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.