R-packages – /branches/Matrix-for-R-2.3.x/INDEX

Rev 3771 – Version 0.995-18 fixing problem with lmer(resp ~ 1|grp,

bates — Wed, 13 Sep 2006 19:50:14 +0000

bates – 3 file(s) modified
Version 0.995-18 fixing problem with lmer(resp ~ 1|grp,

~ /branches/Matrix-for-R-2.3.x/DESCRIPTION
~ /branches/Matrix-for-R-2.3.x/INDEX
~ /branches/Matrix-for-R-2.3.x/R/lmer.R

Rev 3543 – branching an "old-R" compatible version of Matrix

maechler — Sat, 02 Sep 2006 16:36:14 +0000

maechler – 1 file(s) modified
branching an "old-R" compatible version of Matrix

+ /branches/Matrix-for-R-2.3.x (copied from /trunk/Matrix@3542)

Rev 3445 –

bates — Sun, 20 Aug 2006 16:15:59 +0000

bates – 2 file(s) modified

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX

Rev 3403 – Generalize conversions

bates — Sat, 12 Aug 2006 17:34:00 +0000

bates – 4 file(s) modified
Generalize conversions

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/CsparseMatrix-class.Rd
~ /trunk/Matrix/man/TsparseMatrix-class.Rd

Rev 3356 –

bates — Mon, 31 Jul 2006 23:06:01 +0000

bates – 2 file(s) modified

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX

Rev 3180 – Add isNested and for an identity permutation for nested grouping ...

bates — Sat, 27 May 2006 19:51:01 +0000

bates – 7 file(s) modified
Add isNested and for an identity permutation for nested grouping factors

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 3153 – Initial denom_df attempt

bates — Sat, 20 May 2006 11:34:18 +0000

bates – 4 file(s) modified
Initial denom_df attempt

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 3145 – lowerTriMatrix to tril, upperTriMatrix to triu, added band extractor

bates — Wed, 17 May 2006 17:42:09 +0000

bates – 6 file(s) modified
lowerTriMatrix to tril, upperTriMatrix to triu, added band extractor

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
+ /trunk/Matrix/man/band.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/Csparse.R

Rev 3093 – Extend example and add references for pedigree-class

bates — Tue, 25 Apr 2006 18:43:13 +0000

bates – 2 file(s) modified
Extend example and add references for pedigree-class

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/pedigree-class.Rd

Rev 3082 – document qqmath method for ranef.lmer objects

bates — Wed, 19 Apr 2006 14:22:07 +0000

bates – 3 file(s) modified
document qqmath method for ranef.lmer objects

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer-class.Rd

Rev 3054 – Added qqmath method for ranef.lmer and postVar for ranef methods

bates — Sun, 09 Apr 2006 00:02:26 +0000

bates – 9 file(s) modified
Added qqmath method for ranef.lmer and postVar for ranef methods

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/TODO

Rev 3022 – modifying return value of ranef method and adding residuals method

bates — Tue, 21 Mar 2006 11:07:55 +0000

bates – 4 file(s) modified
modifying return value of ranef method and adding residuals method

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R

Rev 2364 – Fix dpotrf call for BLAS under Mac OS X

bates — Thu, 16 Mar 2006 20:03:41 +0000

bates – 4 file(s) modified
Fix dpotrf call for BLAS under Mac OS X

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/src/dpoMatrix.c

Rev 2355 – Update documentation to new lmer class structure

bates — Mon, 13 Mar 2006 13:05:33 +0000

bates – 4 file(s) modified
Update documentation to new lmer class structure

~ /trunk/Matrix/Done
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer-class.Rd
~ /trunk/Matrix/TODO

Rev 2304 – Used cholmod_vertcat and cholmod_horzcat for cbind2 and rbind2 in the ...

bates — Mon, 20 Feb 2006 22:47:20 +0000

bates – 6 file(s) modified
Used cholmod_vertcat and cholmod_horzcat for cbind2 and rbind2 in the dsparseMatrix virtual class

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/dsparseMatrix.R
~ /trunk/Matrix/R/Tsparse.R
~ /trunk/Matrix/src/Csparse.c
~ /trunk/Matrix/src/Csparse.h
~ /trunk/Matrix/src/init.c

Rev 2259 – Fix trivial memory leaks

bates — Tue, 24 Jan 2006 21:03:04 +0000

bates – 4 file(s) modified
Fix trivial memory leaks

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lgeMatrix-class.Rd
~ /trunk/Matrix/src/iohb.c
~ /trunk/Matrix/src/mmio.c

