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Revision 2203 - Directory Listing
Modified Sat Jun 14 20:09:17 2008 UTC (11 years, 4 months ago) by mmaechler
C based encodeInd() -> faster indexing; any()/all() for nsparse; printSpMatrix2(); show(<diag>)

Revision 2195 - Directory Listing
Modified Fri May 30 15:08:31 2008 UTC (11 years, 4 months ago) by dmbates
Use Calloc not Alloca for potentially large allocations in dgeMatrix_exp

Revision 2183 - Directory Listing
Modified Thu Apr 24 10:58:51 2008 UTC (11 years, 6 months ago) by mmaechler
slight change in class-definition of [d]diMatrix; better pos.definite checks for dpo* and dpp*

Revision 2181 - Directory Listing
Modified Thu Apr 24 09:14:58 2008 UTC (11 years, 6 months ago) by mmaechler
fast special case n == 1

Revision 2178 - Directory Listing
Modified Thu Apr 24 06:31:40 2008 UTC (11 years, 6 months ago) by mmaechler
deal with integer 'matrix' in crossprod

Revision 2175 - Directory Listing
Modified Wed Apr 23 11:23:50 2008 UTC (11 years, 6 months ago) by mmaechler
more determinant(); MANY consistency cleanups, found by checkMatrix(); .. (see ChangeLog)

Revision 2166 - Directory Listing
Modified Wed Apr 2 15:06:02 2008 UTC (11 years, 6 months ago) by maechler
move declaration such that old gcc does not complain

Revision 2161 - Directory Listing
Modified Sat Mar 29 14:08:25 2008 UTC (11 years, 6 months ago) by maechler
make work with 2.7.0 version that do not have rcond

Revision 2157 - Directory Listing
Modified Tue Mar 25 15:00:01 2008 UTC (11 years, 6 months ago) by maechler
BunchKaufman(); fix <ddi> o <numeric> bug; Version++

Revision 2156 - Directory Listing
Modified Tue Mar 25 09:26:59 2008 UTC (11 years, 6 months ago) by maechler
trivial update of Csparse to version 2.2.1 (Nov.2007)

Revision 2155 - Directory Listing
Modified Sun Mar 23 16:41:02 2008 UTC (11 years, 7 months ago) by bates
Correct the call to chm_factor_to_SEXP (wrong kind of free used).

Revision 2153 - Directory Listing
Modified Sat Mar 22 21:22:41 2008 UTC (11 years, 7 months ago) by maechler
dsCMatrix_LDL_D() now also uses internal_chm_factor()

Revision 2151 - Directory Listing
Modified Thu Mar 20 23:31:22 2008 UTC (11 years, 7 months ago) by maechler
several cosmetics

Revision 2148 - Directory Listing
Modified Thu Mar 20 21:29:57 2008 UTC (11 years, 7 months ago) by bates
Cleaned up code in dsCMatrix.c; don't cache factorizations with Imult nonzero

Revision 2147 - Directory Listing
Modified Wed Mar 19 15:34:36 2008 UTC (11 years, 7 months ago) by bates
Hidden function ldetL2up to evaluate log-determinant of updated Cholesky factor for a vector of multiples of the identity

Revision 2146 - Directory Listing
Modified Wed Mar 19 14:03:07 2008 UTC (11 years, 7 months ago) by bates
Use CHOLMOD to copy factor in CHMfactor_update

Revision 2145 - Directory Listing
Modified Wed Mar 19 14:00:47 2008 UTC (11 years, 7 months ago) by bates
Add Imult argument to Cholesky

Revision 2144 - Directory Listing
Modified Tue Mar 18 23:08:12 2008 UTC (11 years, 7 months ago) by maechler
.symDiagonal(), is.na() and more diagonalMatrix "Ops"

Revision 2142 - Directory Listing
Modified Tue Mar 18 15:02:23 2008 UTC (11 years, 7 months ago) by bates
update method for CHMfactor; change return type of exported C function chm_factor_update

Revision 2140 - Directory Listing
Modified Tue Mar 18 01:03:48 2008 UTC (11 years, 7 months ago) by bates
Added chm_factor_update, documentation and tests

Revision 2138 - Directory Listing
Modified Mon Mar 17 23:23:30 2008 UTC (11 years, 7 months ago) by maechler
update to CHOLMOD version 1.6 (Nov.2007)

Revision 2137 - Directory Listing
Modified Mon Mar 17 22:21:24 2008 UTC (11 years, 7 months ago) by maechler
my fast determinant(<dsC..>) versions

Revision 2134 - Directory Listing
Modified Mon Mar 17 18:53:43 2008 UTC (11 years, 7 months ago) by bates
Log-determinant of the parent matrix from a CHMfactor object as chm_factor_ldetL2; documentation and support

Revision 2127 - Directory Listing
Modified Fri Mar 7 14:08:04 2008 UTC (11 years, 7 months ago) by maechler
fix the infamous expm() bug also in "Matrix" (duh!)

Revision 2125 - Directory Listing
Modified Fri Mar 7 07:58:26 2008 UTC (11 years, 7 months ago) by maechler
diagN2U() for preserving (unit-)triangularity in sparse (triang.)matrix multiplication

Revision 2124 - Directory Listing
Modified Thu Mar 6 08:19:40 2008 UTC (11 years, 7 months ago) by maechler
need  La_(norm|rcond)_type  definitions also for R-devel  {for now}

Revision 2121 - Directory Listing
Modified Tue Mar 4 22:01:33 2008 UTC (11 years, 7 months ago) by maechler
+ forgotten Rversion.h

Revision 2120 - Directory Listing
Modified Tue Mar 4 21:44:41 2008 UTC (11 years, 7 months ago) by maechler
use diagU2N in more places; also new Tsparse_diagU2N()

Revision 2119 - Directory Listing
Modified Tue Mar 4 21:44:04 2008 UTC (11 years, 7 months ago) by maechler
use CALLDEF and RREGDEF macros

Revision 2118 - Directory Listing
Modified Tue Mar 4 21:42:55 2008 UTC (11 years, 7 months ago) by maechler
remove unused dtTMatrix_as_dgCMatrix

Revision 2117 - Directory Listing
Modified Mon Mar 3 14:35:25 2008 UTC (11 years, 7 months ago) by maechler
s/norm_type/La_norm_type/ in order to move to R-devel

Revision 2115 - Directory Listing
Modified Sat Feb 23 09:23:17 2008 UTC (11 years, 8 months ago) by maechler
+ forceSymmetric(); generalize ddense_to_symmetric to dense_to_s.. and ddense_band to dense_band allowing simplified methods;  Matrix() and many man/*Rd : replace many as(*, <specific>) by as(*, <virtual superclass>)

Revision 2114 - Directory Listing
Modified Mon Feb 18 17:15:41 2008 UTC (11 years, 8 months ago) by bates
-Wall additions

Revision 2113 - Directory Listing
Modified Mon Feb 18 08:27:41 2008 UTC (11 years, 8 months ago) by maechler
miscellaneous cleanup; typically indexing and coercion

Revision 2112 - Directory Listing
Modified Mon Feb 18 08:24:46 2008 UTC (11 years, 8 months ago) by maechler
new symmpart(), skewpart()

Revision 2109 - Directory Listing
Modified Sat Jan 26 20:18:03 2008 UTC (11 years, 8 months ago) by maechler
new .Call(Tsparse_to_tCsparse,*)

Revision 2106 - Directory Listing
Modified Wed Jan 23 09:36:04 2008 UTC (11 years, 9 months ago) by maechler
+ "Schur" class and many more Schur methods

Revision 2104 - Directory Listing
Modified Sat Jan 12 16:09:01 2008 UTC (11 years, 9 months ago) by bates
Documentation errors caught by doxygen

Revision 2100 - Directory Listing
Modified Wed Jan 2 17:47:09 2008 UTC (11 years, 9 months ago) by bates
Corrected function documentation

Revision 2083 - Directory Listing
Modified Mon Oct 8 13:41:45 2007 UTC (12 years ago) by maechler
SHLIB_EXT also needed in some Debian circumstances

Revision 2061 - Directory Listing
Modified Sat Sep 1 20:37:11 2007 UTC (12 years, 1 month ago) by maechler
make alloca working for Sun

Revision 2049 - Directory Listing
Modified Tue Aug 14 22:22:24 2007 UTC (12 years, 2 months ago) by bates
Remove deprecated function writeHB and its methods; switch writeMM to use CHOLMOD code; repair readMM

Revision 2045 - Directory Listing
Modified Tue Aug 14 13:07:10 2007 UTC (12 years, 2 months ago) by bates
declare alloca

Revision 2038 - Directory Listing
Modified Mon Aug 6 16:43:03 2007 UTC (12 years, 2 months ago) by bates
Duplicate the contents of the RHS before Lapack call

Revision 2036 - Directory Listing
Modified Mon Aug 6 12:03:47 2007 UTC (12 years, 2 months ago) by maechler
add more x

Revision 2025 - Directory Listing
Modified Thu Aug 2 08:48:44 2007 UTC (12 years, 2 months ago) by maechler
R_cholmod_printf() instead of Rprintf()  just so pointers match

Revision 2019 - Directory Listing
Modified Wed Aug 1 15:44:06 2007 UTC (12 years, 2 months ago) by bates
Change API for numeric_as_chm_dense and N_AS_CHM_DN

Revision 2018 - Directory Listing
Modified Wed Aug 1 15:22:05 2007 UTC (12 years, 2 months ago) by maechler
fix <dge> %*% <dtr> + misc.cosmetics

Revision 2015 - Directory Listing
Modified Wed Jul 25 14:17:24 2007 UTC (12 years, 3 months ago) by maechler
(mostly) patches from Brian re potential changes in R-devel

Revision 2007 - Directory Listing
Modified Thu Jul 19 19:45:48 2007 UTC (12 years, 3 months ago) by bates
Export triplet_to_sparse, documentation, use typedefs

Revision 2005 - Directory Listing
Modified Wed Jul 18 14:46:20 2007 UTC (12 years, 3 months ago) by maechler
norm() for sparse; systematic checking of norm() and all "Summary" methods

Revision 1986 - Directory Listing
Modified Tue Jul 10 19:30:28 2007 UTC (12 years, 3 months ago) by bates
Fix a "thinko" in the new code for dgeMatrix_colsums

Revision 1974 - Directory Listing
Modified Mon Jul 9 20:45:14 2007 UTC (12 years, 3 months ago) by bates
Untangle horrible code in dgeMatrix_colsums to fix a subtle bug (Kurt Hornik and Ingo Feinerer)

Revision 1973 - Directory Listing
Modified Mon Jul 9 19:43:42 2007 UTC (12 years, 3 months ago) by maechler
"cleaned" dgeMatrix_colsums() - but did not solve the bug

Revision 1968 - Directory Listing
Modified Sat Jul 7 22:49:12 2007 UTC (12 years, 3 months ago) by maechler
Rsparse validation methods; finally make use of slot_dup() macro; fix R_to_C (symmetric)

Revision 1965 - Directory Listing
Modified Sat Jul 7 20:06:05 2007 UTC (12 years, 3 months ago) by bates
Include cholmod_matrixops.h for declaration of cholmod_symmetry

Revision 1960 - Directory Listing
Modified Fri Jul 6 16:54:43 2007 UTC (12 years, 3 months ago) by maechler
merge 'branches/Matrix-APIchange' back into the trunk

Revision 1945 - Directory Listing
Modified Wed Jul 4 18:07:07 2007 UTC (12 years, 3 months ago) by maechler
not dropping dimnames (notably of sparse matrices)

Revision 1921 - Directory Listing
Modified Sat Jun 23 18:08:17 2007 UTC (12 years, 4 months ago) by maechler
colSums() etc update (fix for lgC*)

Revision 1920 - Directory Listing
Modified Sat Jun 23 09:43:30 2007 UTC (12 years, 4 months ago) by maechler
use template instead of huge macro for [diln]gcMatrix_colSums

Revision 1917 - Directory Listing
Modified Thu Jun 21 21:32:39 2007 UTC (12 years, 4 months ago) by maechler
update + comment

Revision 1911 - Directory Listing
Modified Tue Jun 19 16:16:58 2007 UTC (12 years, 4 months ago) by maechler
colSums, ... rowMeans for all Matrices; notably sparse ones via [diln]gCMatrix_colSums C code

Revision 1908 - Directory Listing
Modified Mon Jun 18 16:14:06 2007 UTC (12 years, 4 months ago) by bates
Modified dgCMatrix_colSums for sparseVector result

Revision 1907 - Directory Listing
Modified Mon Jun 18 16:12:45 2007 UTC (12 years, 4 months ago) by bates
Added Matrix_lengthSym

Revision 1906 - Directory Listing
Modified Sat Jun 16 19:26:30 2007 UTC (12 years, 4 months ago) by maechler
no longer use backquote (" ` ") in messages

