2011-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version): 0.999375-41
	(Depends): Matrix(>= 0.9996875-1)

2011-07-22  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION: Long overdue release (apologies, Dieter)

2011-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION, NAMESPACE, R/AllGeneric.R, R/drop1-etc.R, R/newmethods.R,
	  tests/drop.R, tests/lmer-1.Rout.save, tests/nlmer.Rout.save: drop1()
	  etc lme4 & lme4a - cosmetics; renamed file

2011-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* inst/doc/Implementation.Rnw, inst/doc/PLSvGLS.Rnw,
	  inst/doc/Theory.Rnw: aargh.. strip.white=true -- R 2.14 compatibly
	* inst/doc/Implementation.Rnw, inst/doc/PLSvGLS.Rnw,
	  inst/doc/Theory.Rnw: Sweave strip.white="true" -- R 2.14 compatibly
	  correct

2011-04-11  Douglas Bates <bates@stat.wisc.edu>

	* NAMESPACE, R/newmethods.R: Minor changes to names for S3 methods and
	  to exports

2011-04-09  Ben Bolker <bbolker@gmail.com>

	* NAMESPACE: changes for new methods
	* R/newmethods.R, tests/drop.R: first attempt at methods (terms,
	  extractAIC, drop1)

2011-03-11  Douglas Bates <bates@stat.wisc.edu>

	* R/carryOver.R: Changes to the lagged_factor function, which I forgot
	  to commit.
	* NAMESPACE: Allow for exportPattern, currently commented out, in
	  debugging applications

2011-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>

	* ChangeLog, DESCRIPTION, R/lmer.R, ToDo, man/mer-class.Rd,
	  tests/simulate.R: cosmetic - including Version++ --> 0.999375-39,
	  preparing for a release with changed simulate() behavior

2011-02-28  Ben Bolker <bbolker@gmail.com>

	* R/lmer.R: simulate(): return data.frame even for nsim=1 - compatibly
	with other simulate() methods.

2011-02-13  Ben Bolker <bbolker@gmail.com>

	* tests/simulate.R: New tests for simulate()

	* R/lmer.R, data/PB.rda, man/cbpp_PB.Rd, man/mer-class.Rd,
	  man/simulate.Rd, man/sleepstudy_PB.Rd: added simulate method for GLMMs
	  split refit() and simulate() docs out to a separate file
	  for testing/example convenience, add parametric bootstrap results as
	  data

2011-02-08  Douglas Bates  <bates@stat.wisc.edu>

	* R/carryOver.R (lagged_factor): Correct undiscovered error in
	lagging of the variables (this file contains private functions
	that were used by Harold Doran and me).

	* DESCRIPTION: Add Ben to the list of authors and change the
	maintainer address.  Bump version number and date.

2010-11-09  Douglas Bates  <bates@stat.wisc.edu>

	* R/lmer.R (glmer): Forbid the use of "quasi" families in glmer.

2010-10-21  Martin Maechler  <maechler@stat.math.ethz.ch>

	* tests/lmer-1.R (.unsafe.BLAS): allow to set  identical <- all.equal
	for some tests {mainly for Mac OSX i386}

2010-06-03  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Date, Version): 0.999375-34

	* R/lmer.R (glmer_finalize): for a glmer(), allow q == n

	* tests/lmer-1.R (rPoisGLMMi): test example, originating from Ben Bolker

2009-09-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION (Version, Depends): 0.999375-32; needs latest version of Matrix

	* src/init.c (lme4_R_cholmod_error): now using own CHOLMOD error
	handler, which does reset the 'Common' "as to start".

	* tests/lmer-1.R: re-activate first part of mcmcsamp() examples.

2009-06-02  Douglas Bates <bates@stat.wisc.edu>

	* [r318] R/lmer.R: Duh! Forgot the meaning of "stopifnot" and did not
	  reverse the condition.  Now fixed.
	* [r316] DESCRIPTION: New release
	* [r315] R/lmer.R: More informative error message for lmer_finalize.
	  Also check this condition in glmer_finalize.
	* [r314] src/lmer.c: Suppress check on q > n in update_u.

