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Revision 981 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 11 14:12:19 2005 UTC (14 years, 2 months ago) by bates
File length: 52169 byte(s)
Diff to previous 979
Evaluate model frame before glm model of fixed effects

Revision 979 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 11 00:02:45 2005 UTC (14 years, 2 months ago) by bates
File length: 52089 byte(s)
Diff to previous 978
Added a FIXME - will fix later

Revision 978 - (view) (download) (annotate) - [select for diffs]
Modified Mon Oct 10 13:54:09 2005 UTC (14 years, 2 months ago) by bates
File length: 51402 byte(s)
Diff to previous 973
More mer2 modifications

Revision 973 - (view) (download) (annotate) - [select for diffs]
Modified Fri Oct 7 20:15:08 2005 UTC (14 years, 2 months ago) by maechler
File length: 49028 byte(s)
Diff to previous 963
isSymmetric() & simulate() updates; sparse subsetting

Revision 963 - (view) (download) (annotate) - [select for diffs]
Modified Mon Oct 3 01:44:56 2005 UTC (14 years, 2 months ago) by bates
File length: 48887 byte(s)
Diff to previous 940
Modifications to mer2

Revision 940 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 27 00:50:35 2005 UTC (14 years, 2 months ago) by bates
File length: 48977 byte(s)
Diff to previous 939
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

Revision 939 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 20 17:23:24 2005 UTC (14 years, 2 months ago) by bates
File length: 45556 byte(s)
Diff to previous 902
More careful checking for linear mixed model

Revision 902 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 6 14:07:10 2005 UTC (14 years, 3 months ago) by bates
File length: 45639 byte(s)
Diff to previous 901


Revision 901 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 6 01:26:11 2005 UTC (14 years, 3 months ago) by bates
File length: 45539 byte(s)
Diff to previous 888
Add "start" argument to lmer

Revision 888 - (view) (download) (annotate) - [select for diffs]
Modified Thu Sep 1 13:46:21 2005 UTC (14 years, 3 months ago) by bates
File length: 45433 byte(s)
Diff to previous 879
New simulate method for lmer objects

Revision 879 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 30 14:35:05 2005 UTC (14 years, 3 months ago) by bates
File length: 44313 byte(s)
Diff to previous 878
Added simulate generic and method

Revision 878 - (view) (download) (annotate) - [select for diffs]
Modified Sun Aug 28 13:57:39 2005 UTC (14 years, 3 months ago) by bates
File length: 41182 byte(s)
Diff to previous 864
Add simulate method for lmer

Revision 864 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 18 21:36:49 2005 UTC (14 years, 3 months ago) by bates
File length: 39529 byte(s)
Diff to previous 861
It's 'warning', not 'warn'

Revision 861 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 18 21:29:52 2005 UTC (14 years, 3 months ago) by bates
File length: 39526 byte(s)
Diff to previous 843
Fix column labels on mcmcsamp for glmer objects

Revision 843 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 10 18:24:18 2005 UTC (14 years, 4 months ago) by maechler
File length: 39275 byte(s)
Diff to previous 842
comment

Revision 842 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 9 14:23:37 2005 UTC (14 years, 4 months ago) by bates
File length: 39238 byte(s)
Diff to previous 832
Modify column names for transformed parameters in mcmcsamp

Revision 832 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 8 08:33:55 2005 UTC (14 years, 4 months ago) by maechler
File length: 38505 byte(s)
Diff to previous 824
lmer()`s "model = T/F" and control arguments; add comments and "FIXME"s

Revision 824 - (view) (download) (annotate) - [select for diffs]
Modified Sat Aug 6 20:01:51 2005 UTC (14 years, 4 months ago) by bates
File length: 38689 byte(s)
Diff to previous 820
Allow mcmcsamp on transformed parameters

Revision 820 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jul 27 23:07:04 2005 UTC (14 years, 4 months ago) by bates
File length: 38160 byte(s)
Diff to previous 814
Version 0.98-1