Rev 2199 – modifications to lmer and related classes

bates — Sun, 15 Jan 2006 19:18:20 +0000

bates – 7 file(s) modified
modifications to lmer and related classes

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer-class.Rd
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/tests/lmer.R

Rev 2194 – Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

bates — Fri, 13 Jan 2006 23:47:38 +0000

bates – 10 file(s) modified
Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/src/chm_common.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h
~ /trunk/Matrix/tests/lmer.R

Rev 2146 – Fix due to Peter Dalgaard for segfault with multiple non-nested ...

bates — Sat, 07 Jan 2006 19:52:37 +0000

bates – 5 file(s) modified
Fix due to Peter Dalgaard for segfault with multiple non-nested grouping factors; Version 0.99-5

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/src/dgBCMatrix.c
~ /trunk/Matrix/TODO

Rev 1876 – Modifications to mer2

bates — Mon, 03 Oct 2005 01:44:56 +0000

bates – 9 file(s) modified
Modifications to mer2

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h

Rev 1836 – crossprod and tcrossprod for Tsparse

bates — Mon, 19 Sep 2005 21:10:59 +0000

bates – 8 file(s) modified
crossprod and tcrossprod for Tsparse

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/Csparse.R
~ /trunk/Matrix/R/dgTMatrix.R
~ /trunk/Matrix/R/Tsparse.R
~ /trunk/Matrix/src/Csparse.c
~ /trunk/Matrix/src/Csparse.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/tests/matprod.R

Rev 1792 – Add "start" argument to lmer

bates — Tue, 06 Sep 2005 01:26:11 +0000

bates – 7 file(s) modified
Add "start" argument to lmer

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1775 – Update

bates — Tue, 30 Aug 2005 14:38:31 +0000

bates – 1 file(s) modified
Update

~ /trunk/Matrix/INDEX

Rev 1767 – clean up conversion of graphNEL to sparseMatrix

bates — Sat, 27 Aug 2005 22:50:57 +0000

bates – 4 file(s) modified
clean up conversion of graphNEL to sparseMatrix

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/dgTMatrix.c

Rev 1736 – Release 0.98-5

bates — Thu, 18 Aug 2005 21:31:31 +0000

bates – 5 file(s) modified
Release 0.98-5

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/dsCMatrix-class.Rd
~ /trunk/Matrix/man/sparseMatrix-class.Rd

Rev 1726 – Release 0.98-4

bates — Tue, 16 Aug 2005 18:05:01 +0000

bates – 3 file(s) modified
Release 0.98-4

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX

Rev 1710 – update

bates — Mon, 08 Aug 2005 14:59:54 +0000

bates – 1 file(s) modified
update

~ /trunk/Matrix/INDEX

Rev 1696 – Harwell-Boeing and MatrixMarket formats

bates — Sun, 07 Aug 2005 15:22:33 +0000

bates – 14 file(s) modified
Harwell-Boeing and MatrixMarket formats

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/inst/Copyrights
+ /trunk/Matrix/man/externalFormats.Rd
~ /trunk/Matrix/NAMESPACE
+ /trunk/Matrix/R/HBMM.R
+ /trunk/Matrix/src/HBMM.c
+ /trunk/Matrix/src/HBMM.h
~ /trunk/Matrix/src/init.c
+ /trunk/Matrix/src/iohb.c
+ /trunk/Matrix/src/iohb.h
+ /trunk/Matrix/src/mmio.c
+ /trunk/Matrix/src/mmio.h
~ /trunk/Matrix/src/SOURCES_C.mkf

Rev 1679 – Version 0.98-1

bates — Wed, 27 Jul 2005 23:07:04 +0000

bates – 12 file(s) modified
Version 0.98-1

~ /trunk/Matrix/ChangeLog
+ /trunk/Matrix/data/sleepstudy.rda
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer.Rd
+ /trunk/Matrix/man/mcmcsamp.Rd
+ /trunk/Matrix/man/sleepstudy.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/tests/lmer.R

Rev 1633 – Updates to man pages

bates — Mon, 04 Jul 2005 15:28:48 +0000

bates – 1 file(s) modified
Updates to man pages

~ /trunk/Matrix/INDEX

Rev 1612 – More work on MCMC (still incomplete)

bates — Sun, 26 Jun 2005 03:42:21 +0000

bates – 3 file(s) modified
More work on MCMC (still incomplete)