2009-05-20  Douglas Bates <bates@stat.wisc.edu>

	* [r312] DESCRIPTION: New release; allow earlier version of Matrix
	  released with R-2.9.0
	* [r311] R/lmer.R: Force copy of fitted model passed to mcmcsamp
	* [r310] man/refit.Rd: Add alias for mer,matrix method

2009-05-12  Douglas Bates <bates@stat.wisc.edu>

	* [r309] tests/nlmer.Rout.save: Slight difference in calculated results
	* [r307] DESCRIPTION, src/lmer.c: Avoid alloca for arrays of size q (C
	  stack overflows); New release

2009-04-28  Douglas Bates <bates@stat.wisc.edu>

	* [r305] R/lmer.R: Refit method for matrix response, contributed
 	  by Ben Bolker

2009-03-24  Douglas Bates <bates@stat.wisc.edu>

	* [r302] DESCRIPTION, man/Penicillin.Rd, src/lmer.c, tests/lmer-1.R,
	  tests/lmer-1.Rout.save: Handle previously ignored offset specification
	  in LMMs; add tests; new version
	* [r301] inst/doc/Theory.Rnw, inst/doc/Theory.pdf: Updates
	* [r300] R/lmer.R: Remove .Internal call and redundant check

2009-01-05  Douglas Bates <bates@stat.wisc.edu>

	* [r275] R/carryOver.R: evaluate the random effects on the AR1 and
	  general models.  (The carryOver function is not exported.)

2008-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>

	* man/ranef.Rd: add 'whichel' argument to help page

	* DESCRIPTION (Date, Version): 0.999375-28 to be released,
	mainly for re-installation against new Matrix.

2008-10-19  Douglas Bates <bates@stat.wisc.edu>

	* [r241] man/lmer.Rd: update

2008-09-26  Douglas Bates <bates@stat.wisc.edu>

	* [r239] DESCRIPTION: New release
	* [r238] R/carryOver.R: Carryover model revisions (unexported)
	* [r237] R/lmer.R, src/lmer.c: Handle weights correctly for LMMs, fix
	  some of the problems reported by Terry Therneau
	* [r236] man/lmer.Rd: Cosmetic
	* [r235] NAMESPACE: Allow for currently unexported predict method
	* [r234] tests/lmer-1.Rout.save, tests/nlmer.R, tests/nlmer.Rout.save:
	  remove some unstable tests which should be more stable in refactored
	  code
	* [r233] inst/doc/Doxyfile, inst/doc/Implementation.pdf,
	  inst/doc/PLSvGLS.pdf, inst/doc/Theory.Rnw, inst/doc/Theory.pdf: Revise
	  Theory.Rnw for the allcoef version

2008-09-15  Douglas Bates <bates@stat.wisc.edu>

	* [r231] R/carryOver.R: Re-write of carryOver with utility functions
	* [r230] src/lmer.c: Changes in update_dev from Bin Dai
	* [r229] R/lmer.R: Added a preliminary, unexported predict method

2008-09-09  Douglas Bates <bates@stat.wisc.edu>

	* [r227] R/lmer.R, src/lmer.c: Add new positions in the deviance slot
	* [r226] inst/doc/Theory.Rnw, inst/doc/Theory.pdf: Revising the
	  computational methods document in new notation
	* [r225] man/mer-class.Rd, man/ranef.Rd: Allow which argument in
	  mer_postVar
	* [r224] R/AllClass.R, R/carryOver.R, R/lmer.R, src/init.c, src/lmer.c,
	  src/lmer.h: Global change of nf (number of factors) to nt (number of
	  terms); Allow which argument in mer_postVar

2008-09-02  Douglas Bates <bates@stat.wisc.edu>

	* [r223] inst/doc/Theory.Rnw: Yet another rewrite of the theory

2008-08-25  Douglas Bates <bates@stat.wisc.edu>

	* [r222] DESCRIPTION, R/AllClass.R, R/lmer.R,
	  inst/doc/Implementation.pdf, inst/doc/PLSvGLS.pdf,
	  inst/doc/Theory.pdf, src/Syms.h, src/init.c, src/lmer.c, src/lmer.h:
	  Incorporate AGQ code from Bin Dai; Fold verbose indicator into dims;
	  add mxit and mxfn to dims
2008-08-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* NAMESPACE: importFrom(stats, AIC) + comments on import(stats)

2008-08-13  Douglas Bates <bates@stat.wisc.edu>

        * [r212] pkg/R/lmer.R: Don't call LMM code on GLMMs or NLMMs in the
          anova method (Antje Nuthmann)

2008-08-08  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/lmer.R (lmerFactorList): check matrix validity: error out
	instead of later segfault.
	(printMer): improve abbreviation for row/col names of correlation
	matrix.