Revision 1901 - Directory Listing
Modified Sat Jun 16 15:52:56 2007 UTC (12 years, 4 months ago) by bates
added dgCMatrix_colSums for [col,row][Sums,Means]

Revision 1895 - Directory Listing
Modified Fri Jun 15 18:19:23 2007 UTC (12 years, 4 months ago) by bates
added lm.fit.sparse (unexported), coercion of "factor" to dgCMatrix and dgCMatrix_cholsol

Revision 1893 - Directory Listing
Modified Thu Jun 14 10:46:10 2007 UTC (12 years, 4 months ago) by maechler
more strict validity checking for Csparse

Revision 1884 - Directory Listing
Modified Thu Jun 7 08:51:52 2007 UTC (12 years, 4 months ago) by maechler
modularize Makefile(.win)  [checked on Uwe`s server]

Revision 1882 - Directory Listing
Modified Wed Jun 6 14:18:12 2007 UTC (12 years, 4 months ago) by maechler
a bit more sync between the two Makefiles

Revision 1879 - Directory Listing
Modified Tue Jun 5 17:10:33 2007 UTC (12 years, 4 months ago) by bates
Remove reference to the no longer available CCOLAMD

Revision 1876 - Directory Listing
Modified Tue Jun 5 16:53:04 2007 UTC (12 years, 4 months ago) by bates
Update to version 3.0.0 of SuiteSparse

Revision 1875 - Directory Listing
Modified Tue Jun 5 16:50:18 2007 UTC (12 years, 4 months ago) by bates
update to CSparse version 2.2.0

Revision 1874 - Directory Listing
Modified Tue Jun 5 16:49:30 2007 UTC (12 years, 4 months ago) by bates
add ./UFconfig to the include path for compilation

Revision 1873 - Directory Listing
Modified Tue Jun 5 16:48:45 2007 UTC (12 years, 4 months ago) by bates
Update to version 3.0.0 of SuiteSparse

Revision 1869 - Directory Listing
Modified Tue Jun 5 15:03:49 2007 UTC (12 years, 4 months ago) by bates
Modify for new organization of CSparse package

Revision 1867 - Directory Listing
Modified Mon Jun 4 17:13:02 2007 UTC (12 years, 4 months ago) by bates
Remove warnings after change to const char* CHAR

Revision 1862 - Directory Listing
Modified Sun Jun 3 14:42:03 2007 UTC (12 years, 4 months ago) by bates
Yet another cholmod export - cholmod_ssmult

Revision 1847 - Directory Listing
Modified Sat May 19 19:23:28 2007 UTC (12 years, 5 months ago) by bates
Write 1-based, not 0-based, indices in writeMM

Revision 1844 - Directory Listing
Modified Wed May 16 20:40:34 2007 UTC (12 years, 5 months ago) by bates
Added solve methods for CHMfactor class

Revision 1836 - Directory Listing
Modified Mon May 14 13:14:49 2007 UTC (12 years, 5 months ago) by maechler
also remove zpotf2.f et al  from Makefile.win

Revision 1828 - Directory Listing
Modified Wed Apr 25 22:23:31 2007 UTC (12 years, 5 months ago) by bates
Export another CHOLMOD function

Revision 1827 - Directory Listing
Modified Wed Apr 25 22:22:41 2007 UTC (12 years, 5 months ago) by bates
Remove superfluous Lapack files

Revision 1808 - Directory Listing
Modified Thu Mar 29 21:59:20 2007 UTC (12 years, 6 months ago) by bates
Consistency of bounds

Revision 1798 - Directory Listing
Modified Sat Mar 24 14:52:47 2007 UTC (12 years, 7 months ago) by maechler
better dtC inversion from Kasper K

Revision 1787 - Directory Listing
Modified Fri Feb 16 20:02:19 2007 UTC (12 years, 8 months ago) by bates
Prepare for 0.9975-11 release

Revision 1771 - Directory Listing
Modified Tue Feb 6 17:41:42 2007 UTC (12 years, 8 months ago) by maechler
forgot free(.) in R_to_C; other cosmetic

Revision 1766 - Directory Listing
Modified Mon Feb 5 16:35:49 2007 UTC (12 years, 8 months ago) by maechler
port Doug`s fix to R_to_CMatrix and reactivate .Call()s

Revision 1763 - Directory Listing
Modified Sun Feb 4 21:57:00 2007 UTC (12 years, 8 months ago) by bates
Use strdup, not automatic character arrays

Revision 1761 - Directory Listing
Modified Sun Feb 4 19:33:36 2007 UTC (12 years, 8 months ago) by bates
Fix a cut-and-paste error

Revision 1760 - Directory Listing
Modified Sat Feb 3 21:13:22 2007 UTC (12 years, 8 months ago) by maechler
Rsparse coercions now all via R-level "workaround"; to and from  *virtual* rather than specific classes

Revision 1758 - Directory Listing
Modified Sat Feb 3 16:34:51 2007 UTC (12 years, 8 months ago) by maechler
workaround platform-dependent segfault in R_to_CMatrix

Revision 1751 - Directory Listing
Modified Tue Jan 30 17:41:02 2007 UTC (12 years, 8 months ago) by maechler
drop(); tweaks to Ops & indexing; Rsparse coercions for less exceptions in tests/Class+Meth.R

Revision 1750 - Directory Listing
Modified Mon Jan 29 21:10:53 2007 UTC (12 years, 8 months ago) by maechler
more revisiting "FIXME"..

Revision 1747 - Directory Listing
Modified Mon Jan 29 20:17:33 2007 UTC (12 years, 8 months ago) by maechler
many more coercions for diag(), "!", etc; see ChangeLog

Revision 1746 - Directory Listing
Modified Mon Jan 29 16:04:38 2007 UTC (12 years, 8 months ago) by maechler
new DEPS.mkf + reminder on how to

Revision 1736 - Directory Listing
Modified Tue Jan 23 17:09:41 2007 UTC (12 years, 9 months ago) by maechler
+ SET_Dimnames; more dimnames setting and other cosmetic

Revision 1725 - Directory Listing
Modified Wed Jan 17 08:01:10 2007 UTC (12 years, 9 months ago) by maechler
accomplished quite a few small FIXMEs; see ChangeLog

Revision 1716 - Directory Listing
Modified Sat Jan 6 02:01:24 2007 UTC (12 years, 9 months ago) by bates
export cholmod_scale

Revision 1712 - Directory Listing
Modified Wed Dec 27 21:19:24 2006 UTC (12 years, 9 months ago) by maechler
use Lapack 3.1 version for zpot*.f

Revision 1711 - Directory Listing
Modified Wed Dec 27 11:23:41 2006 UTC (12 years, 9 months ago) by maechler
+ include

Revision 1710 - Directory Listing
Modified Tue Dec 26 15:57:06 2006 UTC (12 years, 9 months ago) by maechler
more "[<-" fixes; validity of triangular sparse

Revision 1708 - Directory Listing
Modified Fri Dec 22 19:53:37 2006 UTC (12 years, 10 months ago) by maechler
rbind2() / cbind2() methods fixes + new Auxiliaries

Revision 1703 - Directory Listing
Modified Fri Dec 15 10:16:51 2006 UTC (12 years, 10 months ago) by bates
Export cholmod_change_factor and cholmod_factor_to_sparse

Revision 1691 - Directory Listing
Modified Sun Dec 10 13:54:15 2006 UTC (12 years, 10 months ago) by bates
Convert LDL to LL before conversion to sparseMatrix; clean up docs

Revision 1688 - Directory Listing
Modified Sat Dec 9 00:29:45 2006 UTC (12 years, 10 months ago) by bates
export cholmod_analyze_p; new version

Revision 1686 - Directory Listing
Modified Mon Dec 4 16:20:46 2006 UTC (12 years, 10 months ago) by bates
Check Lapack error code in dgeMatrix_matrix_solve

Revision 1681 - Directory Listing
Modified Wed Nov 29 15:55:03 2006 UTC (12 years, 10 months ago) by bates
Check error code from dgetri in dgeMatrix_solve (Barry Rowlingson)

Revision 1675 - Directory Listing
Modified Tue Nov 7 17:10:51 2006 UTC (12 years, 11 months ago) by maechler
better comment

Revision 1673 - Directory Listing
Modified Mon Nov 6 20:54:26 2006 UTC (12 years, 11 months ago) by maechler
host of changes; mostly indexing(sub-set & -assign) for symmetric and [ cbind(i,j) ]

Revision 1666 - Directory Listing
Modified Sat Nov 4 17:47:31 2006 UTC (12 years, 11 months ago) by maechler
updated to CSparse 2.0.3 (via our CSparse_install.sh)

Revision 1665 - Directory Listing
Modified Fri Nov 3 23:18:07 2006 UTC (12 years, 11 months ago) by maechler
fully-sparse solve() for dsC; indexing & comparison fixes

Revision 1664 - Directory Listing
Modified Fri Nov 3 13:38:32 2006 UTC (12 years, 11 months ago) by bates
Fixed typo

Revision 1663 - Directory Listing
Modified Thu Nov 2 18:22:11 2006 UTC (12 years, 11 months ago) by maechler
oops -- forgot this update in last revision

Revision 1661 - Directory Listing
Modified Thu Nov 2 13:10:50 2006 UTC (12 years, 11 months ago) by maechler
2nd round of cleanup for <sparse>_validate()

Revision 1660 - Directory Listing
Modified Thu Nov 2 11:05:35 2006 UTC (12 years, 11 months ago) by maechler
tcrossprod(<Csp>, <Csp>); dimnames for [t]crossprod; validity now ensures correct length(Dimnames[[j]])

Revision 1659 - Directory Listing
Modified Wed Nov 1 17:50:15 2006 UTC (12 years, 11 months ago) by maechler
extend Csparse_Csparse_crossprod for tcrossprod (need test!); isSymmetric improved; misc.

Revision 1657 - Directory Listing
Modified Wed Nov 1 16:29:53 2006 UTC (12 years, 11 months ago) by bates
crossprod(<CsparseMatrix>,<CsparseMatrix>) added

Revision 1655 - Directory Listing
Modified Mon Oct 30 17:16:27 2006 UTC (12 years, 11 months ago) by maechler
another set of fixes/improvements; the last prompted by Harri Kiiveri

Revision 1654 - Directory Listing
Modified Fri Oct 27 16:58:15 2006 UTC (12 years, 11 months ago) by maechler
miscellaneous "fixes" mostly in ChangeLog and/or related to diagonalMatrix

Revision 1646 - Directory Listing
Modified Sun Oct 22 22:42:40 2006 UTC (13 years ago) by bates
Export yet another cholmod routine

Revision 1641 - Directory Listing
Modified Fri Oct 20 15:04:40 2006 UTC (13 years ago) by bates
Change cholmod to use Rprintf and R's error handler

Revision 1634 - Directory Listing
Modified Mon Oct 16 13:42:29 2006 UTC (13 years ago) by bates
Export cholmod_sort

Revision 1629 - Directory Listing
Modified Fri Oct 13 12:51:11 2006 UTC (13 years ago) by bates
minor corrections

Revision 1624 - Directory Listing
Modified Wed Oct 11 15:00:11 2006 UTC (13 years ago) by bates
Remove Harwell-Boeing format for writing

Revision 1618 - Directory Listing
Modified Fri Oct 6 15:44:01 2006 UTC (13 years ago) by maechler
Matrix(0, d,d) should also give sparse (not diagonal); general_to_symmetric; notably for lsC*; more coercions; first cut at Csparse_drop()

Revision 1613 - Directory Listing
Modified Wed Oct 4 22:41:49 2006 UTC (13 years ago) by bates
New release to export more CCallable functions

Revision 1598 - Directory Listing
Modified Fri Sep 29 09:39:34 2006 UTC (13 years ago) by maechler
comments & not_yet code

Revision 1595 - Directory Listing
Modified Thu Sep 28 22:32:23 2006 UTC (13 years ago) by bates
Add missing include file

Revision 1594 - Directory Listing
Modified Thu Sep 28 22:31:21 2006 UTC (13 years ago) by bates
Export more functions from cholmod for use in Zt_create

Revision 1591 - Directory Listing
Modified Thu Sep 28 15:28:20 2006 UTC (13 years ago) by maechler
validate tweaks for packed matrices

Revision 1589 - Directory Listing
Modified Wed Sep 27 15:57:12 2006 UTC (13 years ago) by maechler
*correct* (!) SUBDIRS

Revision 1575 - Directory Listing
Modified Mon Sep 18 14:47:40 2006 UTC (13 years, 1 month ago) by maechler
check 'x' slot in l.CMatrix_validate

Revision 1574 - Directory Listing
Modified Mon Sep 18 13:28:50 2006 UTC (13 years, 1 month ago) by maechler
comments only

