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Revision 1167 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 15 21:13:54 2006 UTC (13 years, 10 months ago) by bates
File length: 13735 byte(s)
Diff to previous 1164
Removing rcond slot from Matrix objects

Revision 1164 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jan 14 23:40:42 2006 UTC (13 years, 10 months ago) by maechler
File length: 13775 byte(s)
Diff to previous 1162
new dMatrix_validate and dense_nonpacked_validate

Revision 1162 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jan 13 23:47:38 2006 UTC (13 years, 10 months ago) by bates
File length: 13643 byte(s)
Diff to previous 1156
Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

Revision 1156 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 12 23:39:56 2006 UTC (13 years, 10 months ago) by bates
File length: 13667 byte(s)
Diff to previous 1143
Remove redundant registration of dspMatrix_trf; incorporate wts and wrkres slots in mer class

Revision 1143 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 12 03:17:24 2006 UTC (13 years, 10 months ago) by bates
File length: 13641 byte(s)
Diff to previous 1098
Switch to supernodal Cholesky representation of mer objects

Revision 1098 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 29 11:38:59 2005 UTC (13 years, 11 months ago) by maechler
File length: 14084 byte(s)
Diff to previous 1067
some 2-argument-tcrossprod methods (and test svn)

Revision 1067 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 28 16:27:29 2005 UTC (14 years ago) by bates
File length: 14084 byte(s)
Diff to previous 1059
Added crossprod method for Csparse and dense

Revision 1059 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 23 22:20:13 2005 UTC (14 years ago) by bates
File length: 14012 byte(s)
Diff to previous 983
Matrix multiplication and coersion at higher level

Revision 983 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Oct 11 15:19:20 2005 UTC (14 years, 1 month ago) by bates
File length: 13954 byte(s)
Diff to previous 978
Remove references to Pattern.[ch]

Revision 978 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Oct 10 13:54:09 2005 UTC (14 years, 1 month ago) by bates
File length: 13975 byte(s)
Diff to previous 977
More mer2 modifications

Revision 977 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 7 22:14:47 2005 UTC (14 years, 2 months ago) by bates
File length: 13775 byte(s)
Diff to previous 967
mer2_initial

Revision 967 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 6 03:07:23 2005 UTC (14 years, 2 months ago) by bates
File length: 13725 byte(s)
Diff to previous 963
More updates on lmer - still not quite correct

Revision 963 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Oct 3 01:44:56 2005 UTC (14 years, 2 months ago) by bates
File length: 13533 byte(s)
Diff to previous 956
Modifications to mer2

Revision 956 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 30 17:28:00 2005 UTC (14 years, 2 months ago) by maechler
File length: 13533 byte(s)
Diff to previous 945
more coercions; particularly "d" <-> "l"; more tests (and more FIXMEs!); fixing two "index-0 bugs"; ...

Revision 945 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Sep 28 08:54:28 2005 UTC (14 years, 2 months ago) by maechler
File length: 13475 byte(s)
Diff to previous 940
+ logical dense matrices; more coercions

Revision 940 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 27 00:50:35 2005 UTC (14 years, 2 months ago) by bates
File length: 13036 byte(s)
Diff to previous 928
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

Revision 928 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 19 21:10:59 2005 UTC (14 years, 2 months ago) by bates
File length: 13036 byte(s)
Diff to previous 923
crossprod and tcrossprod for Tsparse

Revision 923 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Sep 18 23:41:45 2005 UTC (14 years, 2 months ago) by bates
File length: 13036 byte(s)
Diff to previous 922
More progress on incorporating CHOLMOD - still not passing CMD check

Revision 922 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Sep 18 16:33:54 2005 UTC (14 years, 2 months ago) by bates
File length: 12916 byte(s)
Diff to previous 919
Added CHOLMOD-based C functions.  Still need methods defined in R and some error checking

Revision 919 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Sep 16 17:27:06 2005 UTC (14 years, 2 months ago) by maechler
File length: 12378 byte(s)
Diff to previous 912
new compressed_non_0_ij()

Revision 912 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 15 14:53:55 2005 UTC (14 years, 2 months ago) by bates
File length: 12309 byte(s)
Diff to previous 901
Adding CHOLMOD and related source packages

Revision 901 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 6 01:26:11 2005 UTC (14 years, 3 months ago) by bates
File length: 12134 byte(s)
Diff to previous 890
Add "start" argument to lmer

Revision 890 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 1 17:18:08 2005 UTC (14 years, 3 months ago) by maechler
File length: 12076 byte(s)
Diff to previous 888
add triangularMatrix_validate and symmetric* to C code and make (re!)use of it - not quite everywhere?