	* tests/lmer-1.R: regression test against seg.fault

2008-08-06  Douglas Bates <bates@stat.wisc.edu>

        * [r210] pkg/DESCRIPTION, pkg/man/ranef.Rd: Change qqmath examples to
          dotplot, new release

2008-08-03  Douglas Bates <bates@stat.wisc.edu>

        * [r209] pkg/NAMESPACE, pkg/R/lmer.R: Add dotplot method for the (S3)
          ranef.mer class

2008-07-31  Douglas Bates <bates@stat.wisc.edu>

        * [r206] pkg/src/init.c, pkg/src/lmer.c, pkg/src/lmer.h: Added lme4_ghq
          function based on Fortran sources.

2008-07-27  Douglas Bates <bates@stat.wisc.edu>

        * [r204] pkg/data/VerbAgg.rda, pkg/man/VerbAgg.Rd: Reduce back to a data
          set with factors only

2008-07-25  Douglas Bates <bates@stat.wisc.edu>

	* [r202] DESCRIPTION, src/lmer.c: Implement cloglog inverse link
	  function, new release
	* [r201] DESCRIPTION, R/jml.R, data/VerbAgg.rda, man/VerbAgg.Rd: Add
	  VerbAgg data set and documentation. Prepare for release

2008-07-17  Douglas Bates <bates@stat.wisc.edu>

	* [r197] R/lmer.R: Use dummy call in new("mer", ...) not huge call that
	  is later overwritten
	* [r196] src/init.c: Switch to CALLDEF macro

2008-07-12  Douglas Bates <bates@stat.wisc.edu>

	* [r193] inst/doc/Implementation.pdf, inst/doc/PLSvGLS.pdf,
	  inst/doc/Theory.pdf: Updates of vignettes

2008-07-11  Douglas Bates <bates@stat.wisc.edu>

	* [r192] DESCRIPTION, R/lmer.R: Remove mc from list with doFit = FALSE
	  and in arguments to lmer_finalize and glmer_finalize. New version

2008-07-10  Douglas Bates <bates@stat.wisc.edu>

	* [r190] inst/doc/Implementation.pdf, inst/doc/PLSvGLS.Rnw,
	  inst/doc/PLSvGLS.pdf, inst/doc/Theory.pdf: Add a section on the
	  hatMatrix to PLSvGLS. Update PDFs
	* [r189] DESCRIPTION, R/lmer.R, man/lmer.Rd: incorporate doFit argument
	  in lmer and friends. Create glmer_finalize function. New release
	* [r188] tests/nlmer.R, tests/nlmer.Rout.save: nlmer tests and results
	  updated to new methods
	* [r187] src/lmer.c: Correction, from Bin Dai, to calculation of
	  deviance for NLMMs

2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r183] DESCRIPTION: aargh! forgot to commit the Matrix(>= 0.999375-10)
	  dependency

2008-06-26  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r182] ChangeLog, DESCRIPTION, tests/nlmer.R, tests/nlmer.Rout.save:
	  higher tolerance in nlmer tests; Version .999375-20

	* DESCRIPTION (Version): 0.999375-20 ready for CRAN

	* tests/nlmer.R (allEQ): test with high tolerance.

