ChangeLog

2012-01-07  Douglas Bates <bates@stat.wisc.edu>

	* man/GHrule.Rd, man/NelderMead-class.Rd, man/NelderMead.Rd,
	  man/golden-class.Rd, man/golden.Rd, man/lmer.Rd, man/mkdevfun.Rd:
	  Documentation updates.
	* R/lmer.R, R/profile.R, tests/lmer-1.R: Nlmer now working (for nAGQ=1).
	  Updated tests and got profile working again.
	* R/AllClass.R, R/lmer.R, src/external.cpp, src/optimizer.h: Allowed
	  setting options in the NelderMead optimizer. Switched so that this is
	  the default in glmer.
	* R/AllClass.R, R/lmer.R, src/external.cpp, src/predModule.cpp: More
	  work on nlmer.

2011-12-31  Douglas Bates <bates@stat.wisc.edu>

	* src/predModule.cpp: Add an explicit copy of the mapped sparse matrix
	  to a sparse matrix in updateL

2011-12-28  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Change maximum iterations error to a warning.
	* DESCRIPTION: New version number.
	* R/lmer.R: Allowed choice of optimizer in glmer at least.
	* R/AllClass.R: Extended and exported the NelderMead class
	* src/external.cpp, src/optimizer.cpp, src/optimizer.h: Removed
	  debugging code, added methods to NelderMead to set convergence
	  characteristics and exported same.

2011-12-22  Douglas Bates <bates@stat.wisc.edu>

	* NAMESPACE, R/AllClass.R, src/external.cpp, src/optimizer.cpp,
	  src/optimizer.h: Tuned the Nelder-Mead optimizer a bit and got rid of
	  some of the noise.
	* R/lmer.R, man/lmer.Rd, src/external.cpp: Incorporated aGQ code in the
	  glmer function itself. Eliminated the doFit argument which is
	  redundant when devFunOnly is also used.

2011-12-21  Douglas Bates <bates@stat.wisc.edu>

	* src/external.cpp: Added the glmerAGQ function and did some cleanup.
	* src/predModule.cpp: Delete some debugging code.
	* R/lmer.R: Updates in glmer, aGQ not yet added but soon will be.
	* R/GHrule.R: Rename the knots on the z scale as 'z', not 'k'
	* NAMESPACE: Export the golden class and class generator object

2011-12-16  Douglas Bates <bates@stat.wisc.edu>

	* src/respModule.cpp, src/respModule.h: Clean up declarations by
	  declaring a typedef for Eigen::Map<Eigen::VectorXd>

2011-12-15  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Adopt new version of the merPredD$new function that uses S.
	* R/GHrule.R: Added an R function, based on SparseGrid:::GQN to evaluate
	  a matrix of nodes, weights and log-density for Gauss-Hermite
	  quadrature against a Gaussian density.
	* R/AllClass.R, src/optimizer.h: Added a reverse-communication golden
	  search algorithm class

2011-12-12  Douglas Bates <bates@stat.wisc.edu>

	* src/external.cpp: Fat-finger error. I meant to commit this file and
	  not glmFamily.h
	* src/glmFamily.h, src/optimizer.cpp, src/optimizer.h: Added simple
	  optimizers (Golden search for bounded 1-dimensional and Nelder-Mead
	  for multidimensional).

2011-12-07  Douglas Bates <bates@stat.wisc.edu>

	* R/AllClass.R, R/lmer.R, src/external.cpp, src/predModule.cpp,
	  src/predModule.h: Allow regeneration of pointers in merPredD objects.

2011-12-06  Douglas Bates <bates@stat.wisc.edu>

	* R/AllClass.R, R/lmer.R, src/external.cpp, src/predModule.cpp,
	  src/predModule.h: Add many more fields to the merPredD class and allow
	  for serialize/unserialize. Lower the default tolPwrss as per testing
	  by Ben.

2011-12-05  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION, R/AllClass.R, R/lmer.R, man/lmer.Rd, man/mkdevfun.Rd,
	  man/refitML.Rd, src/external.cpp, src/predModule.cpp,
	  src/predModule.h, src/respModule.cpp, src/respModule.h: Use mapped
	  objects in C++ structures so that serialize/unserialize will work.