Revision 888 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 1 13:46:21 2005 UTC (14 years, 3 months ago) by bates
File length: 11926 byte(s)
Diff to previous 879
New simulate method for lmer objects

Revision 879 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 30 14:35:05 2005 UTC (14 years, 3 months ago) by bates
File length: 11874 byte(s)
Diff to previous 874
Added simulate generic and method

Revision 874 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Aug 27 21:27:51 2005 UTC (14 years, 3 months ago) by maechler
File length: 11980 byte(s)
Diff to previous 866
prepare graphNEL coercion both for directed and undir.

Revision 866 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Aug 19 16:58:26 2005 UTC (14 years, 3 months ago) by maechler
File length: 11980 byte(s)
Diff to previous 862
new lcrc_to_matrix code

Revision 862 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 18 21:31:07 2005 UTC (14 years, 3 months ago) by bates
File length: 11927 byte(s)
Diff to previous 852
Coercion method for graphNEL to sparseMatrix class

Revision 852 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 16 17:52:16 2005 UTC (14 years, 3 months ago) by bates
File length: 11859 byte(s)
Diff to previous 835
Move readHB and readMM to R code and allow the use of connections

Revision 835 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 8 13:33:18 2005 UTC (14 years, 4 months ago) by bates
File length: 11847 byte(s)
Diff to previous 825
Add writeHB and writeMM methods and generic

Revision 825 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Aug 7 15:22:33 2005 UTC (14 years, 4 months ago) by bates
File length: 11697 byte(s)
Diff to previous 824
Harwell-Boeing and MatrixMarket formats

Revision 824 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Aug 6 20:01:51 2005 UTC (14 years, 4 months ago) by bates
File length: 11533 byte(s)
Diff to previous 815
Allow mcmcsamp on transformed parameters

Revision 815 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jul 24 23:53:40 2005 UTC (14 years, 4 months ago) by bates
File length: 11479 byte(s)
Diff to previous 813
Added lmer_MCMCsamp to the C sources

Revision 813 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 21 16:41:42 2005 UTC (14 years, 4 months ago) by bates
File length: 11427 byte(s)
Diff to previous 812
New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

Revision 812 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 21 14:59:04 2005 UTC (14 years, 4 months ago) by bates
File length: 11373 byte(s)
Diff to previous 804
Added an rWishart function, which should later be moved to the stats package

Revision 804 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 7 20:05:47 2005 UTC (14 years, 5 months ago) by bates
File length: 11317 byte(s)
Diff to previous 783
Preparing for glmmMCMC

Revision 783 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jun 26 03:41:37 2005 UTC (14 years, 5 months ago) by bates
File length: 11301 byte(s)
Diff to previous 782
Reinstate check on number of arguments

Revision 782 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 24 23:06:33 2005 UTC (14 years, 5 months ago) by bates
File length: 11312 byte(s)
Diff to previous 781
Adding MCMC capability (currently incomplete)

Revision 781 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 24 15:38:43 2005 UTC (14 years, 5 months ago) by bates
File length: 11300 byte(s)
Diff to previous 776
Further development on AGQ and MCMC for glmm models

Revision 776 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 13 19:45:04 2005 UTC (14 years, 5 months ago) by bates
File length: 11192 byte(s)
Diff to previous 775
Setting up for AGQ

Revision 775 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 13 01:22:28 2005 UTC (14 years, 5 months ago) by bates
File length: 11146 byte(s)
Diff to previous 774
Factoring C code in preparation for AGQ

Revision 774 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Jun 10 18:40:54 2005 UTC (14 years, 5 months ago) by bates
File length: 11536 byte(s)
Diff to previous 766
Moving devLaplace calculations to C code

Revision 766 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 7 23:03:34 2005 UTC (14 years, 6 months ago) by bates
File length: 11542 byte(s)
Diff to previous 761
Isolating and cleaning up the mer, lmer, and glmer functions

Revision 761 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 6 15:51:24 2005 UTC (14 years, 6 months ago) by bates
File length: 11534 byte(s)
Diff to previous 749
Use mer objects; Replace REML slot by method slot