2008-06-25  Douglas Bates <bates@stat.wisc.edu>

	* [r180] DESCRIPTION, R/lmer.R, src/init.c, src/lmer.c,
	  src/lmer.h: Fix single-argument anova method; new version

2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r179] R/lmer.R: expand(<mer>, .) fix {in Tblock()}; using
	  Matrix:::.diag2tT() for now
	* [r178] tests/nlmer-conv.R, tests/nlmer.R,
	  tests/nlmer.Rout.save: split convergence monitoring from "normal"
	  nlmer tests

2008-06-24  Douglas Bates <bates@stat.wisc.edu>

	* [r177] man/mer-class.Rd, man/merMCMC-class.Rd,
	  man/refit.Rd: Updates and corrections

2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r176] tests/lmer-1.R, tests/lmer-1.Rout.save,
	  tests/lmer.R, tests/lmer.Rout.save: rename tests/lmer.R
	  (easier to distinguish from R/lmer.R)

2008-06-24  Douglas Bates <bates@stat.wisc.edu>

	* [r174] DESCRIPTION: New version
	* [r173] inst/doc/Implementation.pdf, inst/doc/PLSvGLS.Rnw,
	  inst/doc/PLSvGLS.pdf, inst/doc/Theory.pdf: Updates, add PDF files to
	  SVN archive.
	* [r172] inst/doc/Implementation.Rnw, inst/doc/Notes.Rnw,
	  inst/doc/PLSvGLS.Rnw: Use a less vague name
	* [r171] inst/doc/Notes.Rnw: Clean up text

2008-06-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r170] NAMESPACE: comments (about "resid") only
	* [r169] tests/lmer.Rout.save: update (oops)
	* [r168] tests/lmer-conv.R, tests/lmer.R, tests/lmer.Rout.save: lmer
	  tests: move convergence part to new separate lmer-conv.R

2008-06-22  Douglas Bates <bates@stat.wisc.edu>

	* [r166] DESCRIPTION: New release
	* [r165] R/lmer.R, man/mer-class.Rd: Added sparse expand method for mer
	  and an example of its use

2008-06-21  Douglas Bates <bates@stat.wisc.edu>

	* [r161] NAMESPACE, R/lmer.R, man/fixef.Rd, man/hatTrace.Rd,
	  man/lmList-class.Rd, man/lmList.Rd, man/lmer.Rd, man/mcmcsamp.Rd,
	  man/mer-class.Rd, man/merMCMC-class.Rd, man/ranef.Rd: Removed
	  visibility of hatTrace and the confint method for mer objects. Major
	  documentation cleanup.
	* [r160] NEWS: Added a NEWS file
	* [r157] tests/lmer.R, tests/lmer.Rout.save: Get rid of calls to
	  system.time in tests - results are not reproducible
	* [r156] NAMESPACE, R/AllGeneric.R, R/gsummary.R, R/lmList.R, R/lmer.R,
	  man/cbpp.Rd, man/gsummary.Rd, man/pooledSD.Rd, man/ranef.Rd: Remove
	  gsummary; fold pooledSD into lmList; add drop argument to ranef;
	  shorten long title in cbpp docs

2008-06-20  Douglas Bates <bates@stat.wisc.edu>

	* [r155] data/Pastes.rda, data/Penicillin.rda, man/Dyestuff.Rd,
	  man/Pastes.Rd, man/Penicillin.Rd: Added Dyestuff2, Pastes and
	  Penicillin data sets. Updated documentation

2008-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>

	* [r153] R/lmer.R: more cleanup in 'method' back compatibility ; typo in
	  message
	* [r152] R/lmer.R: method: s/Laplacian/Laplace/ for back compatibility

2008-06-19  Douglas Bates <bates@stat.wisc.edu>

	* [r151] src/Syms.h, src/init.c, src/lmer.c: Insert hooks for AGQ code
	* [r150] tests/lmer.Rout.save, tests/nlmer.Rout.save: Add saved test
	  output files for comparisons
	* [r149] tests/lmer.R: Replace method argument by REML
	* [r148] R/AllClass.R, R/lmer.R, man/cake.Rd, man/lmer.Rd: Replace
	  method argument by REML or nAGQ, as appropriate
	* [r147] DESCRIPTION: Add Martin and Bin as authors; new version

2008-06-18  Bin Dai <dai@stat.wisc.edu>

	* [r146] R/AllClass.R, R/lmer.R, src/lmer.c: Get ready for AGQ

2008-06-16  Bin Dai <dai@stat.wisc.edu>

	* [r145] R/lmer.R, src/lmer.c: Basic methods lines added
	* [r144] R/AllClass.R, src/Syms.h, src/init.c, src/lmer.c: test of svn