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c

Rev 1610 – Adding MCMC capability (currently incomplete)

bates — Fri, 24 Jun 2005 23:06:33 +0000

bates – 5 file(s) modified
Adding MCMC capability (currently incomplete)

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1609 – Further development on AGQ and MCMC for glmm models

bates — Fri, 24 Jun 2005 15:38:43 +0000

bates – 5 file(s) modified
Further development on AGQ and MCMC for glmm models

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1598 – Release 0.96-3

bates — Sun, 19 Jun 2005 14:59:30 +0000

bates – 3 file(s) modified
Release 0.96-3

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R

Rev 1587 – Prepare for release 0.96-1

bates — Thu, 09 Jun 2005 16:57:55 +0000

bates – 6 file(s) modified
Prepare for release 0.96-1

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
x /trunk/Matrix/man/lmerControl.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/lmer.c

Rev 1583 – Moving lmer to the Matrix package

bates — Wed, 08 Jun 2005 23:47:45 +0000

bates – 15 file(s) modified
Moving lmer to the Matrix package

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
+ /trunk/Matrix/man/BIC.Rd (copied from /trunk/lme4/man/BIC.Rd@1563)
+ /trunk/Matrix/man/fixef.Rd (copied from /trunk/lme4/man/fixef.Rd@1565)
+ /trunk/Matrix/man/lmer-class.Rd (copied from /trunk/lme4/man/lmer-class.Rd@1565)
+ /trunk/Matrix/man/lmer.Rd (copied from /trunk/lme4/man/lmer.Rd@1565)
+ /trunk/Matrix/man/lmerControl.Rd (copied from /trunk/lme4/man/lmerControl.Rd@1563)
+ /trunk/Matrix/man/ranef.Rd (copied from /trunk/lme4/man/ranef.Rd@1563)
+ /trunk/Matrix/man/VarCorr-class.Rd (copied from /trunk/lme4/man/VarCorr-class.Rd@1563)
+ /trunk/Matrix/man/VarCorr.Rd (copied from /trunk/lme4/man/VarCorr.Rd@1563)
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/AllGeneric.R
+ /trunk/Matrix/R/lmer.R (copied from /trunk/lme4/R/lmer.R@1578)
+ /trunk/Matrix/tests/lmer.R (copied from /trunk/lme4/tests/lmer.R@1565)

Rev 1473 – More logical sparse matrix methods

bates — Tue, 10 May 2005 01:42:05 +0000

bates – 9 file(s) modified
More logical sparse matrix methods

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/dMatrix-class.Rd
x /trunk/Matrix/man/lgCMatrix-class.Rd
+ /trunk/Matrix/man/lsparseMatrix-classes.Rd (copied from /trunk/Matrix/man/lgCMatrix-class.Rd@1471)
~ /trunk/Matrix/R/lgCMatrix.R
+ /trunk/Matrix/R/lsCMatrix.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lgCMatrix.c
~ /trunk/Matrix/src/lgCMatrix.h

Rev 1467 – Getting ready for a release

bates — Mon, 09 May 2005 01:24:35 +0000

bates – 7 file(s) modified
Getting ready for a release

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/dgCMatrix.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lgCMatrix.c
~ /trunk/Matrix/src/lgCMatrix.h

Rev 1381 – Release 0.95-6

bates — Mon, 18 Apr 2005 14:34:33 +0000

bates – 17 file(s) modified
Release 0.95-6

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/dgeMatrix.c
~ /trunk/Matrix/src/init.c
+ /trunk/Matrix/src/lgCMatrix.c
+ /trunk/Matrix/src/lgCMatrix.h
+ /trunk/Matrix/src/lgTMatrix.c
+ /trunk/Matrix/src/lgTMatrix.h
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/Metis_utils.c
~ /trunk/Matrix/src/Metis_utils.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/SOURCES_C.mkf

Rev 1315 – Added dgRMatrix methods and documentation

bates — Mon, 28 Mar 2005 14:03:32 +0000

bates – 8 file(s) modified
Added dgRMatrix methods and documentation

~ /trunk/Matrix/INDEX
+ /trunk/Matrix/man/dgRMatrix-class.Rd
~ /trunk/Matrix/R/dgCMatrix.R
+ /trunk/Matrix/R/dgRMatrix.R
~ /trunk/Matrix/src/dgCMatrix.c
~ /trunk/Matrix/src/dgCMatrix.h
~ /trunk/Matrix/src/dtCMatrix.c
~ /trunk/Matrix/src/init.c