of calculation of update in glmer conditional modes 2007-07-13 21:34 Douglas Bates <bates@stat.wisc.edu> * [r4613] inst/doc/Theory.Rnw: Use Poisson mixed model as example of GLMM * [r4614] man/lmer.Rd: Incorporate glmer example * [r4615] R/lmer.R: Add mkdims utility for lmer and glmer 2007-07-12 20:11 Douglas Bates <bates@stat.wisc.edu> * [r4607] R/lmer.R, man/cbpp.Rd: glmer skeleton and test 2007-07-11 20:30 Douglas Bates <bates@stat.wisc.edu> * [r4602] src/lmer.c: Part of the extension of lmer to correlated random effects * [r4603] inst/doc/Theory.Rnw: Minor cleanup * [r4604] src/init.c, src/lmer.c, src/lmer.h: Correct ordering of operations in PSTp_dense_mult; allow external access to mer_update_VtL 2007-07-10 16:36 Douglas Bates <bates@stat.wisc.edu> * [r4591] inst/doc/Theory.Rnw, inst/doc/lme4.bib: Move definitive version of vignette sources to this branch * [r4592] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Clean up the code. 2007-07-09 23:08 Douglas Bates <bates@stat.wisc.edu> * [r4576] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Change name famType to ftyp and Nested to nest in the dims vector (output form is easier to read) * [r4577] inst/doc/Implementation.Rnw, inst/doc/Theory.Rnw: updates of vignettes * [r4584] src/lmer.c: Use Alloca macro, call update_VtL from within lmer_update_dev and not in update_deviance 2007-07-06 16:34 Douglas Bates <bates@stat.wisc.edu> * [r4562] man/lmer-class.Rd: Move nlmer class documentation to lmer-class.Rd * [r4563] R/lmer.R, src/lmer.c, src/pedigree.c: Got new lmer running on models with independent r.e.'s 2007-07-05 23:05 Douglas Bates <bates@stat.wisc.edu> * [r4557] NAMESPACE, R/AllClass.R, R/carryOver.R, R/lmer.R, R/mlirt.R, man/VarCorr.Rd, man/fixef.Rd, man/hatTrace.Rd, man/lmer-class.Rd, man/lmer.Rd, man/mcmcsamp.Rd, man/nlmer-class.Rd, man/nlmer.Rd, man/ranef.Rd, src/init.c, src/lmer.c, src/lmer.h: First cut at the docs and some methods including printing 2007-07-04 18:38 Douglas Bates <bates@stat.wisc.edu> * [r4546] R/AllClass.R, R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Replaced the C functions glmer_create and nlmer_create by R code 2007-07-03 14:43 Douglas Bates <bates@stat.wisc.edu> * [r4539] inst/doc/Doxyfile: Added Doxyfile (not yet working to my satisfaction). * [r4540] inst/doc/Doxyfile: Change version number (should take this from the DESCRIPTION file). * [r4541] src/lmer.c: Use a macro to obtain the L slot as a CHM_FR object 2007-07-02 22:38 Douglas Bates <bates@stat.wisc.edu> * [r4537] R/AllClass.R, R/lmer.R, ToDo, src/Syms.h, src/init.c, src/lmer.c, src/lmer.h: Got a version that runs a simple model fit! Hooray! 2007-06-29 03:41 Douglas Bates <bates@stat.wisc.edu> * [r4516] src/Syms.h, src/init.c, src/lmer2.c: rationalizing the symbols * [r4517] src/Syms.h, src/lme4_utils.h, src/lmer.c, src/lmer.h, src/lmer2.c, src/lmer2.h: re-arranging file names 2007-06-28 21:00 Douglas Bates <bates@stat.wisc.edu> * [r4514] ChangeLog, DESCRIPTION, NAMESPACE, R/AllClass.R, R/lmer.R, inst/doc/Theory.Rnw, man/gsummary.Rd, man/lmList.Rd, src/Syms.h, src/Wishart.c, src/Wishart.h, src/glmer.c, src/glmer.h, src/init.c, src/lme4_utils.c, src/lme4_utils.h, src/lmer.c, src/lmer.h, src/lmer2.c, src/lmer2.h, src/pedigree.h: Switch lmer2 to lmer, glmer and nlmer * [r4515] src/unused: incorporated useful parts into lmer.c 2007-06-20 14:08 Douglas Bates <bates@stat.wisc.edu> * [r4490] R/lmer.R: Do not throw an error when nlev[i] == nobs for the Poisson family * [r4491] inst/doc/Theory.Rnw: Tighten up the description of GLMMs * [r4492] DESCRIPTION: Version 0.99875-2 2007-06-11 19:02 Douglas Bates <bates@stat.wisc.edu> * [r4449] DESCRIPTION, inst/doc/Theory.Rnw, inst/doc/lme4.bib: Added Theory vignette, release 0.99875-1 2007-06-07 21:15 Douglas Bates <bates@stat.wisc.edu> * [r4446] DESCRIPTION, NAMESPACE, R/AllClass.R, R/lmer.R, man/VarCorr.Rd, man/nlmer-class.Rd, man/nlmer.Rd, src/init.c, src/lmer2.c, src/lmer2.h: A working nlmer - hooray! 2007-06-03 19:16 Douglas Bates <bates@stat.wisc.edu> * [r4414] R/AllClass.R, R/lmer.R, src/init.c, src/lmer2.c, src/lmer2.h: More modifications to nlmer