Revision 814 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 21 23:05:52 2005 UTC (14 years, 4 months ago) by bates
File length: 37578 byte(s)
Diff to previous 813
Working version of the glmmMCMC producing an mcmc object

Revision 813 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 21 16:41:42 2005 UTC (14 years, 4 months ago) by bates
File length: 38735 byte(s)
Diff to previous 812
New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

Revision 812 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 21 14:59:04 2005 UTC (14 years, 4 months ago) by bates
File length: 38549 byte(s)
Diff to previous 811
Added an rWishart function, which should later be moved to the stats package

Revision 811 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 14 15:37:41 2005 UTC (14 years, 4 months ago) by bates
File length: 38469 byte(s)
Diff to previous 810
Modifications to glmmMCMC

Revision 810 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 14 13:48:38 2005 UTC (14 years, 4 months ago) by bates
File length: 38872 byte(s)
Diff to previous 809
Modifications to glmmMCMC

Revision 809 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jul 12 23:00:50 2005 UTC (14 years, 4 months ago) by bates
File length: 37987 byte(s)
Diff to previous 806
Release 0.97-4 with fix suggested by DTL

Revision 806 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jul 8 15:38:43 2005 UTC (14 years, 5 months ago) by bates
File length: 37947 byte(s)
Diff to previous 804
Preliminary version of glmmMCMC

Revision 804 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 7 20:05:47 2005 UTC (14 years, 5 months ago) by bates
File length: 37507 byte(s)
Diff to previous 802
Preparing for glmmMCMC

Revision 802 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jul 6 23:55:39 2005 UTC (14 years, 5 months ago) by bates
File length: 37667 byte(s)
Diff to previous 801
got glmer_fixed_update working

Revision 801 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jul 6 16:24:33 2005 UTC (14 years, 5 months ago) by bates
File length: 37622 byte(s)
Diff to previous 799
Updates for release 0.97-2

Revision 799 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jul 5 00:37:34 2005 UTC (14 years, 5 months ago) by bates
File length: 37567 byte(s)
Diff to previous 787
Increase default maxIter and calculate nAGQ more carefully

Revision 787 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jun 30 16:59:12 2005 UTC (14 years, 5 months ago) by bates
File length: 37341 byte(s)
Diff to previous 784
Still modifying glmer_devAGQ

Revision 784 - (view) (download) (annotate) - [select for diffs]
Modified Sun Jun 26 03:42:21 2005 UTC (14 years, 5 months ago) by bates
File length: 37379 byte(s)
Diff to previous 782
More work on MCMC (still incomplete)

Revision 782 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jun 24 23:06:33 2005 UTC (14 years, 5 months ago) by bates
File length: 37269 byte(s)
Diff to previous 781
Adding MCMC capability (currently incomplete)

Revision 781 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jun 24 15:38:43 2005 UTC (14 years, 5 months ago) by bates
File length: 36817 byte(s)
Diff to previous 780
Further development on AGQ and MCMC for glmm models

Revision 780 - (view) (download) (annotate) - [select for diffs]
Modified Sun Jun 19 14:59:30 2005 UTC (14 years, 5 months ago) by bates
File length: 34386 byte(s)
Diff to previous 779
Release 0.96-3

Revision 779 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jun 15 15:52:19 2005 UTC (14 years, 5 months ago) by bates
File length: 34421 byte(s)
Diff to previous 777
Adding AGQ (but not yet correct)

Revision 777 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jun 14 04:02:57 2005 UTC (14 years, 5 months ago) by bates
File length: 33940 byte(s)
Diff to previous 776
release 0.96-2

Revision 776 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jun 13 19:45:04 2005 UTC (14 years, 5 months ago) by bates
File length: 34320 byte(s)
Diff to previous 775
Setting up for AGQ