2008-06-01  Douglas Bates <bates@stat.wisc.edu>

	* [r143] inst/doc/Doxyfile: Update project number
	* [r142] NAMESPACE, man/merMCMC-class.Rd: Document and export as.matrix
	  method for merMCMC

2008-05-30  Douglas Bates <bates@stat.wisc.edu>

	* [r139] src/init.c, src/lmer.c, src/lmer.h: Remove Wishart sampling and
	  replace with least-squares based S sampling; Reorganize code in lmer.c
	* [r138] R/lmer.R: Added methods for merMCMC class

2008-05-25  Douglas Bates <bates@stat.wisc.edu>

	* [r137] inst/doc/Implementation.Rnw: Minor cleanup - still many
	  mistakes

2008-05-14  Douglas Bates <bates@stat.wisc.edu>

	* [r130] DESCRIPTION, man/refit.Rd, tests/nlmer.R: Moved nlmer tests to
	  the tests directory, added help page for refit, new release
	* [r129] R/lmer.R: Incorporated patch from Henric Nilsson to fix bug in
	  model names in multiple model anova output

2008-05-13  Douglas Bates <bates@stat.wisc.edu>

	* [r126] R/lmer.R: Allow ranef( , postVar = TRUE) for cases where each
	  r.e. term has a separate factor
2008-04-25  Douglas Bates <bates@stat.wisc.edu>

	* [r124] DESCRIPTION: New release
	* [r123] tests/nlmer.R: Moved extended nlmer tests to tests directory
	* [r122] NAMESPACE, R/AllGeneric.R, R/lmer.R, man/VarCorr.Rd,
	  man/lmer.Rd, man/mer-class.Rd, man/refit.Rd, src/init.c, src/lmer.c,
	  src/lmer.h: Added refit generic and methods and implemented the
	  simulate method. Fixed a problem with family = gaussian reported by
	  Henrik Parn. Reimplemented VarCorr method to avoid problems with
	  indefinite solutions.

2008-04-14  Douglas Bates <bates@stat.wisc.edu>

	* [r121] data/Dyestuff.rda, man/Dyestuff.Rd: Added the Dyestuff data

2008-04-08  Douglas Bates <bates@stat.wisc.edu>

	* [r120] DESCRIPTION, R/lmer.R, src/lmer.h: Restore names to the
	  components of a VarCorr object; allow for more options in the hidden
	  devmat function; Add the Dyestuff example; New release

2008-04-02  Douglas Bates <bates@stat.wisc.edu>

	* [r119] inst/doc/Notes.Rnw: Minor revision - principally grammar and
	  sentence structure
	* [r118] Done, ToDo: Change some of the ToDo tasks to Done
	* [r117] DESCRIPTION, R/lmer.R: Added the hidden function devmat; New
	  release.

2008-03-31  Douglas Bates <bates@stat.wisc.edu>

        * [r115] DESCRIPTION: New release
        * [r114] tests/lmer.R: Clean up tests for new form of the flist slot
        * [r113] R/carryOver.R, R/mlirt.R: Remove defunct constructions to pass
          codeTools checks
        * [r112] NAMESPACE, R/AllClass.R, R/lmer.R, man/mer-class.Rd,
          src/lmer.c: Change form of flist slot to allow for duplicates; Change
          ranef.mer and coef.mer to S3-classed objects
        * [r111] inst/doc/Implementation.Rnw: Update for recent changes in
          package
        * [r110] inst/doc/Notes.Rnw: New vignette based on notes for Andrew
          Robinson

2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>

        * [r109] man/mer-class.Rd: get rid of codoc() warning

2008-03-26  Douglas Bates <bates@stat.wisc.edu>

        * [r108] DESCRIPTION: New version
        * [r106] NAMESPACE, R/AllClass.R, R/lmer.R, R/mlirt.R, man/VarCorr.Rd,
          man/merMCMC-class.Rd, src/init.c, src/lmer.c, src/lmer.h: Add
          graphical diagnostics for merMCMC class; Remove cnames slot; Initial
          VarCorr for merMCMC

2008-03-17  Douglas Bates <bates@stat.wisc.edu>

        * [r105] DESCRIPTION: New version; update dependencies
        * [r104] src/lmer.c: Move ldetL2 calculations to Matrix package and call
          the exported function from update_L
        * [r103] R/lmer.R: Encapsulate post-model-matrix operations for lmer in
          lmer_finalize.

