2008-09-26 Douglas Bates * [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 * [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 * [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 * [r223] inst/doc/Theory.Rnw: Yet another rewrite of the theory 2008-08-25 Douglas Bates * [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 * NAMESPACE: importFrom(stats, AIC) + comments on import(stats) 2008-08-13 Douglas Bates * [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 * 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 * [r210] pkg/DESCRIPTION, pkg/man/ranef.Rd: Change qqmath examples to dotplot, new release 2008-08-03 Douglas Bates * [r209] pkg/NAMESPACE, pkg/R/lmer.R: Add dotplot method for the (S3) ranef.mer class 2008-07-31 Douglas Bates * [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 * [r204] pkg/data/VerbAgg.rda, pkg/man/VerbAgg.Rd: Reduce back to a data set with factors only 2008-07-25 Douglas Bates * [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 * [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 * [r193] inst/doc/Implementation.pdf, inst/doc/PLSvGLS.pdf, inst/doc/Theory.pdf: Updates of vignettes 2008-07-11 Douglas Bates * [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 * [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 * [r183] DESCRIPTION: aargh! forgot to commit the Matrix(>= 0.999375-10) dependency 2008-06-26 Martin Maechler * [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 * [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 * [r179] R/lmer.R: expand(, .) 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 * [r177] man/mer-class.Rd, man/merMCMC-class.Rd, man/refit.Rd: Updates and corrections 2008-06-24 Martin Maechler * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [r146] R/AllClass.R, R/lmer.R, src/lmer.c: Get ready for AGQ 2008-06-16 Bin Dai * [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 * [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 * [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 * [r137] inst/doc/Implementation.Rnw: Minor cleanup - still many mistakes 2008-05-14 Douglas Bates * [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 * [r126] R/lmer.R: Allow ranef( , postVar = TRUE) for cases where each r.e. term has a separate factor 2008-04-25 Douglas Bates * [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 * [r121] data/Dyestuff.rda, man/Dyestuff.Rd: Added the Dyestuff data 2008-04-08 Douglas Bates * [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 * [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 * [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 * [r109] man/mer-class.Rd: get rid of codoc() warning 2008-03-26 Douglas Bates * [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 * [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 * [r101] R/AllClass.R: Add classes merExt and lmerStratVar 2008-03-14 Douglas Bates * [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 * [r97] DESCRIPTION, R/AllClass.R, R/lmer.R, man/HPDinterval.Rd: Fix HPDinterval methods (Robert Kushler ) and documentation; New release 2008-03-11 Douglas Bates * [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 * [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 * [r88] src/lmer.c: Weighted LMM without segfault. Use for(int i=...) throughout. 2008-03-01 Douglas Bates * [r87] src/lmer.c: Added macros * [r86] inst/doc/Doxyfile: Update version * [r85] man/merMCMC-class.Rd: Update. 2008-02-29 Douglas Bates * [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 * [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 * [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 * [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 * [r65] R/lmer.R: Omit famName slot value in calls to new("mer",...) 2008-02-01 Douglas Bates * [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 * [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 * [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 * [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 ), 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 * [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 * [r40] inst/doc/Implementation.Rnw: Update to current slot names * [r41] man/lmer.Rd: Add links thanks to 2008-01-06 Douglas Bates * [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 * [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 * [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 * [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 * [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 * [r17] inst/doc/Doxyfile, src/Syms.h, src/init.c: Doxygen reconfiguration, code cleanup based on calling tree 2007-12-19 Douglas Bates * [r16] src/lmer.c: More changes in the logic of cond_mode. Looks like this version works properly! 2007-12-17 Douglas Bates * [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 * [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 * [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 * [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 * [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 * [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 for generalized linear models 2007-11-09 18:33 Douglas Bates * [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 * [r4816] DESCRIPTION, R/lmer.R: Update fitted and resid methods; new version of R 2007-10-04 20:33 Douglas Bates * [r4809] src/lmer.c: remove alloc3DArray (part of R from 2.6.0) 2007-09-26 17:32 Douglas Bates * [r4787] R/lmer.R: Reinstitute the names of variance components from formatVC 2007-09-25 15:08 Douglas Bates * [r4782] src/lmer.h: Provide definition of alloca for Solaris 10 2007-09-11 22:17 Douglas Bates * [r4767] src/init.c, src/lmer.c, src/lmer.h: Cleanup, add new functions for .Call 2007-08-31 10:50 Douglas Bates * [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 * [r4731] src/lmer.h: declare alloca * [r4732] src/lmer.c: unused variable 2007-08-12 13:21 Douglas Bates * [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 * [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 * [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 * [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 * [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 * [r4658] R/lmer.R, src/init.c, src/lmer.c, src/lmer.h: More work on nlmer 2007-07-20 20:41 Douglas Bates * [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 * [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 * [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 * [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 * [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 * [r4607] R/lmer.R, man/cbpp.Rd: glmer skeleton and test 2007-07-11 20:30 Douglas Bates * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [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 * [r4449] DESCRIPTION, inst/doc/Theory.Rnw, inst/doc/lme4.bib: Added Theory vignette, release 0.99875-1 2007-06-07 21:15 Douglas Bates * [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 * [r4414] R/AllClass.R, R/lmer.R, src/init.c, src/lmer2.c, src/lmer2.h: More modifications to nlmer