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Revision 1548 - (view) (download) (annotate) - [select for diffs]
Modified Mon Sep 11 22:13:07 2006 UTC (12 years, 11 months ago) by maechler
File length: 22409 byte(s)
Diff to previous 1507
new nMatrix and subclasses; lsparse change to have x slot; many consequences

Revision 1507 - (view) (download) (annotate) - [select for diffs]
Modified Mon Sep 4 18:41:34 2006 UTC (12 years, 11 months ago) by bates
File length: 17990 byte(s)
Diff to previous 1467
Merging changes from Matrix-nolmer branch

Revision 1467 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 30 21:35:09 2006 UTC (12 years, 11 months ago) by maechler
File length: 21530 byte(s)
Diff to previous 1444
several smallish fixes

Revision 1444 - (view) (download) (annotate) - [select for diffs]
Modified Fri Aug 25 14:39:45 2006 UTC (12 years, 11 months ago) by maechler
File length: 21531 byte(s)
Diff to previous 1443
a bit more "MatrixFactorization" ..

Revision 1443 - (view) (download) (annotate) - [select for diffs]
Modified Fri Aug 25 10:44:48 2006 UTC (12 years, 11 months ago) by maechler
File length: 21195 byte(s)
Diff to previous 1432
1st stab at "MatrixFactorization" class; exporting CHMfactor etc

Revision 1432 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 24 16:21:18 2006 UTC (12 years, 11 months ago) by maechler
File length: 21161 byte(s)
Diff to previous 1425
eliminate classed argument from dup_mM*() and dependencies

Revision 1425 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 23 21:25:32 2006 UTC (13 years ago) by bates
File length: 21145 byte(s)
Diff to previous 1407
Remove classes lCholCMatrix and dCholCMatrix, now using CHMfactor classes instead

Revision 1407 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 21 15:24:47 2006 UTC (13 years ago) by maechler
File length: 21130 byte(s)
Diff to previous 1383
rename class "LU" to "denseLU" and make "LU" virtual

Revision 1383 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 17 13:57:53 2006 UTC (13 years ago) by bates
File length: 21098 byte(s)
Diff to previous 1380
add sparse LU and QR decompositions

Revision 1380 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 15 22:31:30 2006 UTC (13 years ago) by bates
File length: 20901 byte(s)
Diff to previous 1335
Adding dgCMatrix_{lusol,qrsol,QR} but QR still not working

Revision 1335 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jul 31 12:11:35 2006 UTC (13 years ago) by maechler
File length: 20209 byte(s)
Diff to previous 1331
change unused class "correlation" to "corMatrix"

Revision 1331 - (view) (download) (annotate) - [select for diffs]
Modified Sat Jul 22 17:59:53 2006 UTC (13 years, 1 month ago) by maechler
File length: 20211 byte(s)
Diff to previous 1315
many method cleanups; notably some "dgC" -> "Csparse" generaliztations

Revision 1315 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jul 10 16:08:05 2006 UTC (13 years, 1 month ago) by maechler
File length: 20108 byte(s)
Diff to previous 1306
miscellaneous small things, including extended tests; see also ChangeLog

Revision 1306 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 6 15:14:12 2006 UTC (13 years, 1 month ago) by bates
File length: 20035 byte(s)
Diff to previous 1280
Establish new class glmer; modify validity check on pedigree to account for nonparallel patterns of missingness in parents

Revision 1280 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 23 08:01:44 2006 UTC (13 years, 3 months ago) by maechler
File length: 19828 byte(s)
Diff to previous 1276
useDynlib(*, .registration=TRUE)

Revision 1276 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 22 19:14:39 2006 UTC (13 years, 3 months ago) by bates
File length: 20642 byte(s)
Diff to previous 1266
Copy colcount in CHOLMOD supernodal factorization

Revision 1266 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 16 19:11:00 2006 UTC (13 years, 3 months ago) by bates
File length: 20618 byte(s)
Diff to previous 1258
Added check on sire and dam indices to pedigree function and class validation function

Revision 1258 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 21 15:44:39 2006 UTC (13 years, 4 months ago) by maechler
File length: 20381 byte(s)
Diff to previous 1247
make pedigree class more memory-efficient; add pedigree()

Revision 1247 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 13 11:12:51 2006 UTC (13 years, 4 months ago) by bates
File length: 21864 byte(s)
Diff to previous 1234
pedigree class added