Revision 1570 - Directory Listing
Modified Sat Sep 16 16:23:49 2006 UTC (13 years, 1 month ago) by maechler
rename lcsc_to_matrix to ncsc_* and write new lcsc_*()

Revision 1568 - Directory Listing
Modified Sat Sep 16 15:17:27 2006 UTC (13 years, 1 month ago) by maechler
update for "l"Matrix cholmod-handling

Revision 1564 - Directory Listing
Modified Thu Sep 14 15:52:48 2006 UTC (13 years, 1 month ago) by maechler
fixup SUBDIRS

Revision 1563 - Directory Listing
Modified Thu Sep 14 15:52:32 2006 UTC (13 years, 1 month ago) by maechler
omit 'NULL' SOURCES_BLAS

Revision 1560 - Directory Listing
Modified Thu Sep 14 06:54:18 2006 UTC (13 years, 1 month ago) by maechler
comment more (-Wall)

Revision 1558 - Directory Listing
Modified Wed Sep 13 17:02:50 2006 UTC (13 years, 1 month ago) by bates
Remove redundant validation checks

Revision 1555 - Directory Listing
Modified Wed Sep 13 14:47:28 2006 UTC (13 years, 1 month ago) by bates
Move checks on column sorting of CsparseMatrix objects to Csparse_validate

Revision 1554 - Directory Listing
Modified Tue Sep 12 22:01:24 2006 UTC (13 years, 1 month ago) by bates
Remove lsame.f and zherk.f - now part of R's BLAS

Revision 1553 - Directory Listing
Modified Tue Sep 12 22:00:13 2006 UTC (13 years, 1 month ago) by bates
Conditionalize definition of SIZE_T_MAX to avoid warnings under Mac OS X (Tim will add this to the upstream sources)

Revision 1552 - Directory Listing
Modified Tue Sep 12 21:58:30 2006 UTC (13 years, 1 month ago) by bates
updates after removal of Metis, CAMD and CCOLAMD

Revision 1551 - Directory Listing
Modified Tue Sep 12 16:39:13 2006 UTC (13 years, 1 month ago) by maechler
1st fix at "Compare"; other small fixes

Revision 1550 - Directory Listing
Modified Tue Sep 12 13:16:30 2006 UTC (13 years, 1 month ago) by maechler
Memcopy: use (int *) in "l" case

Revision 1549 - Directory Listing
Modified Tue Sep 12 13:14:59 2006 UTC (13 years, 1 month ago) by maechler
obvious fix

Revision 1548 - Directory Listing
Modified Mon Sep 11 22:13:07 2006 UTC (13 years, 1 month ago) by maechler
new nMatrix and subclasses; lsparse change to have x slot; many consequences

Revision 1546 - Directory Listing
Modified Mon Sep 11 14:49:05 2006 UTC (13 years, 1 month ago) by bates
Move the alloc_d**Matrix utility functions from the Matrix package to the lme4 package

Revision 1543 - Directory Listing
Modified Sat Sep 9 13:44:15 2006 UTC (13 years, 1 month ago) by bates
ignoring LDL = FALSE now fixed

Revision 1541 - Directory Listing
Modified Sat Sep 9 12:04:53 2006 UTC (13 years, 1 month ago) by maechler
 fname instead of "fname"

Revision 1537 - Directory Listing
Modified Fri Sep 8 13:16:55 2006 UTC (13 years, 1 month ago) by bates
Remove dependencies on triplet_to_col and its source files

Revision 1534 - Directory Listing
Modified Fri Sep 8 12:21:07 2006 UTC (13 years, 1 month ago) by bates
Remove partitioning algorithms for fill-reducing permutation

Revision 1533 - Directory Listing
Modified Fri Sep 8 12:19:19 2006 UTC (13 years, 1 month ago) by bates
hide symbols with a pragma (using an __attribute__ may be better)

Revision 1528 - Directory Listing
Modified Thu Sep 7 03:49:23 2006 UTC (13 years, 1 month ago) by bates
Cleanup

Revision 1523 - Directory Listing
Modified Wed Sep 6 22:33:39 2006 UTC (13 years, 1 month ago) by bates
Cleanup

Revision 1517 - Directory Listing
Modified Wed Sep 6 13:34:03 2006 UTC (13 years, 1 month ago) by bates
Cleanup

Revision 1515 - Directory Listing
Modified Tue Sep 5 22:13:15 2006 UTC (13 years, 1 month ago) by bates
Update to version 1.2 of CHOLMOD and latest versions of its dependent packages

Revision 1514 - Directory Listing
Modified Tue Sep 5 20:15:56 2006 UTC (13 years, 1 month ago) by bates
Moved to ../../inst/doc/UFsparse/AMD.txt

Revision 1512 - Directory Listing
Modified Tue Sep 5 10:08:20 2006 UTC (13 years, 1 month ago) by maechler
add FLIBS

Revision 1511 - Directory Listing
Modified Tue Sep 5 09:12:44 2006 UTC (13 years, 1 month ago) by maechler
remove UMFPACK and LDL also from Makefiles

Revision 1510 - Directory Listing
Modified Mon Sep 4 20:34:43 2006 UTC (13 years, 1 month ago) by bates
Turns out that LDL and UMFPACK were not being used

Revision 1507 - Directory Listing
Modified Mon Sep 4 18:41:34 2006 UTC (13 years, 1 month ago) by bates
Merging changes from Matrix-nolmer branch

Revision 1478 - Directory Listing
Modified Fri Sep 1 23:16:49 2006 UTC (13 years, 1 month ago) by bates
*** empty log message ***

Revision 1470 - Directory Listing
Modified Fri Sep 1 13:30:52 2006 UTC (13 years, 1 month ago) by bates
Remove unused name in ddense_band

Revision 1466 - Directory Listing
Modified Wed Aug 30 03:35:53 2006 UTC (13 years, 1 month ago) by bates
housekeeping

Revision 1465 - Directory Listing
Modified Wed Aug 30 03:05:59 2006 UTC (13 years, 1 month ago) by bates
housekeeping

Revision 1464 - Directory Listing
Modified Wed Aug 30 03:05:06 2006 UTC (13 years, 1 month ago) by bates
housekeeping

Revision 1463 - Directory Listing
Modified Tue Aug 29 22:30:57 2006 UTC (13 years, 1 month ago) by bates
Promotion of %*% and solve to RHS of ddenseMatrix

Revision 1461 - Directory Listing
Modified Tue Aug 29 16:17:27 2006 UTC (13 years, 1 month ago) by bates
Define and use class_P and mMatrix_as_dgeMatrix

Revision 1458 - Directory Listing
Modified Tue Aug 29 00:04:48 2006 UTC (13 years, 1 month ago) by bates
Remove vestigial classed argument for dsCMatrix_matrix_solve

Revision 1453 - Directory Listing
Modified Sun Aug 27 16:16:35 2006 UTC (13 years, 1 month ago) by bates
Added triu, tril and band for ddenseMatrix objects.

Revision 1451 - Directory Listing
Modified Sat Aug 26 17:25:57 2006 UTC (13 years, 1 month ago) by bates
Added initial version of dgeMatrix_band but may change design

Revision 1449 - Directory Listing
Modified Sat Aug 26 13:00:36 2006 UTC (13 years, 1 month ago) by bates
Remove sections of code that are no longer used

Revision 1448 - Directory Listing
Modified Sat Aug 26 03:29:36 2006 UTC (13 years, 1 month ago) by bates
Move methods to the CsparseMatrix class

Revision 1447 - Directory Listing
Modified Fri Aug 25 20:38:36 2006 UTC (13 years, 1 month ago) by maechler
use setAs("ddenseMatrix", "dgeMatrix", *) instead of older specific ones

Revision 1441 - Directory Listing
Modified Thu Aug 24 21:59:49 2006 UTC (13 years, 2 months ago) by bates
Add ddiMatrix,dtpMatrix, dspMatrix and dppMatrix conversions. Remove no-longer-used functions.

Revision 1440 - Directory Listing
Modified Thu Aug 24 18:34:18 2006 UTC (13 years, 2 months ago) by bates
Use dup_mMatrix_as_dgeMatrix

Revision 1438 - Directory Listing
Modified Thu Aug 24 18:23:36 2006 UTC (13 years, 2 months ago) by bates
Replaced R_ldl etc. by CHOLMOD functions

Revision 1437 - Directory Listing
Modified Thu Aug 24 18:23:11 2006 UTC (13 years, 2 months ago) by bates
Replaced R_ldl etc. by CHOLMOD functions

Revision 1436 - Directory Listing
Modified Thu Aug 24 18:22:39 2006 UTC (13 years, 2 months ago) by bates
Use dup_mMatrix_as_dgeMatrix

Revision 1433 - Directory Listing
Modified Thu Aug 24 18:19:36 2006 UTC (13 years, 2 months ago) by bates
Replaced by CHOLMOD functions

Revision 1432 - Directory Listing
Modified Thu Aug 24 16:21:18 2006 UTC (13 years, 2 months ago) by maechler
eliminate classed argument from dup_mM*() and dependencies

Revision 1430 - Directory Listing
Modified Wed Aug 23 22:13:34 2006 UTC (13 years, 2 months ago) by bates
Paring down dependencies

Revision 1428 - Directory Listing
Modified Wed Aug 23 21:32:30 2006 UTC (13 years, 2 months ago) by bates
Disable chol methods for lsCMatrix class temporarily; Comment out old code in src/lsCMatrix.[ch]

Revision 1427 - Directory Listing
Modified Wed Aug 23 21:29:22 2006 UTC (13 years, 2 months ago) by bates
Add Cholesky generic and method for dsCMatrix.  Use CHOLMOD for chol().

Revision 1426 - Directory Listing
Modified Wed Aug 23 21:27:04 2006 UTC (13 years, 2 months ago) by bates
Ensure 'factors' slot exists in result of dgeMatrix_crossprod (may need to do this in other places).

Revision 1425 - Directory Listing
Modified Wed Aug 23 21:25:32 2006 UTC (13 years, 2 months ago) by bates
Remove classes lCholCMatrix and dCholCMatrix, now using CHMfactor classes instead

Revision 1424 - Directory Listing
Modified Wed Aug 23 14:26:19 2006 UTC (13 years, 2 months ago) by maechler
comments; cosmetic

Revision 1421 - Directory Listing
Modified Tue Aug 22 22:50:38 2006 UTC (13 years, 2 months ago) by bates
Comment out vestigial functions

Revision 1419 - Directory Listing
Modified Tue Aug 22 22:49:17 2006 UTC (13 years, 2 months ago) by bates
use diag_P and uplo_P macros

Revision 1418 - Directory Listing
Modified Tue Aug 22 22:47:37 2006 UTC (13 years, 2 months ago) by bates
Comment out vestigial functions

Revision 1417 - Directory Listing
Modified Tue Aug 22 22:46:07 2006 UTC (13 years, 2 months ago) by bates
Use CHOLMOD for dsCMatrix_chol and dsCMatrix_matrix_solve.

Revision 1416 - Directory Listing
Modified Tue Aug 22 22:44:14 2006 UTC (13 years, 2 months ago) by bates
Move check_class to Mutils.h and some bug fixes

Revision 1415 - Directory Listing
Modified Tue Aug 22 18:06:54 2006 UTC (13 years, 2 months ago) by bates
Misunderstood effect of make_d_matrix_triangular and make_d_matrix_symmetric.  Now fixed.  Use _NOT_A_CLASS_ instead of dmatrix for the name of the class that should not occur.

Revision 1413 - Directory Listing
Modified Tue Aug 22 17:25:24 2006 UTC (13 years, 2 months ago) by bates
register dup_mMatrix_as_dgeMatrix for coercions.

Revision 1412 - Directory Listing
Modified Tue Aug 22 17:23:39 2006 UTC (13 years, 2 months ago) by bates
updated for general types of classed Matrices, matrices or numeric or logical vectors.

Revision 1410 - Directory Listing
Modified Tue Aug 22 01:00:03 2006 UTC (13 years, 2 months ago) by bates
Use dup_mMatrix_as_dgeMatrix

Revision 1409 - Directory Listing
Modified Tue Aug 22 00:57:22 2006 UTC (13 years, 2 months ago) by bates
update validation tests, fix -Wall warnings

Revision 1407 - Directory Listing
Modified Mon Aug 21 15:24:47 2006 UTC (13 years, 2 months ago) by maechler
rename class "LU" to "denseLU" and make "LU" virtual

Revision 1404 - Directory Listing
Modified Mon Aug 21 14:38:50 2006 UTC (13 years, 2 months ago) by bates
Fix memory leak caught by valgrind.