2008-03-17  Douglas Bates <bates@stat.wisc.edu>

        * [r101] R/AllClass.R: Add classes merExt and lmerStratVar

2008-03-14  Douglas Bates <bates@stat.wisc.edu>

        * [r100] R/lmer.R: Fix from Henric Nilsson for fitted and resid methods
          under na.action = na.exclude
        * [r99] R/AllClass.R, R/AllGeneric.R, man/mer-class.Rd,
          man/merMCMC-class.Rd: Cleanup in code; documentation update
        * [r98] R/lmer.R: Coercion of merMCMC to matrix

2008-03-12  Douglas Bates <bates@stat.wisc.edu>

        * [r97] DESCRIPTION, R/AllClass.R, R/lmer.R, man/HPDinterval.Rd: Fix
          HPDinterval methods (Robert Kushler <kushler@oakland.edu>) and
          documentation; New release

2008-03-11  Douglas Bates <bates@stat.wisc.edu>

        * [r94] DESCRIPTION, NAMESPACE, R/pedigree.R, man/HPDinterval.Rd,
          man/merMCMC-class.Rd, man/pooledSD.Rd: Update NAMESPACE and
          documentation; move pedigree functions to pedigreemm package; New
          release
        * [r93] R/AllClass.R, R/pedigree.R, man/pedigree-class.Rd,
          man/pedigree.Rd, src/init.c, src/lmer.c, src/lmer.h: Move pedigree
          class and methods for the class to the pedigreemm package

2008-03-10  Douglas Bates <bates@stat.wisc.edu>

        * [r90] DESCRIPTION: New alpha release
        * [r89] NAMESPACE, R/AllGeneric.R, R/lmList.R, R/lmer.R, src/init.c,
          src/lmer.c, src/lmer.h: More macros; use sigmaML and sigmaREML
          components in deviance slot; fix MCMC_ST for order and mer_MCMCsamp
          for df in sigma sample

2008-03-03  Douglas Bates <bates@stat.wisc.edu>

        * [r88] src/lmer.c: Weighted LMM without segfault. Use for(int i=...)
          throughout.

2008-03-01  Douglas Bates <bates@stat.wisc.edu>

        * [r87] src/lmer.c: Added macros
        * [r86] inst/doc/Doxyfile: Update version
        * [r85] man/merMCMC-class.Rd: Update.

2008-02-29  Douglas Bates <bates@stat.wisc.edu>

        * [r82] man/merMCMC-class.Rd: documentation for merMCMC class
        * [r81] src/lmer.c: update doxygen documentation
        * [r80] DESCRIPTION: New release so others can try mcmcsamp
        * [r79] NAMESPACE, R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c,
          src/lmer.c, src/lmer.h: Create and incorporate merMCMC class. mcmcsamp
          is running again but the results look wrong.

2008-02-14  Douglas Bates <bates@stat.wisc.edu>

        * [r77] DESCRIPTION: new release
        * [r76] R/lmer.R: disable mcmcsamp until fixed
        * [r75] inst/doc/Implementation.Rnw: update for new slot names
        * [r74] src/lmer.c: more macros
        * [r73] man/mer-class.Rd: add model.matrix and model.frame to examples

2008-02-11  Douglas Bates <bates@stat.wisc.edu>

        * [r71] R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c, src/lmer.c:
          Change slot names RCXy and RXy to RZX and RX
        * [r70] NAMESPACE, R/lmer.R: Add methods for model.matrix and
          model.frame
        * [r69] R/jml.R: Change parameterization to remove the intercept term

2008-02-05  Douglas Bates <bates@stat.wisc.edu>

        * [r67] R/AllClass.R, R/jml.R, src/Syms.h, src/init.c, src/lmer.c,
          src/lmer.h: Added sparseRasch function and some auxillaries
        * [r66] R/lmer.R: Moved names of elements of dims and deviance slots to
          separate variables. Changed initialization in VecFromNames

2008-02-03  Douglas Bates <bates@stat.wisc.edu>

        * [r65] R/lmer.R: Omit famName slot value in calls to new("mer",...)