Revision 775 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jun 13 01:22:28 2005 UTC (14 years, 5 months ago) by bates
File length: 34087 byte(s)
Diff to previous 774
Factoring C code in preparation for AGQ

Revision 774 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jun 10 18:40:54 2005 UTC (14 years, 6 months ago) by bates
File length: 35572 byte(s)
Diff to previous 772
Moving devLaplace calculations to C code

Revision 772 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jun 9 16:57:55 2005 UTC (14 years, 6 months ago) by bates
File length: 37563 byte(s)
Diff to previous 769
Prepare for release 0.96-1

Revision 769 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jun 8 23:47:45 2005 UTC (14 years, 6 months ago) by bates
File length: 37587 byte(s)
Copied from: branches/trunk-lme4/R/lmer.R revision 767
Diff to previous 767
Moving lmer to the Matrix package

Revision 767 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jun 7 23:05:00 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 38819 byte(s)
Diff to previous 755
Move more of glmm calculations to C code

Revision 755 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jun 6 15:37:45 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 37275 byte(s)
Diff to previous 754
Use the mer class explicitly and combine code for lmer and glmer creation

Revision 754 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 30 18:40:45 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 46178 byte(s)
Diff to previous 752
Release 0.95-10

Revision 752 - (view) (download) (annotate) - [select for diffs]
Modified Sun May 29 02:14:58 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 46114 byte(s)
Diff to previous 751
Release 0.95-9

Revision 751 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 24 17:49:33 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 46431 byte(s)
Diff to previous 750
Add optimization through port

Revision 750 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 20 13:15:58 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 45109 byte(s)
Diff to previous 727
Release 0.95-8

Revision 727 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 13 15:14:14 2005 UTC (14 years, 6 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 45095 byte(s)
Diff to previous 721
Release 0.95-7

Revision 721 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 9 02:13:25 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 43757 byte(s)
Diff to previous 717
added glmer class

Revision 717 - (view) (download) (annotate) - [select for diffs]
Modified Sun May 8 18:58:05 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 42564 byte(s)
Diff to previous 711
commented out code for Laplace approx in R

Revision 711 - (view) (download) (annotate) - [select for diffs]
Modified Thu May 5 04:12:44 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 42406 byte(s)
Diff to previous 710
Updates related to Laplace approximation

Revision 710 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 3 16:10:17 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 42160 byte(s)
Diff to previous 708
added option to calculate parts of Laplace approximation in C code. Currently doesn't work

Revision 708 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 2 21:29:55 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 41791 byte(s)
Diff to previous 707
to reduce overhead of calling as.matrix on ranef()'s, now using
.Call("lmer_ranef") directly

Revision 707 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 2 17:27:53 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 41856 byte(s)
Diff to previous 706
updated Laplace calculations

Revision 706 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 29 15:42:12 2005 UTC (14 years, 7 months ago) by deepayan
Original Path: branches/trunk-lme4/R/lmer.R
File length: 41561 byte(s)
Diff to previous 704
added code for Laplace approximation, essentially porting the ssclme version

Revision 704 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 21 22:01:09 2005 UTC (14 years, 7 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 30644 byte(s)
Diff to previous 691
Release 0.95-6

Revision 691 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 15 14:37:38 2005 UTC (14 years, 7 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 30005 byte(s)
Diff to previous 690
Release 0.95-5

Revision 690 - (view) (download) (annotate) - [select for diffs]
Modified Tue Apr 5 22:17:04 2005 UTC (14 years, 8 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 29655 byte(s)
Diff to previous 689
Release 0.95-2

Revision 689 - (view) (download) (annotate) - [select for diffs]
Modified Sat Apr 2 14:41:46 2005 UTC (14 years, 8 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 29741 byte(s)
Diff to previous 601
Release of lme_0.95-1

Revision 601 - (view) (download) (annotate) - [select for diffs]
Modified Fri Mar 4 03:52:38 2005 UTC (14 years, 9 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 20775 byte(s)
Diff to previous 571
C function lmer_fitted added