Revision 1399 - Directory Listing
Modified Sun Aug 20 16:14:07 2006 UTC (13 years, 2 months ago) by bates
Fix thinko in sparseQR_resid_fitted

Revision 1397 - Directory Listing
Modified Sun Aug 20 03:24:10 2006 UTC (13 years, 2 months ago) by bates
Check length of q before trying to store it

Revision 1396 - Directory Listing
Modified Sun Aug 20 03:17:19 2006 UTC (13 years, 2 months ago) by bates
Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid and qr.fitted

Revision 1395 - Directory Listing
Modified Sun Aug 20 03:15:25 2006 UTC (13 years, 2 months ago) by bates
Added dup_mMatrix_as_dgeMatrix utility

Revision 1394 - Directory Listing
Modified Sat Aug 19 12:16:16 2006 UTC (13 years, 2 months ago) by maechler
add comment on why Rdefines.h

Revision 1393 - Directory Listing
Modified Fri Aug 18 17:00:10 2006 UTC (13 years, 2 months ago) by maechler
using R_VERSION (useful more generally) - does not help

Revision 1386 - Directory Listing
Modified Thu Aug 17 22:30:40 2006 UTC (13 years, 2 months ago) by bates
Remove code that is no longer used

Revision 1385 - Directory Listing
Modified Thu Aug 17 22:30:01 2006 UTC (13 years, 2 months ago) by bates
Added solve methods for dgCMatrix and documentation

Revision 1384 - Directory Listing
Modified Thu Aug 17 13:59:21 2006 UTC (13 years, 2 months ago) by bates
Update to version 2.0.1 of Tim Davis's CSparse library

Revision 1383 - Directory Listing
Modified Thu Aug 17 13:57:53 2006 UTC (13 years, 2 months ago) by bates
add sparse LU and QR decompositions

Revision 1382 - Directory Listing
Modified Wed Aug 16 16:34:27 2006 UTC (13 years, 2 months ago) by maechler
new script for CSparse updating

Revision 1381 - Directory Listing
Modified Wed Aug 16 03:17:34 2006 UTC (13 years, 2 months ago) by bates
Repaired Matrix_cs_as_SEXP, cosmetic changes in dgCMatrix_QR

Revision 1380 - Directory Listing
Modified Tue Aug 15 22:31:30 2006 UTC (13 years, 2 months ago) by bates
Adding dgCMatrix_{lusol,qrsol,QR} but QR still not working

Revision 1375 - Directory Listing
Modified Tue Aug 15 18:21:49 2006 UTC (13 years, 2 months ago) by maechler
eliminate sCMatrix_to_gCMatrix now that we have (almost identical) Csparse_symmetric_to_general

Revision 1371 - Directory Listing
Modified Mon Aug 14 21:08:58 2006 UTC (13 years, 2 months ago) by bates
Utilities Csparse_to_logical and Csparse_symmetric_to_general

Revision 1369 - Directory Listing
Modified Mon Aug 14 18:54:04 2006 UTC (13 years, 2 months ago) by bates
Use CHOLMOD code for general methods at CsparseMatrix, TsparseMatrix, denseMatrix or matrix level when possible

Revision 1367 - Directory Listing
Modified Sat Aug 12 17:33:07 2006 UTC (13 years, 2 months ago) by bates
Generalize conversions

Revision 1366 - Directory Listing
Modified Sat Aug 12 17:31:39 2006 UTC (13 years, 2 months ago) by bates
Generalize conversions

Revision 1363 - Directory Listing
Modified Thu Aug 10 18:49:06 2006 UTC (13 years, 2 months ago) by bates
Adjust glmer_init for S4SXP

Revision 1360 - Directory Listing
Modified Tue Aug 8 17:29:03 2006 UTC (13 years, 2 months ago) by bates
crossprod and tcrossprod for TsparseMatrix

Revision 1353 - Directory Listing
Modified Tue Aug 8 14:54:12 2006 UTC (13 years, 2 months ago) by bates
tcrossprod result has stype = -1 (perhaps this should change).

Revision 1352 - Directory Listing
Modified Mon Aug 7 18:31:12 2006 UTC (13 years, 2 months ago) by bates
Set stype in C function Csparse_crossprod and avoid R-level conversions

Revision 1342 - Directory Listing
Modified Tue Aug 1 20:26:45 2006 UTC (13 years, 2 months ago) by bates
hatTrace and warnings about boundary convergence

Revision 1336 - Directory Listing
Modified Mon Jul 31 23:05:04 2006 UTC (13 years, 2 months ago) by bates
Add hatTrace function

Revision 1331 - Directory Listing
Modified Sat Jul 22 17:59:53 2006 UTC (13 years, 3 months ago) by maechler
many method cleanups; notably some "dgC" -> "Csparse" generaliztations

Revision 1330 - Directory Listing
Modified Fri Jul 21 08:28:18 2006 UTC (13 years, 3 months ago) by maechler
pass verbose argument to (gl)mer_MCMCsamp() and use it in C code

Revision 1323 - Directory Listing
Modified Mon Jul 17 18:34:45 2006 UTC (13 years, 3 months ago) by bates
Add coersion from CHMfactor to sparseMatrix

Revision 1318 - Directory Listing
Modified Mon Jul 17 13:06:55 2006 UTC (13 years, 3 months ago) by maechler
dsTMatrix_as_dgTMatrix(): do not copy the diag TWICE

Revision 1317 - Directory Listing
Modified Tue Jul 11 22:02:10 2006 UTC (13 years, 3 months ago) by bates
Fix the problem of applying INTEGER to the x slot of the value.

Revision 1315 - Directory Listing
Modified Mon Jul 10 16:08:05 2006 UTC (13 years, 3 months ago) by maechler
miscellaneous small things, including extended tests; see also ChangeLog

Revision 1314 - Directory Listing
Modified Mon Jul 10 15:23:48 2006 UTC (13 years, 3 months ago) by maechler
add lgCMatrix_diag()

Revision 1310 - Directory Listing
Modified Thu Jul 6 15:27:14 2006 UTC (13 years, 3 months ago) by bates
Remove definitions of unused identifiers

Revision 1309 - Directory Listing
Modified Thu Jul 6 15:25:55 2006 UTC (13 years, 3 months ago) by bates
mcmcsamp for glmer objects

Revision 1308 - Directory Listing
Modified Thu Jul 6 15:25:21 2006 UTC (13 years, 3 months ago) by bates
mcmcsamp for glmer objects

Revision 1307 - Directory Listing
Modified Thu Jul 6 15:16:45 2006 UTC (13 years, 3 months ago) by bates
Correction in pedigree_inbreeding (which is not currently being used or fully tested)

Revision 1296 - Directory Listing
Modified Sat Jun 10 18:06:33 2006 UTC (13 years, 4 months ago) by bates
Re-aligned deviance column in mcmcsamp output (and no longer use index of -1); added calculations of mer_hat_trace

Revision 1294 - Directory Listing
Modified Thu Jun 8 16:06:02 2006 UTC (13 years, 4 months ago) by bates
Many changes in mcmcsample and other places

Revision 1284 - Directory Listing
Modified Sat May 27 20:01:11 2006 UTC (13 years, 4 months ago) by bates
More careful checks in subbars and friends, code for calculating inbreeding coefficients directly from the pedigree

Revision 1283 - Directory Listing
Modified Sat May 27 19:51:01 2006 UTC (13 years, 4 months ago) by bates
Add isNested and for an identity permutation for nested grouping factors

Revision 1282 - Directory Listing
Modified Wed May 24 17:00:12 2006 UTC (13 years, 5 months ago) by maechler
eliminate a few old "FIXME"s (and add a new one :-)

Revision 1279 - Directory Listing
Modified Tue May 23 08:01:11 2006 UTC (13 years, 5 months ago) by maechler
make compilable

Revision 1278 - Directory Listing
Modified Mon May 22 22:30:11 2006 UTC (13 years, 5 months ago) by bates
Begin isNested

Revision 1277 - Directory Listing
Modified Mon May 22 19:16:12 2006 UTC (13 years, 5 months ago) by bates
Add an implementation of mer_denom_df

Revision 1275 - Directory Listing
Modified Mon May 22 18:58:08 2006 UTC (13 years, 5 months ago) by bates
Compile the check module for CHOLMOD

Revision 1273 - Directory Listing
Modified Mon May 22 18:56:23 2006 UTC (13 years, 5 months ago) by bates
Copy colcount in CHOLMOD supernodal factorization

Revision 1272 - Directory Listing
Modified Sat May 20 11:34:18 2006 UTC (13 years, 5 months ago) by bates
Initial denom_df attempt

Revision 1271 - Directory Listing
Modified Thu May 18 06:47:09 2006 UTC (13 years, 5 months ago) by maechler
some  "sparse <-> graph"  updates

Revision 1267 - Directory Listing
Modified Tue May 16 19:12:13 2006 UTC (13 years, 5 months ago) by bates
single argument [t]crossprod now returns a symmetric matrix

Revision 1265 - Directory Listing
Modified Mon May 15 22:36:59 2006 UTC (13 years, 5 months ago) by bates
Generics lowerTriMatrix and upperTriMatrix and C function Csparse_band

Revision 1262 - Directory Listing
Modified Sun Apr 30 15:40:39 2006 UTC (13 years, 5 months ago) by bates
Add special solve method for unit upper triangular matrices

Revision 1261 - Directory Listing
Modified Sun Apr 30 15:39:44 2006 UTC (13 years, 5 months ago) by bates
Add chol method for pedigree objects

Revision 1256 - Directory Listing
Modified Wed Apr 19 14:19:29 2006 UTC (13 years, 6 months ago) by bates
nz component of cs structure should be -1 for a compressed column-oriented matrix

Revision 1252 - Directory Listing
Modified Sat Apr 15 13:47:09 2006 UTC (13 years, 6 months ago) by bates
Remove redundant #include "cs.h" directives.

Revision 1251 - Directory Listing
Modified Sat Apr 15 13:08:26 2006 UTC (13 years, 6 months ago) by bates
Add CSparse-based solve methods for dtCMatrix class

Revision 1250 - Directory Listing
Modified Sat Apr 15 13:01:24 2006 UTC (13 years, 6 months ago) by bates
Add CSparse library and utilities

Revision 1248 - Directory Listing
Modified Thu Apr 13 22:05:22 2006 UTC (13 years, 6 months ago) by bates
C code for inverse of sparse, unit, lower triangular matrices (pattern only at present)

Revision 1243 - Directory Listing
Modified Sun Apr 9 00:02:26 2006 UTC (13 years, 6 months ago) by bates
Added qqmath method for ranef.lmer and postVar for ranef methods

Revision 1236 - Directory Listing
Modified Thu Mar 23 15:16:17 2006 UTC (13 years, 7 months ago) by bates
Propagate DimNames in dsyMatrix_as_dspMatrix

Revision 1231 - Directory Listing
Modified Sat Mar 18 17:41:34 2006 UTC (13 years, 7 months ago) by bates
Trivial change in documentation of a function

Revision 1230 - Directory Listing
Modified Thu Mar 16 20:03:41 2006 UTC (13 years, 7 months ago) by bates
Fix dpotrf call for BLAS under Mac OS X

Revision 1223 - Directory Listing
Modified Tue Mar 7 11:06:46 2006 UTC (13 years, 7 months ago) by maechler
lmer(): dropped non-sensical 'x' and 'y' arguments

Revision 1219 - Directory Listing
Modified Wed Feb 22 08:21:09 2006 UTC (13 years, 8 months ago) by maechler
use R_ARCH for R-devel

Revision 1218 - Directory Listing
Modified Mon Feb 20 22:47:20 2006 UTC (13 years, 8 months ago) by bates
Used cholmod_vertcat and cholmod_horzcat for cbind2 and rbind2 in the dsparseMatrix virtual class

Revision 1213 - Directory Listing
Modified Tue Feb 7 23:44:07 2006 UTC (13 years, 8 months ago) by bates
Fix case of cbind(successes, failures) for lmer fitting a GLMM (see Changelog)

Revision 1209 - Directory Listing
Modified Wed Jan 25 23:42:57 2006 UTC (13 years, 8 months ago) by bates
Use coersion for transpose of dtCMatrix class

Revision 1208 - Directory Listing
Modified Wed Jan 25 15:19:29 2006 UTC (13 years, 8 months ago) by bates
Move dtTMatrix_to_dtCMatrix to CHOLMOD code

Revision 1206 - Directory Listing
Modified Tue Jan 24 23:02:36 2006 UTC (13 years, 8 months ago) by bates
Initialize result of dgeMatrix_crossprod

Revision 1205 - Directory Listing
Modified Tue Jan 24 21:03:04 2006 UTC (13 years, 8 months ago) by bates
Fix trivial memory leaks

Revision 1204 - Directory Listing
Modified Tue Jan 24 17:48:18 2006 UTC (13 years, 8 months ago) by bates
Fix trivial memory leak