2008-02-01  Douglas Bates <bates@stat.wisc.edu>

        * [r64] DESCRIPTION: Version 0.999375-3
        * [r63] man/cbpp.Rd: Remove unmatched brace from previous \dontrun
          specification
        * [r62] R/AllClass.R: Remove defunct famName slot

2008-01-31  Douglas Bates <bates@stat.wisc.edu>

        * [r61] src/Syms.h, src/init.c: delete references to defunct pnames
          symbol
        * [r60] R/lmer.R: Coerce offset and weights to double, use correct
          offset in call to glm.fit in glmer - reported by
          David.Duffy@qimr.edu.au
        * [r59] ChangeLog:

2008-01-30  Douglas Bates <bates@stat.wisc.edu>

	* [r56] DESCRIPTION, inst/doc/Doxyfile: New release
	* [r57] R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c, src/lmer.c,
	  src/lmer.h: Orthogonalize link and var. Create A in R code. Change
	  slot priorWt to pWt.

2008-01-25  Douglas Bates <bates@stat.wisc.edu>

	* [r50] ToDo: Remove items that are now done
	* [r51] man/cbpp.Rd: Run both examples again
	* [r52] R/jml.R: Split off the creation of the binary response matrix
	* [r53] R/lmer.R: Bug #90 (fix due to Steven McKinney
	  <smckinney@bccrc.ca>), modify slots; V instead of v and pnames
	* [r54] R/AllClass.R: Modify slots; V instead of v and pnames
	* [r55] src/Syms.h, src/init.c, src/lmer.c: Modify slots; V instead of v
	  and pnames. Zero the accumulator in update_L so that nlmer works
	  again.

2008-01-21  Douglas Bates <bates@stat.wisc.edu>

	* [r44] R/jml.R: A pure R version of joint maximum likelihood estimation
	  of the parameters in the Rasch model
	* [r45] R/mlirt.R: Spelling correction
	* [r46] inst/doc/Doxyfile: Do not save dot files
	* [r47] inst/doc/Implementation.Rnw: Update to class definitions in
	  0.999375-1
	* [r48] DESCRIPTION: Alpha release of version 1.0
	* [r49] R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c, src/lmer.c,
	  src/lmer.h: Clean up mer class. Some of the items on the feature
	  request and bug lists.

2008-01-07  Douglas Bates <bates@stat.wisc.edu>

	* [r40] inst/doc/Implementation.Rnw: Update to current slot names
	* [r41] man/lmer.Rd: Add links thanks to <gregor.gorjanc@bfro.uni-lj.si>

2008-01-06  Douglas Bates <bates@stat.wisc.edu>

	* [r36] src/Syms.h, src/init.c, src/lmer.c: Add macros, fix bug in
	  update_RX, correct declarations with R_INLINE
	* [r37] R/AllClass.R, R/lmer.R: Change name RVXy to RCXy

2008-01-03  Douglas Bates <bates@stat.wisc.edu>

	* [r29] NAMESPACE, R/AllClass.R, R/lmer.R, man/VarCorr.Rd, man/lmer.Rd,
	  man/mcmcsamp.Rd, src/Syms.h, src/init.c, src/lmer.c, src/lmer.h:
	  Remove lmer, nlmer and glmer classes. All necessary slots are now in
	  mer.
	* [r31] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Remove isREML
	  macro, clean up code in mer_postVar now that useSc is saved.
	* [r32] src/Syms.h, src/init.c, src/lmer.c: change TSPp_*_mult to
	  update_ranef with a single argument

2008-01-02  Douglas Bates <bates@stat.wisc.edu>

	* [r25] man/lmer-class.Rd: Update documentation for new class
	  definitions
	* [r26] man/mer-class.Rd: Move to name given in the file
	* [r27] man/lmer-class.Rd:

2007-12-27  Douglas Bates <bates@stat.wisc.edu>

	* [r20] inst/doc/Doxyfile, www/doxygen, many others: Update doxygen
	  configuration, add doxygen html directory
	* [r21] R/lmer.R, src/Syms.h, src/init.c, src/lmer.c, src/lmer.h:
	  Consolidation of functions, doxygen-style documentation
	* [r22] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Move
	  nlmer_create_A to R code