Revision 749 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 20 03:17:14 2005 UTC (14 years, 6 months ago) by bates
File length: 11553 byte(s)
Diff to previous 739
Release 0.95-10

Revision 739 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 17 17:42:04 2005 UTC (14 years, 6 months ago) by bates
File length: 13003 byte(s)
Diff to previous 723
Adding logical sparse matrix methods

Revision 723 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 10 01:42:05 2005 UTC (14 years, 6 months ago) by bates
File length: 12220 byte(s)
Diff to previous 718
More logical sparse matrix methods

Revision 718 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon May 9 01:24:35 2005 UTC (14 years, 7 months ago) by bates
File length: 12156 byte(s)
Diff to previous 714
Getting ready for a release

Revision 714 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 6 23:52:34 2005 UTC (14 years, 7 months ago) by bates
File length: 12030 byte(s)
Diff to previous 709
Added colSums and friends for dgeMatrix class

Revision 709 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue May 3 16:08:26 2005 UTC (14 years, 7 months ago) by deepayan
File length: 11970 byte(s)
Diff to previous 705
changes related to Laplace approximation, including new function to compute parts of the deviance in C code, which doesn't currently work

Revision 705 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 29 14:42:39 2005 UTC (14 years, 7 months ago) by deepayan
File length: 11656 byte(s)
Diff to previous 692
additions related to the Laplace approximation in glmm lmer models

Revision 692 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 18 14:34:33 2005 UTC (14 years, 7 months ago) by bates
File length: 11502 byte(s)
Diff to previous 686
Release 0.95-6

Revision 686 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 31 21:19:35 2005 UTC (14 years, 8 months ago) by bates
File length: 11329 byte(s)
Diff to previous 683
Create "fallback" methods for any kind of numeric, dense matrix

Revision 683 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 31 17:10:16 2005 UTC (14 years, 8 months ago) by bates
File length: 11329 byte(s)
Diff to previous 677
Moving methods for operations with numeric to the Matrix class and with integer to the dMatrix class

Revision 677 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 28 14:03:32 2005 UTC (14 years, 8 months ago) by bates
File length: 11329 byte(s)
Diff to previous 675
Added dgRMatrix methods and documentation

Revision 675 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Mar 26 11:16:05 2005 UTC (14 years, 8 months ago) by maechler
File length: 11315 byte(s)
Diff to previous 654
export csc_tcrossprod - and add examples & test for tcrossprod()

Revision 654 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 16 16:18:33 2005 UTC (14 years, 8 months ago) by bates
File length: 11261 byte(s)
Diff to previous 652
Generalize matrix multiplication and solve methods

Revision 652 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 16 01:08:36 2005 UTC (14 years, 8 months ago) by bates
File length: 11341 byte(s)
Diff to previous 637
Updates to multiplication and other methods

Revision 637 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Mar 15 00:41:24 2005 UTC (14 years, 8 months ago) by bates
File length: 11502 byte(s)
Diff to previous 631
Coercions and methods for dppMatrix and dspMatrix classes

Revision 631 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Mar 13 04:34:52 2005 UTC (14 years, 8 months ago) by bates
File length: 10174 byte(s)
Diff to previous 628
Add BunchKaufman factorization

Revision 628 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 10 17:57:47 2005 UTC (14 years, 8 months ago) by maechler
File length: 10054 byte(s)
Diff to previous 622
more  %*% methods; some dimnames in C (untested); checks extended

Revision 622 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 7 12:45:59 2005 UTC (14 years, 9 months ago) by bates
File length: 9984 byte(s)
Diff to previous 613
Wrong number of args in lmer_update_mm

Revision 613 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Mar 5 21:13:40 2005 UTC (14 years, 9 months ago) by maechler
File length: 9936 byte(s)
Diff to previous 603
+ Matrix_DimnamesSym

Revision 603 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Mar 4 12:53:01 2005 UTC (14 years, 9 months ago) by bates
File length: 9890 byte(s)
Diff to previous 597
Define %*% method for dtpMatrix and matrix properly

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Modified Thu Mar 3 19:58:59 2005 UTC (14 years, 9 months ago) by bates
File length: 9756 byte(s)
Diff to previous 591
Methods and coercions for the dtpMatrix class

Revision 591 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 3 05:16:09 2005 UTC (14 years, 9 months ago) by bates
File length: 9696 byte(s)
Diff to previous 587
C functions for dtpMatrix class