Revision 1200 - Directory Listing
Modified Mon Jan 23 16:01:20 2006 UTC (13 years, 9 months ago) by maechler
make*_(triangular|symmetric) : now for ldense* as well

Revision 1196 - Directory Listing
Modified Sun Jan 22 14:52:05 2006 UTC (13 years, 9 months ago) by bates
fix valgrind-detected memory leak

Revision 1195 - Directory Listing
Modified Sun Jan 22 14:16:38 2006 UTC (13 years, 9 months ago) by bates
Be more conservative by running cholmod_sort before cholmod_nnz

Revision 1194 - Directory Listing
Modified Sun Jan 22 14:16:04 2006 UTC (13 years, 9 months ago) by bates
Fixing memory leaks

Revision 1193 - Directory Listing
Modified Sat Jan 21 21:43:13 2006 UTC (13 years, 9 months ago) by bates
Free memory allocated in csc_tcrossprod

Revision 1191 - Directory Listing
Modified Fri Jan 20 19:47:10 2006 UTC (13 years, 9 months ago) by bates
Use cholmod_copy in csc_tcrossprod

Revision 1190 - Directory Listing
Modified Fri Jan 20 19:46:38 2006 UTC (13 years, 9 months ago) by bates
Clean up documentation

Revision 1187 - Directory Listing
Modified Thu Jan 19 22:10:55 2006 UTC (13 years, 9 months ago) by maechler
fix that other old bug that crept into 2nd last fix

Revision 1186 - Directory Listing
Modified Thu Jan 19 22:06:38 2006 UTC (13 years, 9 months ago) by maechler
+ "{"

Revision 1185 - Directory Listing
Modified Thu Jan 19 22:02:53 2006 UTC (13 years, 9 months ago) by maechler
restitute cholmod_common declaration to setting 0.99-6

Revision 1180 - Directory Listing
Modified Thu Jan 19 00:43:37 2006 UTC (13 years, 9 months ago) by bates
Over to Martin for release 0.995-2

Revision 1177 - Directory Listing
Modified Wed Jan 18 07:35:10 2006 UTC (13 years, 9 months ago) by maechler
ALL_CFLAGS += -O2

Revision 1176 - Directory Listing
Modified Wed Jan 18 07:31:41 2006 UTC (13 years, 9 months ago) by maechler
correct LAPACK_LIBS (didn't change all in r2189)

Revision 1175 - Directory Listing
Modified Tue Jan 17 23:41:36 2006 UTC (13 years, 9 months ago) by bates
Munging the data frame

Revision 1174 - Directory Listing
Modified Mon Jan 16 20:03:48 2006 UTC (13 years, 9 months ago) by maechler
make Matrix() "smart" -- with help of quite a few new setAs(. , .) settings

Revision 1167 - Directory Listing
Modified Sun Jan 15 21:13:54 2006 UTC (13 years, 9 months ago) by bates
Removing rcond slot from Matrix objects

Revision 1164 - Directory Listing
Modified Sat Jan 14 23:40:42 2006 UTC (13 years, 9 months ago) by maechler
new dMatrix_validate and dense_nonpacked_validate

Revision 1162 - Directory Listing
Modified Fri Jan 13 23:47:38 2006 UTC (13 years, 9 months ago) by bates
Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

Revision 1158 - Directory Listing
Modified Fri Jan 13 13:13:09 2006 UTC (13 years, 9 months ago) by maechler
Linking change for R-devel (windows), thanks to BDR

Revision 1156 - Directory Listing
Modified Thu Jan 12 23:39:56 2006 UTC (13 years, 9 months ago) by bates
Remove redundant registration of dspMatrix_trf; incorporate wts and wrkres slots in mer class

Revision 1151 - Directory Listing
Modified Thu Jan 12 07:31:55 2006 UTC (13 years, 9 months ago) by maechler
use "$(MAKE)", not "make" in Makefiles; needed eg on *BSD for "gmake"

Revision 1143 - Directory Listing
Modified Thu Jan 12 03:17:24 2006 UTC (13 years, 9 months ago) by bates
Switch to supernodal Cholesky representation of mer objects

Revision 1142 - Directory Listing
Modified Thu Jan 12 03:10:29 2006 UTC (13 years, 9 months ago) by bates
Remove dgBCMatrix.[ch] and dependencies

Revision 1141 - Directory Listing
Modified Thu Jan 12 03:02:46 2006 UTC (13 years, 9 months ago) by bates
Change malloc to Calloc in chm_common.c and correspondingly free to Free there and elsewhere

Revision 1119 - Directory Listing
Modified Sat Jan 7 19:52:37 2006 UTC (13 years, 9 months ago) by bates
Fix due to Peter Dalgaard for segfault with multiple non-nested grouping factors; Version 0.99-5

Revision 1101 - Directory Listing
Modified Thu Dec 29 20:05:37 2005 UTC (13 years, 9 months ago) by maechler
dgeMatrix_matrix_crossprod(*, trans)

Revision 1098 - Directory Listing
Modified Thu Dec 29 11:38:59 2005 UTC (13 years, 9 months ago) by maechler
some 2-argument-tcrossprod methods (and test svn)

Revision 1067 - Directory Listing
Modified Mon Nov 28 16:27:29 2005 UTC (13 years, 10 months ago) by bates
Added crossprod method for Csparse and dense

Revision 1059 - Directory Listing
Modified Wed Nov 23 22:20:13 2005 UTC (13 years, 11 months ago) by bates
Matrix multiplication and coersion at higher level

Revision 1053 - Directory Listing
Modified Mon Nov 14 22:21:04 2005 UTC (13 years, 11 months ago) by bates
Release 0.99-2

Revision 1048 - Directory Listing
Modified Sat Nov 12 16:44:04 2005 UTC (13 years, 11 months ago) by bates
Test for both BLAS_LIBS and LAPACK_LIBS

Revision 1047 - Directory Listing
Modified Sat Nov 12 12:35:55 2005 UTC (13 years, 11 months ago) by maechler
revert to original (-r1820)

Revision 1046 - Directory Listing
Modified Sat Nov 12 12:07:53 2005 UTC (13 years, 11 months ago) by maechler
lsame.f needed for z*.f - only if not BLAS_LIBS

Revision 1041 - Directory Listing
Modified Fri Nov 11 21:45:50 2005 UTC (13 years, 11 months ago) by maechler
use $(.)

Revision 1033 - Directory Listing
Modified Wed Nov 9 22:39:33 2005 UTC (13 years, 11 months ago) by bates
typo

Revision 1032 - Directory Listing
Modified Wed Nov 9 17:55:53 2005 UTC (13 years, 11 months ago) by maechler
need for "extern" (by Brian)

Revision 1031 - Directory Listing
Modified Wed Nov 9 17:50:06 2005 UTC (13 years, 11 months ago) by maechler
using malloc & free & variable "dofree"

Revision 1030 - Directory Listing
Modified Wed Nov 9 17:48:24 2005 UTC (13 years, 11 months ago) by maechler
Windows "make" extensions (based on Brian`s)

Revision 1029 - Directory Listing
Modified Wed Nov 9 15:26:22 2005 UTC (13 years, 11 months ago) by maechler
use free() to clean up after  as_cholmod_*() since these use malloc() - as in Brian`s patch

Revision 1026 - Directory Listing
Modified Tue Nov 8 23:12:38 2005 UTC (13 years, 11 months ago) by bates
Moving CHOLMOD User Guide

Revision 1025 - Directory Listing
Modified Tue Nov 8 23:11:59 2005 UTC (13 years, 11 months ago) by bates
Moving CHOLMOD User Guide

Revision 1024 - Directory Listing
Modified Tue Nov 8 23:09:13 2005 UTC (13 years, 11 months ago) by bates
New version of Makefile.win

Revision 1023 - Directory Listing
Modified Tue Nov 8 23:07:36 2005 UTC (13 years, 11 months ago) by bates
Remove entire UFconfig directory

Revision 1022 - Directory Listing
Modified Tue Nov 8 20:49:59 2005 UTC (13 years, 11 months ago) by bates
Modifying CHOLMOD Makefiles and directories

Revision 1021 - Directory Listing
Modified Tue Nov 8 19:40:59 2005 UTC (13 years, 11 months ago) by bates
Removing unused directory

Revision 1020 - Directory Listing
Modified Tue Nov 8 19:40:36 2005 UTC (13 years, 11 months ago) by bates
Removing unused directory

Revision 1019 - Directory Listing
Modified Tue Nov 8 19:28:07 2005 UTC (13 years, 11 months ago) by bates


Revision 1018 - Directory Listing
Modified Tue Nov 8 19:27:47 2005 UTC (13 years, 11 months ago) by bates


Revision 1017 - Directory Listing
Modified Tue Nov 8 19:17:19 2005 UTC (13 years, 11 months ago) by bates


Revision 1016 - Directory Listing
Modified Tue Nov 8 19:13:56 2005 UTC (13 years, 11 months ago) by bates
Removing the test matrix directory

Revision 1014 - Directory Listing
Modified Tue Nov 8 18:21:28 2005 UTC (13 years, 11 months ago) by bates
Moving AMD docs to inst/doc

Revision 1013 - Directory Listing
Modified Tue Nov 8 13:33:44 2005 UTC (13 years, 11 months ago) by bates
Use Calloc/Free, not malloc/Free

Revision 989 - Directory Listing
Modified Tue Oct 25 17:39:26 2005 UTC (13 years, 11 months ago) by bates
munging the Makefiles

Revision 984 - Directory Listing
Modified Tue Oct 11 18:08:46 2005 UTC (14 years ago) by bates
Tidying up

Revision 983 - Directory Listing
Modified Tue Oct 11 15:19:20 2005 UTC (14 years ago) by bates
Remove references to Pattern.[ch]

Revision 982 - Directory Listing
Modified Tue Oct 11 15:18:23 2005 UTC (14 years ago) by bates
Remove references to Pattern.[ch]

Revision 980 - Directory Listing
Modified Tue Oct 11 14:11:44 2005 UTC (14 years ago) by bates
Remove Pattern sources that are no longer needed

Revision 979 - Directory Listing
Modified Tue Oct 11 00:02:45 2005 UTC (14 years ago) by bates
Added a FIXME - will fix later

Revision 978 - Directory Listing
Modified Mon Oct 10 13:54:09 2005 UTC (14 years ago) by bates
More mer2 modifications

Revision 977 - Directory Listing
Modified Fri Oct 7 22:14:47 2005 UTC (14 years ago) by bates
mer2_initial

Revision 975 - Directory Listing
Modified Fri Oct 7 20:18:14 2005 UTC (14 years ago) by maechler
comment

Revision 971 - Directory Listing
Modified Fri Oct 7 15:40:21 2005 UTC (14 years ago) by maechler
add BLAS zherk.f because it's not (yet) in R

Revision 970 - Directory Listing
Modified Fri Oct 7 14:20:23 2005 UTC (14 years ago) by bates
Added a factorization in mer2_create so the permutation could be applied to Z'X and Z'y

Revision 969 - Directory Listing
Modified Thu Oct 6 23:34:20 2005 UTC (14 years ago) by bates
Permutation of Z'X and Z'y in mer2_factor

Revision 968 - Directory Listing
Modified Thu Oct 6 23:33:25 2005 UTC (14 years ago) by bates
nrow, not ncol

Revision 967 - Directory Listing
Modified Thu Oct 6 03:07:23 2005 UTC (14 years ago) by bates
More updates on lmer - still not quite correct

Revision 966 - Directory Listing
Modified Thu Oct 6 03:06:40 2005 UTC (14 years ago) by bates
Routines missing from the lapack module sources

Revision 964 - Directory Listing
Modified Mon Oct 3 20:35:52 2005 UTC (14 years ago) by maechler
new and better error mesage when info

Revision 963 - Directory Listing
Modified Mon Oct 3 01:44:56 2005 UTC (14 years ago) by bates
Modifications to mer2

Revision 960 - Directory Listing
Modified Sat Oct 1 20:10:45 2005 UTC (14 years ago) by maechler
cosmetic

Revision 957 - Directory Listing
Modified Sat Oct 1 20:08:04 2005 UTC (14 years ago) by maechler
check return value from cholmod_aat()   {fix seg.fault}

Revision 956 - Directory Listing
Modified Fri Sep 30 17:28:00 2005 UTC (14 years ago) by maechler
more coercions; particularly "d" <-> "l"; more tests (and more FIXMEs!); fixing two "index-0 bugs"; ...