Revision 1234 - (view) (download) (annotate) - [select for diffs]
Modified Tue Mar 21 12:33:28 2006 UTC (13 years, 5 months ago) by bates
File length: 20933 byte(s)
Diff to previous 1227
Change name of lmer.ranef class to ranef.lmer, add coef.lmer and update plot methods for these classes

Revision 1227 - (view) (download) (annotate) - [select for diffs]
Modified Wed Mar 15 17:42:03 2006 UTC (13 years, 5 months ago) by maechler
File length: 20892 byte(s)
Diff to previous 1226
use  isPacked() [internal] instead of private class "packedMatrix"

Revision 1226 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 13 14:07:58 2006 UTC (13 years, 5 months ago) by maechler
File length: 20819 byte(s)
Diff to previous 1222
sparse: "[<-" and better arithmetic; other tweaks

Revision 1222 - (view) (download) (annotate) - [select for diffs]
Modified Tue Mar 7 11:05:08 2006 UTC (13 years, 5 months ago) by maechler
File length: 20818 byte(s)
Diff to previous 1201
lmer(): non-trivial summary() method -> summary.*mer classes

Revision 1201 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 23 16:04:12 2006 UTC (13 years, 6 months ago) by maechler
File length: 20418 byte(s)
Diff to previous 1189
Class cleanup; particularly ldense* ones

Revision 1189 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 20 18:13:39 2006 UTC (13 years, 7 months ago) by maechler
File length: 20301 byte(s)
Diff to previous 1174
"dsy" no longer extends "dge"; other small fixes

Revision 1174 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 16 20:03:48 2006 UTC (13 years, 7 months ago) by maechler
File length: 20191 byte(s)
Diff to previous 1166
make Matrix() "smart" -- with help of quite a few new setAs(. , .) settings

Revision 1166 - (view) (download) (annotate) - [select for diffs]
Modified Sun Jan 15 19:18:20 2006 UTC (13 years, 7 months ago) by bates
File length: 20215 byte(s)
Diff to previous 1165
modifications to lmer and related classes

Revision 1165 - (view) (download) (annotate) - [select for diffs]
Modified Sat Jan 14 23:41:55 2006 UTC (13 years, 7 months ago) by maechler
File length: 20320 byte(s)
Diff to previous 1160
new coercion to dtr* and dsy* using isSymmetric() and isTriangular(); fix validity checking; some class descriptions

Revision 1160 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 13 23:45:45 2006 UTC (13 years, 7 months ago) by bates
File length: 20280 byte(s)
Diff to previous 1156
Updating the list of slots on factorable and non-factorable classes

Revision 1156 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 12 23:39:56 2006 UTC (13 years, 7 months ago) by bates
File length: 20136 byte(s)
Diff to previous 1150
Remove redundant registration of dspMatrix_trf; incorporate wts and wrkres slots in mer class

Revision 1150 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 12 03:41:25 2006 UTC (13 years, 7 months ago) by bates
File length: 19556 byte(s)
Diff to previous 1127
Switch to supernodal Cholesky representation of mer objects

Revision 1127 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jan 10 18:11:23 2006 UTC (13 years, 7 months ago) by maechler
File length: 19846 byte(s)
Diff to previous 1109
add ", drop = FALSE" in lmer.coef constructions; plus a few comments

Revision 1109 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jan 3 16:42:31 2006 UTC (13 years, 7 months ago) by maechler
File length: 19730 byte(s)
Diff to previous 1037
"diagonalMatrix" class and subclasses with a few methods; very basic "ltTMatrix" methods

Revision 1037 - (view) (download) (annotate) - [select for diffs]
Modified Fri Nov 11 14:57:22 2005 UTC (13 years, 9 months ago) by bates
File length: 18685 byte(s)
Diff to previous 984
Adding PACKAGE = to .Call lines

Revision 984 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 11 18:08:46 2005 UTC (13 years, 10 months ago) by bates
File length: 17718 byte(s)
Diff to previous 967
Tidying up

Revision 967 - (view) (download) (annotate) - [select for diffs]
Modified Thu Oct 6 03:07:23 2005 UTC (13 years, 10 months ago) by bates
File length: 17715 byte(s)
Diff to previous 963
More updates on lmer - still not quite correct