Revision 587 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 2 18:19:15 2005 UTC (14 years, 9 months ago) by bates
File length: 9235 byte(s)
Diff to previous 582
dsTMatrix_as_dsCMatrix

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Modified Mon Feb 28 18:15:21 2005 UTC (14 years, 9 months ago) by bates
File length: 9165 byte(s)
Diff to previous 557
Internationalization and localization

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Modified Thu Feb 17 01:18:02 2005 UTC (14 years, 9 months ago) by bates
File length: 9181 byte(s)
Diff to previous 546
Coercions and methods for the dsTMatrix class

Revision 546 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Feb 15 22:09:12 2005 UTC (14 years, 9 months ago) by bates
File length: 9026 byte(s)
Diff to previous 543
Methods and coercions for the dtTMatrix class

Revision 543 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Feb 12 13:37:46 2005 UTC (14 years, 9 months ago) by bates
File length: 8871 byte(s)
Diff to previous 536
Changes for non-nested vector-valued random effects

Revision 536 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 10 08:15:12 2005 UTC (14 years, 9 months ago) by bates
File length: 8821 byte(s)
Diff to previous 495
rearranging utility functions in the C code

Revision 495 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Feb 3 18:48:31 2005 UTC (14 years, 10 months ago) by bates
File length: 8721 byte(s)
Diff to previous 488
Initial implementation of the Schur generic

Revision 488 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 2 19:11:51 2005 UTC (14 years, 10 months ago) by bates
File length: 8667 byte(s)
Diff to previous 485
renaming and rearranging classes

Revision 485 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 2 17:20:55 2005 UTC (14 years, 10 months ago) by bates
File length: 8521 byte(s)
Diff to previous 478
renaming and rearranging classes

Revision 478 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 2 14:33:51 2005 UTC (14 years, 10 months ago) by bates
File length: 8493 byte(s)
Diff to previous 476
Renaming and reorganizing classes

Revision 476 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Feb 2 11:51:24 2005 UTC (14 years, 10 months ago) by bates
File length: 8365 byte(s)
Diff to previous 461
Change name of slot from factorization to factors

Revision 461 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sat Jan 29 14:09:38 2005 UTC (14 years, 10 months ago) by bates
File length: 8375 byte(s)
Diff to previous 451
Add expm function

Revision 451 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Sun Jan 23 10:05:53 2005 UTC (14 years, 10 months ago) by bates
File length: 8273 byte(s)
Diff to previous 422
New coercion method for cscBlocked objects

Revision 422 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 4 23:45:15 2005 UTC (14 years, 11 months ago) by bates
File length: 8205 byte(s)
Diff to previous 417
Check in prior to leaving for Zuerich

Revision 417 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 3 19:14:22 2005 UTC (14 years, 11 months ago) by bates
File length: 8151 byte(s)
Diff to previous 415
Change to the lmer representation

Revision 415 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jan 3 19:05:11 2005 UTC (14 years, 11 months ago) by bates
File length: 8153 byte(s)
Diff to previous 410
Change to the lmer representation

Revision 410 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 28 14:51:42 2004 UTC (14 years, 11 months ago) by bates
File length: 8461 byte(s)
Diff to previous 397
Working on the lmer classes

Revision 397 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 16 19:15:32 2004 UTC (14 years, 11 months ago) by bates
File length: 8213 byte(s)
Diff to previous 390
Add arguments to ssclme_to_lme

Revision 390 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Dec 14 19:58:55 2004 UTC (14 years, 11 months ago) by bates
File length: 8212 byte(s)
Diff to previous 329
Add a coercion for tripletMatrix to matrix

Revision 329 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Nov 12 21:01:19 2004 UTC (15 years ago) by bates
File length: 8152 byte(s)
Diff to previous 305
Keep symbols and filenames consistent

Revision 305 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Oct 27 21:36:19 2004 UTC (15 years, 1 month ago) by bates
File length: 8665 byte(s)
Diff to previous 298
updates and downdates

Revision 298 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Oct 8 13:47:20 2004 UTC (15 years, 2 months ago) by bates
File length: 8607 byte(s)
Diff to previous 297
added validate functions

Revision 297 - (view) (download) (as text) (annotate) - [select for diffs]
Added Mon Oct 4 17:13:42 2004 UTC (15 years, 2 months ago) by bates
File length: 8519 byte(s)
Add registration of .Call functions

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