Revision 955 - Directory Listing
Modified Thu Sep 29 19:32:14 2005 UTC (14 years ago) by maechler
duh: LIB was not a name

Revision 952 - Directory Listing
Modified Wed Sep 28 19:19:19 2005 UTC (14 years ago) by maechler
packed_to_full_(double|int) and full_to_packed_*

Revision 951 - Directory Listing
Modified Wed Sep 28 12:42:51 2005 UTC (14 years ago) by maechler
use uplo_P() and diag_P() macros instead of *_value() functions

Revision 950 - Directory Listing
Modified Wed Sep 28 12:42:11 2005 UTC (14 years ago) by maechler
+ include

Revision 945 - Directory Listing
Modified Wed Sep 28 08:54:28 2005 UTC (14 years ago) by maechler
+ logical dense matrices; more coercions

Revision 944 - Directory Listing
Modified Wed Sep 28 08:54:00 2005 UTC (14 years ago) by maechler
fix longstanding typo; new dsT*_as_dgT*

Revision 943 - Directory Listing
Modified Wed Sep 28 08:52:22 2005 UTC (14 years ago) by maechler
+ uplo_value(), diag_value()

Revision 940 - Directory Listing
Modified Tue Sep 27 00:50:35 2005 UTC (14 years ago) by bates
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

Revision 932 - Directory Listing
Modified Mon Sep 19 23:04:52 2005 UTC (14 years, 1 month ago) by bates
Updated DEPS.mkf and some include files

Revision 930 - Directory Listing
Modified Mon Sep 19 21:29:37 2005 UTC (14 years, 1 month ago) by bates
corrected error message

Revision 928 - Directory Listing
Modified Mon Sep 19 21:10:59 2005 UTC (14 years, 1 month ago) by bates
crossprod and tcrossprod for Tsparse

Revision 927 - Directory Listing
Modified Mon Sep 19 21:09:49 2005 UTC (14 years, 1 month ago) by bates
Fixed a thinko picked up by the compiler

Revision 926 - Directory Listing
Modified Mon Sep 19 21:08:53 2005 UTC (14 years, 1 month ago) by bates
Keep -Wall quiet

Revision 925 - Directory Listing
Modified Mon Sep 19 19:01:31 2005 UTC (14 years, 1 month ago) by maechler
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 923 - Directory Listing
Modified Sun Sep 18 23:41:45 2005 UTC (14 years, 1 month ago) by bates
More progress on incorporating CHOLMOD - still not passing CMD check

Revision 922 - Directory Listing
Modified Sun Sep 18 16:33:54 2005 UTC (14 years, 1 month ago) by bates
Added CHOLMOD-based C functions.  Still need methods defined in R and some error checking

Revision 921 - Directory Listing
Modified Sat Sep 17 14:27:41 2005 UTC (14 years, 1 month ago) by bates
Sparse Matrix methods using CHOLMOD inside ifdef blocks

Revision 920 - Directory Listing
Modified Fri Sep 16 19:36:51 2005 UTC (14 years, 1 month ago) by bates
Some CHOLMOD utilities

Revision 919 - Directory Listing
Modified Fri Sep 16 17:27:06 2005 UTC (14 years, 1 month ago) by maechler
new compressed_non_0_ij()

Revision 917 - Directory Listing
Modified Thu Sep 15 18:03:55 2005 UTC (14 years, 1 month ago) by bates
Document changes

Revision 916 - Directory Listing
Modified Thu Sep 15 17:52:59 2005 UTC (14 years, 1 month ago) by bates
Actually needed the Check module

Revision 915 - Directory Listing
Modified Thu Sep 15 17:45:23 2005 UTC (14 years, 1 month ago) by bates
Removing unneeded directories

Revision 914 - Directory Listing
Modified Thu Sep 15 17:41:38 2005 UTC (14 years, 1 month ago) by bates
Removing unneeded directories

Revision 913 - Directory Listing
Modified Thu Sep 15 17:38:18 2005 UTC (14 years, 1 month ago) by bates
No need for xerbla in R package

Revision 912 - Directory Listing
Modified Thu Sep 15 14:53:55 2005 UTC (14 years, 1 month ago) by bates
Adding CHOLMOD and related source packages

Revision 903 - Directory Listing
Modified Wed Sep 7 20:43:18 2005 UTC (14 years, 1 month ago) by bates
Remove unnecessary declaration

Revision 901 - Directory Listing
Modified Tue Sep 6 01:26:11 2005 UTC (14 years, 1 month ago) by bates
Add "start" argument to lmer

Revision 896 - Directory Listing
Modified Sat Sep 3 21:57:18 2005 UTC (14 years, 1 month ago) by maechler
more consistency in validation checks

Revision 895 - Directory Listing
Modified Sat Sep 3 21:56:35 2005 UTC (14 years, 1 month ago) by maechler
cosmetic, comment

Revision 894 - Directory Listing
Modified Sat Sep 3 21:55:38 2005 UTC (14 years, 1 month ago) by maechler
comments

Revision 890 - Directory Listing
Modified Thu Sep 1 17:18:08 2005 UTC (14 years, 1 month ago) by maechler
add triangularMatrix_validate and symmetric* to C code and make (re!)use of it - not quite everywhere?

Revision 888 - Directory Listing
Modified Thu Sep 1 13:46:21 2005 UTC (14 years, 1 month ago) by bates
New simulate method for lmer objects

Revision 885 - Directory Listing
Modified Tue Aug 30 20:54:55 2005 UTC (14 years, 1 month ago) by maechler
fix typo in non-validity text

Revision 883 - Directory Listing
Modified Tue Aug 30 14:38:04 2005 UTC (14 years, 1 month ago) by bates
Doxygen documentation for C function

Revision 879 - Directory Listing
Modified Tue Aug 30 14:35:05 2005 UTC (14 years, 1 month ago) by bates
Added simulate generic and method

Revision 878 - Directory Listing
Modified Sun Aug 28 13:57:39 2005 UTC (14 years, 1 month ago) by bates
Add simulate method for lmer

Revision 876 - Directory Listing
Modified Sat Aug 27 22:50:57 2005 UTC (14 years, 1 month ago) by bates
clean up conversion of graphNEL to sparseMatrix

Revision 874 - Directory Listing
Modified Sat Aug 27 21:27:51 2005 UTC (14 years, 1 month ago) by maechler
prepare graphNEL coercion both for directed and undir.

Revision 866 - Directory Listing
Modified Fri Aug 19 16:58:26 2005 UTC (14 years, 2 months ago) by maechler
new lcrc_to_matrix code

Revision 862 - Directory Listing
Modified Thu Aug 18 21:31:07 2005 UTC (14 years, 2 months ago) by bates
Coercion method for graphNEL to sparseMatrix class

Revision 852 - Directory Listing
Modified Tue Aug 16 17:52:16 2005 UTC (14 years, 2 months ago) by bates
Move readHB and readMM to R code and allow the use of connections

Revision 846 - Directory Listing
Modified Wed Aug 10 22:08:35 2005 UTC (14 years, 2 months ago) by bates
Release 0.98-3

Revision 841 - Directory Listing
Modified Tue Aug 9 14:21:32 2005 UTC (14 years, 2 months ago) by bates
Remove second declaration of IOHBterminate

Revision 840 - Directory Listing
Modified Mon Aug 8 16:16:17 2005 UTC (14 years, 2 months ago) by bates
Avoid problems with trying to write to string constants.

Revision 838 - Directory Listing
Modified Mon Aug 8 14:59:38 2005 UTC (14 years, 2 months ago) by bates
writeHarwellBoeing and writeMatrixMarket routines

Revision 835 - Directory Listing
Modified Mon Aug 8 13:33:18 2005 UTC (14 years, 2 months ago) by bates
Add writeHB and writeMM methods and generic

Revision 825 - Directory Listing
Modified Sun Aug 7 15:22:33 2005 UTC (14 years, 2 months ago) by bates
Harwell-Boeing and MatrixMarket formats

Revision 824 - Directory Listing
Modified Sat Aug 6 20:01:51 2005 UTC (14 years, 2 months ago) by bates
Allow mcmcsamp on transformed parameters

Revision 820 - Directory Listing
Modified Wed Jul 27 23:07:04 2005 UTC (14 years, 2 months ago) by bates
Version 0.98-1

Revision 818 - Directory Listing
Modified Tue Jul 26 22:46:14 2005 UTC (14 years, 2 months ago) by bates
updates on lmer_MCMCsamp

Revision 816 - Directory Listing
Modified Tue Jul 26 12:36:10 2005 UTC (14 years, 2 months ago) by bates
Working version of lmer_MCMCsamp - may have chisq in wrong place when sampling sigmasqr

Revision 815 - Directory Listing
Modified Sun Jul 24 23:53:40 2005 UTC (14 years, 3 months ago) by bates
Added lmer_MCMCsamp to the C sources

Revision 814 - Directory Listing
Modified Thu Jul 21 23:05:52 2005 UTC (14 years, 3 months ago) by bates
Working version of the glmmMCMC producing an mcmc object

Revision 813 - Directory Listing
Modified Thu Jul 21 16:41:42 2005 UTC (14 years, 3 months ago) by bates
New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

Revision 812 - Directory Listing
Modified Thu Jul 21 14:59:04 2005 UTC (14 years, 3 months ago) by bates
Added an rWishart function, which should later be moved to the stats package

Revision 808 - Directory Listing
Modified Mon Jul 11 15:05:40 2005 UTC (14 years, 3 months ago) by bates
Release 0.97-3

Revision 806 - Directory Listing
Modified Fri Jul 8 15:38:43 2005 UTC (14 years, 3 months ago) by bates
Preliminary version of glmmMCMC

Revision 805 - Directory Listing
Modified Fri Jul 8 03:47:35 2005 UTC (14 years, 3 months ago) by bates
More work on glmer_ranef_update - still not complete

Revision 804 - Directory Listing
Modified Thu Jul 7 20:05:47 2005 UTC (14 years, 3 months ago) by bates
Preparing for glmmMCMC

Revision 803 - Directory Listing
Modified Thu Jul 7 19:09:49 2005 UTC (14 years, 3 months ago) by murdoch
Get include files from R_HOME/include in Windows

Revision 802 - Directory Listing
Modified Wed Jul 6 23:55:39 2005 UTC (14 years, 3 months ago) by bates
got glmer_fixed_update working

Revision 801 - Directory Listing
Modified Wed Jul 6 16:24:33 2005 UTC (14 years, 3 months ago) by bates
Updates for release 0.97-2

Revision 800 - Directory Listing
Modified Tue Jul 5 00:38:09 2005 UTC (14 years, 3 months ago) by bates
Clean up

Revision 796 - Directory Listing
Modified Mon Jul 4 14:57:28 2005 UTC (14 years, 3 months ago) by bates
Added utilities vecSum and vecIncrement

Revision 795 - Directory Listing
Modified Mon Jul 4 14:56:57 2005 UTC (14 years, 3 months ago) by bates
Added AGQ for glmer class

Revision 790 - Directory Listing
Modified Sat Jul 2 20:57:08 2005 UTC (14 years, 3 months ago) by maechler
emacs-helping comment

Revision 787 - Directory Listing
Modified Thu Jun 30 16:59:12 2005 UTC (14 years, 3 months ago) by bates
Still modifying glmer_devAGQ

Revision 786 - Directory Listing
Modified Tue Jun 28 13:58:41 2005 UTC (14 years, 3 months ago) by bates
Developing AGQ but still not right

Revision 785 - Directory Listing
Modified Sun Jun 26 16:22:56 2005 UTC (14 years, 3 months ago) by bates
Conditional modes now ok for MCMC - still need sampling methods

Revision 784 - Directory Listing
Modified Sun Jun 26 03:42:21 2005 UTC (14 years, 3 months ago) by bates
More work on MCMC (still incomplete)

Revision 783 - Directory Listing
Modified Sun Jun 26 03:41:37 2005 UTC (14 years, 3 months ago) by bates
Reinstate check on number of arguments

Revision 782 - Directory Listing
Modified Fri Jun 24 23:06:33 2005 UTC (14 years, 4 months ago) by bates
Adding MCMC capability (currently incomplete)

Revision 781 - Directory Listing
Modified Fri Jun 24 15:38:43 2005 UTC (14 years, 4 months ago) by bates
Further development on AGQ and MCMC for glmm models

Revision 779 - Directory Listing
Modified Wed Jun 15 15:52:19 2005 UTC (14 years, 4 months ago) by bates
Adding AGQ (but not yet correct)

Revision 778 - Directory Listing
Modified Tue Jun 14 04:05:54 2005 UTC (14 years, 4 months ago) by bates
Non-working version - needs adjustment of deviance by multiplicative factor

Revision 777 - Directory Listing
Modified Tue Jun 14 04:02:57 2005 UTC (14 years, 4 months ago) by bates
release 0.96-2

Revision 776 - Directory Listing
Modified Mon Jun 13 19:45:04 2005 UTC (14 years, 4 months ago) by bates
Setting up for AGQ

Revision 775 - Directory Listing
Modified Mon Jun 13 01:22:28 2005 UTC (14 years, 4 months ago) by bates
Factoring C code in preparation for AGQ