2011-11-29  Douglas Bates <bates@stat.wisc.edu>

	* R/profile.R: More fixing of labels. Fix up strip names to
	  reflect sigma, not log(sigma).

2011-11-29  Douglas Bates <bates@stat.wisc.edu>

	* R/profile.R: Profiling now works for lmer models with variance
	  components only, including the case of a single fixed-effects
	  parameter. Labeling of some plots needs to be corrected.
	* src/predModule.cpp, src/predModule.h: Modifications for the 0-column X
	  matrix case used in profiling.
	* src/Gauss_Hermite.cpp, src/Gauss_Hermite.h, src/external.cpp: Move
	  Gaussian quadrature knot/weight calculations to the Gqr package.

2011-11-28  Douglas Bates <bates@stat.wisc.edu>

	* R/profile.R: Got profile working for cases where the number of
	  fixed-effects is greater than 1. Need a "do nothing gracefully" clause
	  for p == 1.
	* R/lmer.R: Use the value of emptyenv(), not the funtion itself. Add ...
	  to refitML generic and method
	* R/lmer.R: Use separate mkdevfun in glmer. Switch devFunOnly to an
	  integer value where 1 and 2 refer to different stages.

2011-11-17  Douglas Bates <bates@stat.wisc.edu>

	* R/AllClass.R: Correct and extend the allInfo method for the glmResp
	  class.
	* ToDo: Need to come up with a crafty way of creating a copy of the
	  reference class object with the external pointer. It may work to just
	  copy it then set the PTR to be a NULL pointer.

2011-11-16  Douglas Bates <bates@stat.wisc.edu>

	* src/Gauss_Hermite.cpp, src/Gauss_Hermite.h, src/external.cpp: Add
	  another method of creating Gaussian quadrature rules. Export the GHQ
	  class.
	* tests/lmer-1.R: Comment out enough tests to make R CMD check succeed.
	* R/lmer.R: Clean up some functions and methods that were causing
	  problems with the tests.
	* man/glmFamily-class.Rd, man/glmFamily.Rd, man/lmResp-class.Rd,
	  man/lmResp.Rd: Document the class generator object and the reference
	  class (for now).
	* NAMESPACE: Remove redundant S3 method vcov.summary.mer

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

	* src/external.cpp: Correct the argument counts for externally visible
	  glmFamily accessors
	* man/sleepstudy.Rd: disable a test - need to check what rcond(fm@re)
	  did in lme4a
	* man/reTrms.Rd: No longer used
	* man/profile-methods.Rd: Don't run examples until the code has been
	  fixed
	* man/merPredD-class.Rd, man/merPredD.Rd: Try to document reference
	  class generator object this way
	* inst/unitTests/runit.compDev.R, inst/unitTests/runit.link.R,
	  inst/unitTests/runit.lmerResp.R: update tests (compDev is inert at
	  present but could be activated for glmer tests)

2011-11-02  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION: Bump the version number.
	* NAMESPACE, man/glmFamily-class.Rd: Export and document the glmFamily
	  reference class and generator object
	* src/Makevars, src/Makevars.win: Add a Makevars.win file. Make the
	  factory-fresh setting of CPPFLAGS suppress warnings.
	* man/lmerMod-class.Rd, man/merMod-class.Rd, man/merPredD-class.Rd:
	  incorporate documentation for [gn]lmerMod-class in the merMod-class
	  docs; document merPredD-class
	* inst/doc/PLSvGLS.Rnw, inst/doc/PLSvGLS.pdf, inst/doc/Theory.Rnw,
	  inst/doc/Theory.pdf, inst/doc/lme4.bib, vignettes,
	  vignettes/PLSvGLS.Rnw, vignettes/PLSvGLS.pdf, vignettes/Theory.Rnw,
	  vignettes/Theory.pdf, vignettes/lme4.bib: Move vignette sources to a
	  vignettes directory per recommendations for R-2.14.0

2011-10-18  Douglas Bates <bates@stat.wisc.edu>

	* man/mkdevfun.Rd: Cleanup.
	* NAMESPACE: Export S3 method for devcomp.
	* man/lmResp-class.Rd: Document response reference classes and
	  constructor objects
	* man/chmSp.Rd, man/deFeMod.Rd, man/feModule-class.Rd, man/glmFamily.Rd,
	  man/glmerResp.Rd, man/lmerResp-class.Rd, man/lmerResp.Rd,
	  man/reModule-class.Rd, man/reModule.Rd: Remove documentation of
	  no-longer-used classes from Rcpp modules
	* man/cbpp.Rd: From R-2.14.0 on getCall is imported from the stats
	  package.
	* R/lmer.R: Getter and setter for REML field in lmerResp should be reml,
	  not REML.