2007-12-24  Douglas Bates <bates@stat.wisc.edu>

	* [r18] inst/doc/Doxyfile: Add the tree view on the left of the html
	  pages
	* [r19] src/Syms.h, src/init.c, src/lmer.c, src/lmer.h: Removing entry
	  points that are not called

2007-12-21  Douglas Bates <bates@stat.wisc.edu>

	* [r17] inst/doc/Doxyfile, src/Syms.h, src/init.c: Doxygen
	  reconfiguration, code cleanup based on calling tree

2007-12-19  Douglas Bates <bates@stat.wisc.edu>

	* [r16] src/lmer.c: More changes in the logic of cond_mode. Looks like
	  this version works properly!

2007-12-17  Douglas Bates <bates@stat.wisc.edu>

	* [r15] src/init.c, src/lmer.c, src/lmer.h: Factor C code; add more
	  externally callable entry points; still not converging.

2007-12-16  Douglas Bates <bates@stat.wisc.edu>

	* [r11] R/lmer.R, src/lmer.c, src/lmer.h: Code cleanup and name change,
	  continued. Last checkin was premature.
	* [r12] inst/doc/Implementation.Rnw: Change .Call names for consistency
	  with the current names
	* [r13] NAMESPACE: Avoid importing the entire namespace from the stats
	  package
	* [r14] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: Externally
	  callable lmer_profiled_deviance and allowing negative verbose values

2007-12-15  Douglas Bates <bates@stat.wisc.edu>

	* [r10] R/lmer.R, src/init.c, src/lmer.c: Code cleanup; change name of
	  derivative matrix Mt for NLMMs to A

2007-12-06  Douglas Bates <bates@stat.wisc.edu>

	* [r8] R/AllGeneric.R: Remove isNested as a generic
	* [r9] R/lmer.R, src/lmer.c: Remove the mtyp element in the dims slot of
	  mer objects

2007-12-03  Douglas Bates <bates@stat.wisc.edu>

	* [r7] README, R/AllClass.R, R/lmer.R, src/Syms.h, src/init.c,
	  src/lmer.c, src/lmer.h: Modifications to classes and methods for lmer
	  and glmer. Lmer now working but glmer still gives incorrect
	  conditional modes and hence incorrect optima.

2007-11-09  Douglas Bates <bates@stat.wisc.edu>

	* [r2] ChangeLog, DESCRIPTION, Done, NAMESPACE, R/AllClass.R,
	  R/AllGeneric.R, R/carryOver.R, R/gsummary.R, R/lmList.R, R/lmer.R,
	  R/mlirt.R, R/pedigree.R, ToDo, inst, inst/doc, inst/doc/Doxyfile,
	  inst/doc/Implementation.Rnw, inst/doc/Theory.Rnw, inst/doc/lme4.bib,
	  man/BIC.Rd, man/VarCorr-class.Rd, man/VarCorr.Rd, man/cake.Rd,
	  man/cbpp.Rd, man/fixef.Rd, man/gsummary.Rd, man/hatTrace.Rd,
	  man/lmList-class.Rd, man/lmList.Rd, man/lmer-class.Rd, man/lmer.Rd,
	  man/mcmcsamp.Rd, man/pedigree-class.Rd, man/pedigree.Rd,
	  man/pooledSD.Rd, man/ranef.Rd, man/sleepstudy.Rd, src, src/Makevars,
	  src/Syms.h, src/init.c, src/lmer.c, src/lmer.h, src/local_stubs.c,
	  tests, tests/extras.R, tests/lmer.R: Initialize R-forge package to
	  what was the gappy-lmer branch
	* [r3] DESCRIPTION: Update Data:, add MEMSS to Suggests:
	* [r4] data, data/cake.rda, data/cbpp.rda, data/sleepstudy.rda: Add the
	  overlooked data directory
	* [r5] man/lmer.Rd: Add an alias for lmer2 in the documentation
	* [r6] R/lmList.R: Applied patch from Nathaniel Smithh <njs@pobox.com>
	  for generalized linear models

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