Revision 774 - Directory Listing
Modified Fri Jun 10 18:40:54 2005 UTC (14 years, 4 months ago) by bates
Moving devLaplace calculations to C code

Revision 773 - Directory Listing
Modified Thu Jun 9 18:30:33 2005 UTC (14 years, 4 months ago) by bates
Adding flag to skip fixed-effects terms (for use with generalized linear or nonlinear models)

Revision 772 - Directory Listing
Modified Thu Jun 9 16:57:55 2005 UTC (14 years, 4 months ago) by bates
Prepare for release 0.96-1

Revision 766 - Directory Listing
Modified Tue Jun 7 23:03:34 2005 UTC (14 years, 4 months ago) by bates
Isolating and cleaning up the mer, lmer, and glmer functions

Revision 765 - Directory Listing
Modified Tue Jun 7 23:03:19 2005 UTC (14 years, 4 months ago) by bates
Keep -Wall quiet

Revision 764 - Directory Listing
Modified Mon Jun 6 16:03:07 2005 UTC (14 years, 4 months ago) by bates
Keep -Wall quiet

Revision 762 - Directory Listing
Modified Mon Jun 6 15:52:23 2005 UTC (14 years, 4 months ago) by bates
Keep -Wall quiet

Revision 761 - Directory Listing
Modified Mon Jun 6 15:51:24 2005 UTC (14 years, 4 months ago) by bates
Use mer objects; Replace REML slot by method slot

Revision 758 - Directory Listing
Modified Mon Jun 6 15:46:28 2005 UTC (14 years, 4 months ago) by bates
Fix matrix multiplication methods

Revision 753 - Directory Listing
Modified Sun May 29 02:15:35 2005 UTC (14 years, 4 months ago) by bates
Release 0.95-11

Revision 749 - Directory Listing
Modified Fri May 20 03:17:14 2005 UTC (14 years, 5 months ago) by bates
Release 0.95-10

Revision 748 - Directory Listing
Modified Thu May 19 21:29:33 2005 UTC (14 years, 5 months ago) by deepayan
fixed typos

Revision 747 - Directory Listing
Modified Thu May 19 17:43:42 2005 UTC (14 years, 5 months ago) by bates
Incorrect version but I want to transfer it

Revision 746 - Directory Listing
Modified Wed May 18 17:03:17 2005 UTC (14 years, 5 months ago) by bates
Corrected determination of slot sizes for multiple non-nested grouping factors

Revision 745 - Directory Listing
Modified Tue May 17 18:34:27 2005 UTC (14 years, 5 months ago) by bates
Fold bCrosstab.[ch] into lmer.[ch]

Revision 743 - Directory Listing
Modified Tue May 17 17:45:52 2005 UTC (14 years, 5 months ago) by bates
Fold bCrosstab.[ch] into lmer.[ch]

Revision 742 - Directory Listing
Modified Tue May 17 17:45:24 2005 UTC (14 years, 5 months ago) by bates
Fold bCrosstab.[ch] into lmer.[ch]

Revision 741 - Directory Listing
Modified Tue May 17 17:44:02 2005 UTC (14 years, 5 months ago) by bates
collapse some constructions in the code

Revision 740 - Directory Listing
Modified Tue May 17 17:42:35 2005 UTC (14 years, 5 months ago) by bates
Last update before removing these files

Revision 739 - Directory Listing
Modified Tue May 17 17:42:04 2005 UTC (14 years, 5 months ago) by bates
Adding logical sparse matrix methods

Revision 738 - Directory Listing
Modified Tue May 17 17:25:31 2005 UTC (14 years, 5 months ago) by bates
Added Matrix_expand_pointers (callable from R) and moved utility for duplicating slots

Revision 737 - Directory Listing
Modified Tue May 17 17:21:38 2005 UTC (14 years, 5 months ago) by bates
Adding logical sparse matrix methods

Revision 736 - Directory Listing
Modified Tue May 17 17:21:04 2005 UTC (14 years, 5 months ago) by bates
Adding logical sparse matrix methods

Revision 733 - Directory Listing
Modified Tue May 17 17:18:30 2005 UTC (14 years, 5 months ago) by bates
Adding logical sparse matrix methods

Revision 732 - Directory Listing
Modified Tue May 17 17:18:14 2005 UTC (14 years, 5 months ago) by bates
Adding logical sparse matrix methods

Revision 728 - Directory Listing
Modified Sat May 14 00:21:17 2005 UTC (14 years, 5 months ago) by bates
Preparing for release 0.95-10

Revision 726 - Directory Listing
Modified Thu May 12 14:59:04 2005 UTC (14 years, 5 months ago) by bates
Release 0.95-9

Revision 725 - Directory Listing
Modified Tue May 10 14:50:39 2005 UTC (14 years, 5 months ago) by bates
Release 0.95-8 with bug fix for sparse symmetric solve

Revision 723 - Directory Listing
Modified Tue May 10 01:42:05 2005 UTC (14 years, 5 months ago) by bates
More logical sparse matrix methods

Revision 718 - Directory Listing
Modified Mon May 9 01:24:35 2005 UTC (14 years, 5 months ago) by bates
Getting ready for a release

Revision 714 - Directory Listing
Modified Fri May 6 23:52:34 2005 UTC (14 years, 5 months ago) by bates
Added colSums and friends for dgeMatrix class

Revision 711 - Directory Listing
Modified Thu May 5 04:12:44 2005 UTC (14 years, 5 months ago) by deepayan
Updates related to Laplace approximation

Revision 709 - Directory Listing
Modified Tue May 3 16:08:26 2005 UTC (14 years, 5 months ago) by deepayan
changes related to Laplace approximation, including new function to compute parts of the deviance in C code, which doesn't currently work

Revision 705 - Directory Listing
Modified Fri Apr 29 14:42:39 2005 UTC (14 years, 5 months ago) by deepayan
additions related to the Laplace approximation in glmm lmer models

Revision 700 - Directory Listing
Modified Mon Apr 18 20:21:04 2005 UTC (14 years, 6 months ago) by maechler
-Wall

Revision 694 - Directory Listing
Modified Mon Apr 18 17:11:32 2005 UTC (14 years, 6 months ago) by bates
Give a warning, not an error, for detection of exact singularity in the LU decomposition

Revision 692 - Directory Listing
Modified Mon Apr 18 14:34:33 2005 UTC (14 years, 6 months ago) by bates
Release 0.95-6

Revision 688 - Directory Listing
Modified Sat Apr 2 13:18:16 2005 UTC (14 years, 6 months ago) by maechler
no need for \ in %*% in error message

Revision 686 - Directory Listing
Modified Thu Mar 31 21:19:35 2005 UTC (14 years, 6 months ago) by bates
Create "fallback" methods for any kind of numeric, dense matrix

Revision 683 - Directory Listing
Modified Thu Mar 31 17:10:16 2005 UTC (14 years, 6 months ago) by bates
Moving methods for operations with numeric to the Matrix class and with integer to the dMatrix class

Revision 681 - Directory Listing
Modified Thu Mar 31 00:14:36 2005 UTC (14 years, 6 months ago) by bates
Repaired a thinko in the lmer_fitted function

Revision 679 - Directory Listing
Modified Wed Mar 30 14:42:36 2005 UTC (14 years, 6 months ago) by bates
Rename expand_column_pointers to expand_cmpPt (expand compressed pointers)

Revision 677 - Directory Listing
Modified Mon Mar 28 14:03:32 2005 UTC (14 years, 6 months ago) by bates
Added dgRMatrix methods and documentation

Revision 675 - Directory Listing
Modified Sat Mar 26 11:16:05 2005 UTC (14 years, 6 months ago) by maechler
export csc_tcrossprod - and add examples & test for tcrossprod()

Revision 655 - Directory Listing
Modified Wed Mar 16 16:37:05 2005 UTC (14 years, 7 months ago) by maechler
eliminate extraneous declaration for "-Wall"

Revision 654 - Directory Listing
Modified Wed Mar 16 16:18:33 2005 UTC (14 years, 7 months ago) by bates
Generalize matrix multiplication and solve methods

Revision 653 - Directory Listing
Modified Wed Mar 16 16:17:43 2005 UTC (14 years, 7 months ago) by bates
include permutation in expand method for LU

Revision 652 - Directory Listing
Modified Wed Mar 16 01:08:36 2005 UTC (14 years, 7 months ago) by bates
Updates to multiplication and other methods

Revision 649 - Directory Listing
Modified Tue Mar 15 00:59:38 2005 UTC (14 years, 7 months ago) by bates
Validate function stubs for pBunchKaufman and pCholesky classes

Revision 648 - Directory Listing
Modified Tue Mar 15 00:58:37 2005 UTC (14 years, 7 months ago) by bates
Zero the unused triangle in the Cholesky decomposition

Revision 643 - Directory Listing
Modified Tue Mar 15 00:50:48 2005 UTC (14 years, 7 months ago) by bates
Adding many methods for the dsyMatrix class

Revision 639 - Directory Listing
Modified Tue Mar 15 00:44:02 2005 UTC (14 years, 7 months ago) by bates
Coercions and methods for dppMatrix and dspMatrix classes

Revision 637 - Directory Listing
Modified Tue Mar 15 00:41:24 2005 UTC (14 years, 7 months ago) by bates
Coercions and methods for dppMatrix and dspMatrix classes

Revision 635 - Directory Listing
Modified Tue Mar 15 00:40:26 2005 UTC (14 years, 7 months ago) by bates
Coercions and methods for dppMatrix and dspMatrix classes

Revision 633 - Directory Listing
Modified Sun Mar 13 21:01:15 2005 UTC (14 years, 7 months ago) by maechler
comments

Revision 631 - Directory Listing
Modified Sun Mar 13 04:34:52 2005 UTC (14 years, 7 months ago) by bates
Add BunchKaufman factorization

Revision 629 - Directory Listing
Modified Thu Mar 10 19:00:57 2005 UTC (14 years, 7 months ago) by bates
Fix dgeMatrix_dtpMatrix_mm and add test

Revision 628 - Directory Listing
Modified Thu Mar 10 17:57:47 2005 UTC (14 years, 7 months ago) by maechler
more  %*% methods; some dimnames in C (untested); checks extended

Revision 622 - Directory Listing
Modified Mon Mar 7 12:45:59 2005 UTC (14 years, 7 months ago) by bates
Wrong number of args in lmer_update_mm

Revision 614 - Directory Listing
Modified Sat Mar 5 21:14:43 2005 UTC (14 years, 7 months ago) by maechler
L <-> U for transpose

Revision 613 - Directory Listing
Modified Sat Mar 5 21:13:40 2005 UTC (14 years, 7 months ago) by maechler
+ Matrix_DimnamesSym

Revision 605 - Directory Listing
Modified Fri Mar 4 17:29:02 2005 UTC (14 years, 7 months ago) by maechler
do not Calloc()/Free() in "good" case of check_scalar_string()

Revision 604 - Directory Listing
Modified Fri Mar 4 17:27:51 2005 UTC (14 years, 7 months ago) by maechler
check for integer 'x'

Revision 603 - Directory Listing
Modified Fri Mar 4 12:53:01 2005 UTC (14 years, 7 months ago) by bates
Define %*% method for dtpMatrix and matrix properly

Revision 599 - Directory Listing
Modified Fri Mar 4 03:49:53 2005 UTC (14 years, 7 months ago) by bates
Added C function lmer_fitted

Revision 597 - Directory Listing
Modified Thu Mar 3 19:58:59 2005 UTC (14 years, 7 months ago) by bates
Methods and coercions for the dtpMatrix class

Revision 592 - Directory Listing
Modified Thu Mar 3 05:16:50 2005 UTC (14 years, 7 months ago) by bates
Clean up *_validate functions

Revision 591 - Directory Listing
Modified Thu Mar 3 05:16:09 2005 UTC (14 years, 7 months ago) by bates
C functions for dtpMatrix class

Revision 589 - Directory Listing
Modified Wed Mar 2 19:53:53 2005 UTC (14 years, 7 months ago) by bates
more coercions

Revision 588 - Directory Listing
Modified Wed Mar 2 18:19:51 2005 UTC (14 years, 7 months ago) by bates
shorten csc_components_transpose to csc_compTr

Revision 587 - Directory Listing
Modified Wed Mar 2 18:19:15 2005 UTC (14 years, 7 months ago) by bates
dsTMatrix_as_dsCMatrix

Revision 586 - Directory Listing
Modified Tue Mar 1 14:55:03 2005 UTC (14 years, 7 months ago) by maechler
more "-Wall" dummy init.s

Revision 585 - Directory Listing
Modified Tue Mar 1 14:54:38 2005 UTC (14 years, 7 months ago) by maechler
typo in SelectQueue[o]neWay; comment

Revision 582 - Directory Listing
Modified Mon Feb 28 18:15:21 2005 UTC (14 years, 7 months ago) by bates
Internationalization and localization