2011-10-17  Douglas Bates <bates@stat.wisc.edu>

	* src/respModule.cpp, src/respModule.h: Change working weights to be a
	  matrix.
	* src/predModule.cpp: Thinko regarding 0-based indices.

2011-10-14  Douglas Bates <bates@stat.wisc.edu>

	* DESCRIPTION, NAMESPACE, R/AllClass.R, R/lmer.R, src/external.cpp,
	  src/predModule.cpp, src/predModule.h, src/respModule.cpp,
	  src/respModule.h: nlmer added. Increment calculation for PWRSS works
	  but not yet incorporated in R code.

2011-10-03  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Small but important change in checking for object weights in
	  environment rho in mkRespMod2

2011-09-30  Douglas Bates <bates@stat.wisc.edu>

	* R/AllClass.R, R/lmer.R: Use inheritance on reference classes, being
	  careful about package installation. Create a cleaner version of
	  mkRespMod2.
	* NAMESPACE: export more classes
	* DESCRIPTION: new version and date

2011-09-29  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Modify mkRespMod for nlmer response.
	* src/external.cpp: Add isNullExtPtr .Call'able function for Ptr/ptr
	  formulation.
	* NAMESPACE, R/AllClass.R: new organization of response classes. Use
	  Ptr/ptr formulation to generate external pointers.

2011-09-27  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: More components/slots/etc. available in getME()
	* R/AllClass.R, R/lmer.R: Reinstitute the Gp slot in merMod objects

2011-09-23  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/lmer.R, man/ranef.Rd: *must* use lme4Eigen::: inside devFun()
	  [evaluated from C++]
	* man/refitML.Rd: add doc. + example
	* man/Pastes.Rd, man/Penicillin.Rd: reactivate the image(L) plots

2011-09-22  Martin Maechler  <maechler@stat.math.ethz.ch>

	* NAMESPACE, R/AllClass.R, R/lmer.R: tolPwrss - for now

2011-09-22  Douglas Bates <bates@stat.wisc.edu>

	* data/VerbAgg.rda: Correct labels on Gender, use camelCase consistently
	  on item labels.
	* data/sleepstudy.rda: switch to bzip2 compression for smaller file
	  size.

2011-09-21  Douglas Bates <bates@stat.wisc.edu>

	* src/external.cpp: Added a function to check on the SIMD instruction
	  sets in use by Eigen.

2011-09-20  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Do the same number of pwrssUpdate calls with compDev=TRUE or
	  FALSE
	* src/external.cpp, src/predModule.cpp, src/predModule.h: Remove
	  debugging code. solve and solveU methods for merPredD class now return
	  the numerator of the convergence criterion.
	* R/lmer.R: Need to pass the pointer, not the reference class object.
	  Modifications to glmer, pwrssUpdate, etc. to get glmer working.

2011-09-20  Martin Maechler  <maechler@stat.math.ethz.ch>

	* R/lmer.R, man/lmer.Rd, src/external.cpp: non-hardcorded PWRSS
	  tolerance

2011-09-19  Douglas Bates <bates@stat.wisc.edu>

	* NAMESPACE, R/AllClass.R, R/lmer.R, src/external.cpp, src/glmFamily.h,
	  src/respModule.cpp: created a glmFamily reference class and allowed
	  for compiled version of glmer update using working residuals and
	  weights (not currently working properly, use compDev=FALSE argument to
	  glmer)
	* DESCRIPTION: new version and date
	* src/external.cpp, src/predModule.cpp, src/predModule.h,
	  src/respModule.cpp, src/respModule.h: Moved all externally .Call'able
	  function definitions to external.cpp. external.h and init.cpp are no
	  longer needed.