Revision 963 - (view) (download) (annotate) - [select for diffs]
Modified Mon Oct 3 01:44:56 2005 UTC (13 years, 10 months ago) by bates
File length: 17556 byte(s)
Diff to previous 953
Modifications to mer2

Revision 953 - (view) (download) (annotate) - [select for diffs]
Modified Wed Sep 28 19:31:36 2005 UTC (13 years, 10 months ago) by maechler
File length: 17568 byte(s)
Diff to previous 946
move "factors" slot to "Matrix"

Revision 946 - (view) (download) (annotate) - [select for diffs]
Modified Wed Sep 28 08:56:42 2005 UTC (13 years, 10 months ago) by maechler
File length: 17384 byte(s)
Diff to previous 940
some "Summary" methods; some "Compare" group methods; logical dense matrices

Revision 940 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 27 00:50:35 2005 UTC (13 years, 10 months ago) by bates
File length: 16792 byte(s)
Diff to previous 925
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

Revision 925 - (view) (download) (annotate) - [select for diffs]
Modified Mon Sep 19 19:01:31 2005 UTC (13 years, 11 months ago) by maechler
File length: 15909 byte(s)
Diff to previous 922
too many changes: rbind2 for dM*, cbind2(), "Math", "Arith" for sparse ones; more  "s/gTMatrix/TsparseMatrix/" fixes; quite a few more tests, incl some for *all* classes

Revision 922 - (view) (download) (annotate) - [select for diffs]
Modified Sun Sep 18 16:33:54 2005 UTC (13 years, 11 months ago) by bates
File length: 14630 byte(s)
Diff to previous 898
Added CHOLMOD-based C functions.  Still need methods defined in R and some error checking

Revision 898 - (view) (download) (annotate) - [select for diffs]
Modified Sat Sep 3 21:58:37 2005 UTC (13 years, 11 months ago) by maechler
File length: 13767 byte(s)
Diff to previous 887
+ prototypes for validity; pMatrix validity

Revision 887 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 31 20:31:47 2005 UTC (13 years, 11 months ago) by maechler
File length: 15239 byte(s)
Diff to previous 886
uplo &diag slots now go with superclass triangular* or symmetric*

Revision 886 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 31 17:49:47 2005 UTC (13 years, 11 months ago) by maechler
File length: 16008 byte(s)
Diff to previous 876
new classes "index", "symmetricM*" and "triangularM*"; indexing for logical and character indices; new tests; more to do

Revision 876 - (view) (download) (annotate) - [select for diffs]
Modified Sat Aug 27 22:50:57 2005 UTC (13 years, 11 months ago) by bates
File length: 15316 byte(s)
Diff to previous 868
clean up conversion of graphNEL to sparseMatrix

Revision 868 - (view) (download) (annotate) - [select for diffs]
Modified Fri Aug 19 17:01:11 2005 UTC (14 years ago) by maechler
File length: 15272 byte(s)
Diff to previous 856
printing of sparse logicals; "[" reorganization (part 1)

Revision 856 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 16 20:20:13 2005 UTC (14 years ago) by maechler
File length: 15177 byte(s)
Diff to previous 851
small fixups

Revision 851 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 16 17:39:38 2005 UTC (14 years ago) by maechler
File length: 15169 byte(s)
Diff to previous 848
export  dgR*, dsR* & dtR* Matrix - and "fix" stubs

Revision 848 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 11 07:41:59 2005 UTC (14 years ago) by maechler
File length: 15153 byte(s)
Diff to previous 769
+"denseMatrix" class; export defined but unused classes

Revision 769 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jun 8 23:47:45 2005 UTC (14 years, 2 months ago) by bates
File length: 14972 byte(s)
Diff to previous 730
Moving lmer to the Matrix package

Revision 730 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 17 17:16:53 2005 UTC (14 years, 3 months ago) by bates
File length: 11763 byte(s)
Diff to previous 692
Adding logical sparse matrix methods

Revision 692 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 18 14:34:33 2005 UTC (14 years, 4 months ago) by bates
File length: 11564 byte(s)
Diff to previous 676
Release 0.95-6

Revision 676 - (view) (download) (annotate) - [select for diffs]
Modified Sat Mar 26 15:59:18 2005 UTC (14 years, 4 months ago) by maechler
File length: 8579 byte(s)
Diff to previous 665
+ virtual "sparseMatrix" classes