Revision 571 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 25 13:30:34 2005 UTC (14 years, 9 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 20864 byte(s)
Diff to previous 562
Release 0.9-1

Revision 562 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 19:25:47 2005 UTC (14 years, 9 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 20324 byte(s)
Diff to previous 550
Release 0.8-3

Revision 550 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 15 22:15:11 2005 UTC (14 years, 9 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 20272 byte(s)
Diff to previous 545
Use coercion to extract L from an lmer object

Revision 545 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 15 16:06:25 2005 UTC (14 years, 9 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 19520 byte(s)
Diff to previous 468
Updates to extract pieces of lmer objects for debugging

Revision 468 - (view) (download) (annotate) - [select for diffs]
Modified Sat Jan 29 14:18:34 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 18128 byte(s)
Diff to previous 457
Result of all.equal is not necessarily a logical value

Revision 457 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 24 09:12:53 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 18112 byte(s)
Diff to previous 452
Check parameter values before assigning them in the gradient
calculation.  This may save unnecessary decompositions (although it
turns out that the decomposition is fast and the inversion is slow).

Revision 452 - (view) (download) (annotate) - [select for diffs]
Modified Sun Jan 23 10:09:03 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 18087 byte(s)
Diff to previous 449
Allow constant fixed part of formula

Revision 449 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 21 22:01:21 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 17954 byte(s)
Diff to previous 446
Release 0.6-12

Revision 446 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jan 19 19:08:01 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 17019 byte(s)
Diff to previous 435
Add slots and methods

Revision 435 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 13 19:37:26 2005 UTC (14 years, 10 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 10533 byte(s)
Diff to previous 423
Add the lmer generic and methods

Revision 423 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jan 4 23:45:49 2005 UTC (14 years, 11 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 6903 byte(s)
Diff to previous 413
Check in prior to leaving for Zuerich

Revision 413 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 3 18:51:30 2005 UTC (14 years, 11 months ago) by bates
Original Path: branches/trunk-lme4/R/lmer.R
File length: 6779 byte(s)
Copied from: branches/trunk-lme4/R/lmeRep.R revision 411
Diff to previous 411
Switch from lmeRep to lmer

Revision 411 - (view) (download) (annotate) - [select for diffs]
Modified Tue Dec 28 14:52:19 2004 UTC (14 years, 11 months ago) by bates
Original Path: branches/trunk-lme4/R/lmeRep.R
File length: 6823 byte(s)
Diff to previous 382
Updates to GLMM

Revision 382 - (view) (download) (annotate) - [select for diffs]
Modified Sun Dec 12 17:30:29 2004 UTC (14 years, 11 months ago) by bates
Original Path: branches/trunk-lme4/R/lmeRep.R
File length: 6822 byte(s)
Diff to previous 380
Use constrained optimization for the ssclme representation as well as for the lmeRep

Revision 380 - (view) (download) (annotate) - [select for diffs]
Modified Sat Dec 11 13:50:17 2004 UTC (15 years ago) by bates
Original Path: branches/trunk-lme4/R/lmeRep.R
File length: 8503 byte(s)
Diff to previous 362
conditionalize use of analytic gradient in lme1

Revision 362 - (view) (download) (annotate) - [select for diffs]
Modified Sun Dec 5 13:46:51 2004 UTC (15 years ago) by bates
Original Path: branches/trunk-lme4/R/lmeRep.R
File length: 8424 byte(s)
Diff to previous 316
Make verbose really verbose for lme1

Revision 316 - (view) (download) (annotate) - [select for diffs]
Added Tue Nov 2 21:28:48 2004 UTC (15 years, 1 month ago) by bates
Original Path: branches/trunk-lme4/R/lmeRep.R
File length: 8412 byte(s)
Adding lme1 and the lmeRep methods

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