2011-09-19  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Clean up printMer and summary.merMod
	* src/external.cpp, src/external.h, src/lmer.cpp, src/lmer.h: rename
	  lmer.[h,cpp] to external.[h,cpp]
	* R/lmer.R: Initial iterations in glmer (the nAGQ=0L part) now working.
	  Later iterations still need work.

2011-09-16  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Use fac argument in call to sqrL() method. glmer now
	  iterates but does not yet converge.
	* src/predModule.cpp: Add the - u_i on the rhs of the equation in the
	  solve method.
	* R/AllClass.R, src/init.cpp, src/predModule.cpp, src/predModule.h: New
	  'allInfo' method for glmerResp reference class. Added .Call'able
	  extractors for Utr and Vtr to merPredD class.

2011-09-14  Douglas Bates <bates@stat.wisc.edu>

	* R/lmer.R: Modified glmer to return a meaningful object when
	  doFit=FALSE.
	* R/AllClass.R, src/init.cpp, src/respModule.cpp, src/respModule.h:
	  Added methods and new classes for response modules. Modified names of
	  .Call'able functions to make them easier to understand.
	* src/predModule.cpp: Use d_LamtUt instead of recomputing d_Lambdat *
	  d_Ut
	* inst/unitTests/runit.link.R: Modified link/muEta/variance unit tests
	  to use a glmerResp object.

2011-09-13  Douglas Bates <bates@stat.wisc.edu>

	* src/Makevars: Add more explanation about the -DNDEBUG compiler flag
	  and when to use it.
	* R/AllClass.R, R/lmer.R, src/init.cpp, src/predModule.cpp,
	  src/predModule.h, src/respModule.cpp, src/respModule.h: Many more
	  methods added to the reference class definitions, as well as
	  documentation. glmer is now working in the sense that it doesn't
	  segfault, however it is not yet performing the calculations correctly.
	* DESCRIPTION: Remove RcppModule specification.
2011-09-12  Douglas Bates <bates@stat.wisc.edu>

	* src/respModule.h: Clean up calculation of working residuals.
	* R/lmer.R: Still working on glmer, not there yet.
	* R/AllClass.R, src/init.cpp, src/predModule.cpp, src/predModule.h,
	  src/respModule.cpp, src/respModule.h: Added many more R-callable entry
	  points in respModule and predModule, incorporating them as methods in
	  the reference class definitions.
	* src/Makevars: Allow for suppression of assert statements with -DNDEBUG
	  (R CMD check complains)

2011-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION, NAMESPACE, R/AllClass.R, R/lmer.R,
	  inst/unitTests/runTests.R, tests/doRunit.R, tests/drop.R,
	  tests/extras.R, tests/lmer-1.Rout.save, tests/lmer.R,
	  tests/lmer2_ex.R, tests/nlmer-conv.R, tests/nlmer.R, tests/throw.R:
	  more updates
	* man/Dyestuff.Rd, man/VarCorr.Rd, man/cbpp.Rd, man/getME.Rd,
	  man/lmer.Rd, man/lmerMod-class.Rd, man/merMod-class.Rd,
	  man/mkdevfun.Rd, man/ranef.Rd, man/reModule-class.Rd: considerably
	  more documentation

2011-09-11  Douglas Bates <bates@stat.wisc.edu>

	* NAMESPACE, R/AllClass.R, R/lmer.R, src/init.cpp, src/respModule.cpp,
	  src/respModule.h: Added glmerResp class and began glmer function.
	  Still needs work.

2011-09-11  Douglas Bates <bates@stat.wisc.edu>

	* src/predModule.[h,cpp]: Wrote native C++ L() method. Somehow calling
	  ::M_chm_factor_as_SEXP was messing up memory.
	* tests/vcov-etc.R, tests/lmer-conv.R: Test using this package not lme4a
	* R/AllClass.R, src/init.cpp, src/predModule.cpp, src/predModule.h: Add
	  capability of extracting L from a merPredD object

2011-09-10  Martin Maechler  <maechler@stat.math.ethz.ch>

	* DESCRIPTION, NAMESPACE, R/lmer.R, man/Pastes.Rd, man/Penicillin.Rd,
	  man/bootMer.Rd, man/getL.Rd, man/getME.Rd, man/merMod-class.Rd:
	  getME() for all three(!) versions of lme4 -- deprecate getL() where it
	  exists

2011-09-02  Douglas Bates <bates@stat.wisc.edu>

	* src/init.cpp, src/predModule.cpp, src/predModule.h: Drop the check for
	  diagonal Lambda. Cache the value of LamtUt and update it in place with
	  new method updateLamtUt.