Revision 665 - (view) (download) (annotate) - [select for diffs]
Modified Thu Mar 24 13:06:09 2005 UTC (14 years, 5 months ago) by bates
File length: 8393 byte(s)
Diff to previous 664
Removing the ssclme and sscCrosstab classes

Revision 664 - (view) (download) (annotate) - [select for diffs]
Modified Thu Mar 24 13:00:09 2005 UTC (14 years, 5 months ago) by maechler
File length: 10249 byte(s)
Diff to previous 652
make virtual classes "VIRTUAL"

Revision 652 - (view) (download) (annotate) - [select for diffs]
Modified Wed Mar 16 01:08:36 2005 UTC (14 years, 5 months ago) by bates
File length: 10115 byte(s)
Diff to previous 638
Updates to multiplication and other methods

Revision 638 - (view) (download) (annotate) - [select for diffs]
Modified Tue Mar 15 00:43:21 2005 UTC (14 years, 5 months ago) by bates
File length: 10116 byte(s)
Diff to previous 631
permutation matrix class

Revision 631 - (view) (download) (annotate) - [select for diffs]
Modified Sun Mar 13 04:34:52 2005 UTC (14 years, 5 months ago) by bates
File length: 9285 byte(s)
Diff to previous 628
Add BunchKaufman factorization

Revision 628 - (view) (download) (annotate) - [select for diffs]
Modified Thu Mar 10 17:57:47 2005 UTC (14 years, 5 months ago) by maechler
File length: 9123 byte(s)
Diff to previous 610
more  %*% methods; some dimnames in C (untested); checks extended

Revision 610 - (view) (download) (annotate) - [select for diffs]
Modified Fri Mar 4 17:34:19 2005 UTC (14 years, 5 months ago) by maechler
File length: 9121 byte(s)
Diff to previous 593
comments only

Revision 593 - (view) (download) (annotate) - [select for diffs]
Modified Thu Mar 3 05:17:32 2005 UTC (14 years, 5 months ago) by bates
File length: 9122 byte(s)
Diff to previous 538
Remove pdfactor class

Revision 538 - (view) (download) (annotate) - [select for diffs]
Modified Thu Feb 10 13:50:27 2005 UTC (14 years, 6 months ago) by maechler
File length: 9124 byte(s)
Diff to previous 521
add @Dimnames (-> new "mm")

Revision 521 - (view) (download) (annotate) - [select for diffs]
Modified Sat Feb 5 17:04:56 2005 UTC (14 years, 6 months ago) by maechler
File length: 8924 byte(s)
Diff to previous 513
small update

Revision 513 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 4 23:46:08 2005 UTC (14 years, 6 months ago) by maechler
File length: 8909 byte(s)
Diff to previous 498
require() is not needed; ddense.. for "dsp"; cosmetic

Revision 498 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 4 18:15:54 2005 UTC (14 years, 6 months ago) by maechler
File length: 8590 byte(s)
Diff to previous 492
cosmetic

Revision 492 - (view) (download) (annotate) - [select for diffs]
Modified Thu Feb 3 14:24:03 2005 UTC (14 years, 6 months ago) by bates
File length: 8614 byte(s)
Diff to previous 482
Getting package to pass CMD check

Revision 482 - (view) (download) (annotate) - [select for diffs]
Modified Wed Feb 2 15:37:31 2005 UTC (14 years, 6 months ago) by bates
File length: 8564 byte(s)
Diff to previous 477
renaming and rearranging classes

Revision 477 - (view) (download) (annotate) - [select for diffs]
Modified Wed Feb 2 14:14:59 2005 UTC (14 years, 6 months ago) by bates
File length: 8564 byte(s)
Diff to previous 476
Renaming and reorganizing classes

Revision 476 - (view) (download) (annotate) - [select for diffs]
Modified Wed Feb 2 11:51:24 2005 UTC (14 years, 6 months ago) by bates
File length: 9246 byte(s)
Diff to previous 448
Change name of slot from factorization to factors

Revision 448 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 21 21:59:45 2005 UTC (14 years, 7 months ago) by bates
File length: 9276 byte(s)
Diff to previous 440
Release 0.8-23

Revision 440 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jan 19 11:21:28 2005 UTC (14 years, 7 months ago) by bates
File length: 11103 byte(s)
Diff to previous 436
Remove Linv slot in lmer class