2011-08-31  Douglas Bates <bates@stat.wisc.edu>

	* src/init.cpp, src/predModule.cpp, src/predModule.h: Finally got a
	  work-around for the "pruning of sparse product" problem. Also added a
	  diagonalLambda method.
	* R/AllClass.R: Add a "fitted" method to the lmerResp reference class.
	  Re-arrange code.

2011-08-30  Douglas Bates <bates@stat.wisc.edu>

	* src/predModule.cpp, src/predModule.h: Drop some debugging code.
	  Isolate the calculation of LamtUt to try to find out what goes wrong
	  in there.
	* R/lmer.R: Update the ranef method for merPredD storing Lambdat, not
	  Lambda

2011-08-29  Douglas Bates <bates@stat.wisc.edu>

	* R/AllGeneric.R, R/utilities.R, src/init.cpp, src/predModule.cpp,
	  src/respModule.cpp, src/respModule.h: Code cleanup - remove exception
	  declarations, use specific 'using' statements within blocks instead of
	  'using namespace' statements.

2011-08-28  Douglas Bates <bates@stat.wisc.edu>

	* NAMESPACE, src/eigen.h, src/glmFamily.cpp, src/glmFamily.h,
	  src/lmer.cpp, src/predModule.cpp, src/predModule.h,
	  src/respModule.cpp, src/respModule.h: Initialize d_delb and d_delu in
	  predModule to zero (not doing so was causing hard-to-debug errors).
	  Remove exception declarations as suggested for Rcpp. Make declaration
	  of short names for Eigen classes and constants namespace-specific.

2011-08-11  Douglas Bates <bates@stat.wisc.edu>

	* src/predModule.cpp: Using solveInPlace to try to avoid memory
	  problems.

2011-07-31  Douglas Bates <bates@stat.wisc.edu>

	* src/lmer.cpp, src/predModule.cpp, src/predModule.h: Trying to track
	  dowm memory problem in the evaluation of delu. It looks like it is in
	  the CholmodSupport.h file in Eigen but my intended fix apparently
	  didn't succeed.
	* R/AllClass.R: Modified according to John Chambers' suggestions.

2011-07-29  Douglas Bates <bates@stat.wisc.edu>

	* src/respModule.cpp, src/respModule.h: Flailing around trying to find
	  the source of the memory problems. valgrind claims there is an
	  uninitialized value being used in a log call within the Laplace method
	  but I can't find it.
	* src/predModule.h: Remove unneeded template keywords (caught by an old
	  compiler).
	* R/AllClass.R: Realized that the initialize method should return an
	  object.
	* R/AllClass.R, R/lmer.R, src/init.cpp, src/predModule.cpp,
	  src/predModule.h: Switch to Lambdat and Zt and the CHOLMOD
	  factorization. Special code for diagonal Lambda.
	* src/predModule.cpp: One more attempt. Still failing on the boundary
	  when the number of nonzeros changes.

2011-07-28  Douglas Bates <bates@stat.wisc.edu>

	* src/init.cpp, src/predModule.cpp, src/predModule.h: First shot at a
	  version with the Eigen/Matrix/CHOLMOD links. Compiles and loads but
	  not yet tested. Checking in so I can access it from home.
	* src/init.cpp, src/lmer.cpp, src/predModule.cpp, src/predModule.h: More
	  getter methods defined in C++ code and reference class. Remove some
	  debugging code.
	* R/AllClass.R, R/AllGeneric.R, R/lmList.R, R/lmer.R: More changes to
	  use S3 methods when dispatching on the first argument only.
	* DESCRIPTION, NAMESPACE: Change dependencies and imports.

2011-07-26  Douglas Bates <bates@stat.wisc.edu>

	* * initialize this archive.