Revision 436 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 17 12:46:13 2005 UTC (14 years, 7 months ago) by bates
File length: 11179 byte(s)
Diff to previous 433
Add slots to lmer class

Revision 433 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 13 19:35:19 2005 UTC (14 years, 7 months ago) by bates
File length: 11136 byte(s)
Diff to previous 417
Add the bVar slot to the lmer object

Revision 417 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 3 19:14:22 2005 UTC (14 years, 7 months ago) by bates
File length: 11040 byte(s)
Diff to previous 410
Change to the lmer representation

Revision 410 - (view) (download) (annotate) - [select for diffs]
Modified Tue Dec 28 14:51:42 2004 UTC (14 years, 7 months ago) by bates
File length: 12364 byte(s)
Diff to previous 391
Working on the lmer classes

Revision 391 - (view) (download) (annotate) - [select for diffs]
Modified Tue Dec 14 20:00:15 2004 UTC (14 years, 8 months ago) by bates
File length: 10717 byte(s)
Diff to previous 333
Add a coercion for tripletMatrix to matrix

Revision 333 - (view) (download) (annotate) - [select for diffs]
Modified Fri Nov 12 21:10:17 2004 UTC (14 years, 9 months ago) by bates
File length: 10716 byte(s)
Diff to previous 325
Add classes

Revision 325 - (view) (download) (annotate) - [select for diffs]
Modified Sat Nov 6 18:03:00 2004 UTC (14 years, 9 months ago) by bates
File length: 8863 byte(s)
Diff to previous 302
Add blocked/blocked cross-tabulation class

Revision 302 - (view) (download) (annotate) - [select for diffs]
Modified Wed Oct 27 21:32:37 2004 UTC (14 years, 9 months ago) by bates
File length: 8397 byte(s)
Diff to previous 296
Remove PACKAGE="Matrix" in .Call

Revision 296 - (view) (download) (annotate) - [select for diffs]
Modified Mon Oct 4 17:13:29 2004 UTC (14 years, 10 months ago) by bates
File length: 8623 byte(s)
Diff to previous 272
Add registration of .Call functions

Revision 272 - (view) (download) (annotate) - [select for diffs]
Modified Thu Sep 2 23:14:00 2004 UTC (14 years, 11 months ago) by bates
File length: 8688 byte(s)
Diff to previous 268
Add cscBlocked, tweak lmeRep

Revision 268 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 31 19:13:33 2004 UTC (14 years, 11 months ago) by bates
File length: 8583 byte(s)
Diff to previous 263
New version

Revision 263 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 26 16:01:35 2004 UTC (14 years, 11 months ago) by bates
File length: 8576 byte(s)
Diff to previous 257
extending lmeRep to multiple nested grouping factors

Revision 257 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 24 02:08:08 2004 UTC (15 years ago) by bates
File length: 10106 byte(s)
Diff to previous 255
Remove taucs, add lmeRep, new release

Revision 255 - (view) (download) (annotate) - [select for diffs]
Modified Fri Aug 20 16:27:15 2004 UTC (15 years ago) by bates
File length: 10039 byte(s)
Diff to previous 241
Add the lmeRep class

Revision 241 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jul 7 18:23:11 2004 UTC (15 years, 1 month ago) by bates
File length: 8711 byte(s)
Diff to previous 202
Remove pdMat classes

Revision 202 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jun 1 19:38:39 2004 UTC (15 years, 2 months ago) by bates
File length: 8667 byte(s)
Diff to previous 159
Be more careful in calls to require

Revision 159 - (view) (download) (annotate) - [select for diffs]
Modified Sun May 9 22:06:53 2004 UTC (15 years, 3 months ago) by bates
File length: 8650 byte(s)
Diff to previous 13
Remove storage of L-inverse

Revision 13 - (view) (download) (annotate) - [select for diffs]
Modified Tue Mar 23 13:16:19 2004 UTC (15 years, 5 months ago) by bates
File length: 8860 byte(s)
Diff to previous 10
Add diag slot to tscMatrix

Revision 10 - (view) (download) (annotate) - [select for diffs]
Added Mon Mar 22 20:20:05 2004 UTC (15 years, 5 months ago) by bates
File length: 8828 byte(s)
Initial import

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