Revision 576 - Directory Listing
Modified Sat Feb 26 18:18:30 2005 UTC (14 years, 7 months ago) by maechler
prevent segfault {but not "nicely"}

Revision 575 - Directory Listing
Modified Sat Feb 26 18:07:35 2005 UTC (14 years, 7 months ago) by maechler
use "(.)" against "-Wall" warning

Revision 572 - Directory Listing
Modified Fri Feb 25 14:11:54 2005 UTC (14 years, 7 months ago) by bates
Inlined function declarations moved within the conditional expression

Revision 565 - Directory Listing
Modified Tue Feb 22 01:15:45 2005 UTC (14 years, 8 months ago) by bates
Clean up documentation errors exposed by doxygen

Revision 564 - Directory Listing
Modified Sat Feb 19 03:25:17 2005 UTC (14 years, 8 months ago) by bates
Fix compiler warnings

Revision 563 - Directory Listing
Modified Sat Feb 19 02:08:36 2005 UTC (14 years, 8 months ago) by bates
Clean up warnings from compiler

Revision 560 - Directory Listing
Modified Fri Feb 18 14:29:53 2005 UTC (14 years, 8 months ago) by bates
Argument list for cscb_trsm

Revision 559 - Directory Listing
Modified Fri Feb 18 14:29:03 2005 UTC (14 years, 8 months ago) by bates
Changes for non-trivial cscb-trsm

Revision 557 - Directory Listing
Modified Thu Feb 17 01:18:02 2005 UTC (14 years, 8 months ago) by bates
Coercions and methods for the dsTMatrix class

Revision 556 - Directory Listing
Modified Wed Feb 16 20:49:44 2005 UTC (14 years, 8 months ago) by bates
Non-trivial cscb_ldl case

Revision 555 - Directory Listing
Modified Wed Feb 16 20:49:16 2005 UTC (14 years, 8 months ago) by bates
cosmetic changes - reformating

Revision 554 - Directory Listing
Modified Wed Feb 16 13:43:45 2005 UTC (14 years, 8 months ago) by bates
clean up logic

Revision 553 - Directory Listing
Modified Wed Feb 16 13:43:17 2005 UTC (14 years, 8 months ago) by bates
clean up long lines

Revision 551 - Directory Listing
Modified Tue Feb 15 22:28:03 2005 UTC (14 years, 8 months ago) by bates
triangular, triplet sparse matrices

Revision 546 - Directory Listing
Modified Tue Feb 15 22:09:12 2005 UTC (14 years, 8 months ago) by bates
Methods and coercions for the dtTMatrix class

Revision 543 - Directory Listing
Modified Sat Feb 12 13:37:46 2005 UTC (14 years, 8 months ago) by bates
Changes for non-nested vector-valued random effects

Revision 536 - Directory Listing
Modified Thu Feb 10 08:15:12 2005 UTC (14 years, 8 months ago) by bates
rearranging utility functions in the C code

Revision 534 - Directory Listing
Modified Tue Feb 8 08:59:31 2005 UTC (14 years, 8 months ago) by maechler
use mkString(); "uplo" and "diag" must be uppercase

Revision 531 - Directory Listing
Modified Mon Feb 7 11:04:53 2005 UTC (14 years, 8 months ago) by bates
Include the $(SUBSTAMP) target

Revision 526 - Directory Listing
Modified Mon Feb 7 10:50:20 2005 UTC (14 years, 8 months ago) by bates
Include a dependence of the LIB target on the OBJS

Revision 525 - Directory Listing
Modified Mon Feb 7 10:49:20 2005 UTC (14 years, 8 months ago) by bates
Force a call to Make lib in the subdirectories whenever the SHLIB
target is built.  Right now this isn't working properly.

Revision 496 - Directory Listing
Modified Fri Feb 4 18:14:08 2005 UTC (14 years, 8 months ago) by maechler
- get rid of two extraneous declarations
- use the SWAP(.) macro {as in other places}

Revision 495 - Directory Listing
Modified Thu Feb 3 18:48:31 2005 UTC (14 years, 8 months ago) by bates
Initial implementation of the Schur generic

Revision 493 - Directory Listing
Modified Thu Feb 3 18:47:20 2005 UTC (14 years, 8 months ago) by bates
Move the make_named function to Mutils as Matrix_make_named

Revision 492 - Directory Listing
Modified Thu Feb 3 14:24:03 2005 UTC (14 years, 8 months ago) by bates
Getting package to pass CMD check

Revision 491 - Directory Listing
Modified Wed Feb 2 19:40:26 2005 UTC (14 years, 8 months ago) by bates
renaming and rearranging classes

Revision 490 - Directory Listing
Modified Wed Feb 2 19:13:42 2005 UTC (14 years, 8 months ago) by bates
renaming and rearranging classes

Revision 488 - Directory Listing
Modified Wed Feb 2 19:11:51 2005 UTC (14 years, 8 months ago) by bates
renaming and rearranging classes

Revision 485 - Directory Listing
Modified Wed Feb 2 17:20:55 2005 UTC (14 years, 8 months ago) by bates
renaming and rearranging classes

Revision 482 - Directory Listing
Modified Wed Feb 2 15:37:31 2005 UTC (14 years, 8 months ago) by bates
renaming and rearranging classes

Revision 479 - Directory Listing
Modified Wed Feb 2 14:52:26 2005 UTC (14 years, 8 months ago) by bates
Renaming and reorganizing classes

Revision 478 - Directory Listing
Modified Wed Feb 2 14:33:51 2005 UTC (14 years, 8 months ago) by bates
Renaming and reorganizing classes

Revision 476 - Directory Listing
Modified Wed Feb 2 11:51:24 2005 UTC (14 years, 8 months ago) by bates
Change name of slot from factorization to factors

Revision 466 - Directory Listing
Modified Sat Jan 29 14:14:31 2005 UTC (14 years, 8 months ago) by bates
Add an externally accessible entry point to lmer_Crosstab

Revision 465 - Directory Listing
Modified Sat Jan 29 14:14:01 2005 UTC (14 years, 8 months ago) by bates
Add an externally accessible entry point to lmer_Crosstab

Revision 464 - Directory Listing
Modified Sat Jan 29 14:12:53 2005 UTC (14 years, 8 months ago) by bates
Clean up Lind calculation

Revision 463 - Directory Listing
Modified Sat Jan 29 14:11:34 2005 UTC (14 years, 8 months ago) by bates
Make make clean cleaner

Revision 461 - Directory Listing
Modified Sat Jan 29 14:09:38 2005 UTC (14 years, 8 months ago) by bates
Add expm function

Revision 451 - Directory Listing
Modified Sun Jan 23 10:05:53 2005 UTC (14 years, 9 months ago) by bates
New coercion method for cscBlocked objects

Revision 448 - Directory Listing
Modified Fri Jan 21 21:59:45 2005 UTC (14 years, 9 months ago) by bates
Release 0.8-23

Revision 447 - Directory Listing
Modified Fri Jan 21 12:17:56 2005 UTC (14 years, 9 months ago) by bates
Change char flags to cblas enum types

Revision 445 - Directory Listing
Modified Wed Jan 19 19:06:24 2005 UTC (14 years, 9 months ago) by bates
Off-diagonals from L, not ZZpO

Revision 444 - Directory Listing
Modified Wed Jan 19 19:05:15 2005 UTC (14 years, 9 months ago) by bates
Off-diagonals from L, not ZZpO

Revision 443 - Directory Listing
Modified Wed Jan 19 11:28:00 2005 UTC (14 years, 9 months ago) by bates
Remove references to the Linv slot.  Change to the extended parent
pairs.  Extensive changes in lmer_invert.  These still probably have
errors but this check in is to provide a checkpoint.

Revision 442 - Directory Listing
Modified Wed Jan 19 11:25:39 2005 UTC (14 years, 9 months ago) by bates
Remove any references to Linv.  Rewrite routines to use a solution
from L rather than multiplication by the inverse.  Change calling
sequences to use the Parent array.  Change the parent arrays to
extended parent pairs.

Revision 441 - Directory Listing
Modified Wed Jan 19 11:22:07 2005 UTC (14 years, 9 months ago) by bates
See if use of cblas would be a good idea

Revision 439 - Directory Listing
Modified Wed Jan 19 11:20:32 2005 UTC (14 years, 9 months ago) by bates
See if use of cblas would be a good idea

Revision 438 - Directory Listing
Modified Mon Jan 17 12:48:32 2005 UTC (14 years, 9 months ago) by bates
Remove mistaken transpose

Revision 437 - Directory Listing
Modified Mon Jan 17 12:47:29 2005 UTC (14 years, 9 months ago) by bates
Remove Linv references

Revision 434 - Directory Listing
Modified Thu Jan 13 19:36:12 2005 UTC (14 years, 9 months ago) by bates
Added and modified many functions to do solutions rather than inversions.

Revision 432 - Directory Listing
Modified Thu Jan 13 19:34:37 2005 UTC (14 years, 9 months ago) by bates
Define the AZERO macro

Revision 431 - Directory Listing
Modified Thu Jan 13 19:34:03 2005 UTC (14 years, 9 months ago) by bates
Use the AZERO macro

Revision 430 - Directory Listing
Modified Thu Jan 13 19:32:26 2005 UTC (14 years, 9 months ago) by bates
Add definitions of cscb_trsm and cscb_trcbsm

Revision 429 - Directory Listing
Modified Thu Jan 13 19:31:10 2005 UTC (14 years, 9 months ago) by bates
Many changes with respect to the representation and calculation steps.

Revision 425 - Directory Listing
Modified Wed Jan 5 15:26:34 2005 UTC (14 years, 9 months ago) by bates
decrement when counting down

Revision 424 - Directory Listing
Modified Wed Jan 5 13:50:30 2005 UTC (14 years, 9 months ago) by bates
Minor typos

Revision 422 - Directory Listing
Modified Tue Jan 4 23:45:15 2005 UTC (14 years, 9 months ago) by bates
Check in prior to leaving for Zuerich

Revision 417 - Directory Listing
Modified Mon Jan 3 19:14:22 2005 UTC (14 years, 9 months ago) by bates
Change to the lmer representation

Revision 415 - Directory Listing
Modified Mon Jan 3 19:05:11 2005 UTC (14 years, 9 months ago) by bates
Change to the lmer representation

Revision 412 - Directory Listing
Modified Tue Dec 28 15:06:55 2004 UTC (14 years, 9 months ago) by bates


Revision 410 - Directory Listing
Modified Tue Dec 28 14:51:42 2004 UTC (14 years, 9 months ago) by bates
Working on the lmer classes

Revision 397 - Directory Listing
Modified Thu Dec 16 19:15:32 2004 UTC (14 years, 10 months ago) by bates
Add arguments to ssclme_to_lme

Revision 390 - Directory Listing
Modified Tue Dec 14 19:58:55 2004 UTC (14 years, 10 months ago) by bates
Add a coercion for tripletMatrix to matrix

Revision 387 - Directory Listing
Modified Mon Dec 13 16:00:04 2004 UTC (14 years, 10 months ago) by bates
Keep -Wall happy

Revision 386 - Directory Listing
Modified Mon Dec 13 15:59:24 2004 UTC (14 years, 10 months ago) by bates
Fix bug in multivariate/multiple groups case

Revision 379 - Directory Listing
Modified Sat Dec 11 13:48:29 2004 UTC (14 years, 10 months ago) by bates
make -Wall happy

Revision 378 - Directory Listing
Modified Sat Dec 11 13:47:45 2004 UTC (14 years, 10 months ago) by bates
make -Wall happy

Revision 377 - Directory Listing
Modified Sat Dec 11 13:46:42 2004 UTC (14 years, 10 months ago) by bates
make -Wall happy

Revision 376 - Directory Listing
Modified Sat Dec 11 13:44:01 2004 UTC (14 years, 10 months ago) by bates
declaration of R_alloc

Revision 373 - Directory Listing
Modified Sun Dec 5 13:54:32 2004 UTC (14 years, 10 months ago) by bates
Fixed nested scalar r.e., multivariate bug still outstanding

Revision 372 - Directory Listing
Modified Sun Dec 5 13:53:29 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 371 - Directory Listing
Modified Sun Dec 5 13:52:25 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 370 - Directory Listing
Modified Sun Dec 5 13:52:06 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 369 - Directory Listing
Modified Sun Dec 5 13:51:27 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 368 - Directory Listing
Modified Sun Dec 5 13:50:54 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 367 - Directory Listing
Modified Sun Dec 5 13:50:43 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 366 - Directory Listing
Modified Sun Dec 5 13:49:51 2004 UTC (14 years, 10 months ago) by bates
R-specific versions of ldl

Revision 359 - Directory Listing
Modified Sat Nov 27 17:58:23 2004 UTC (14 years, 10 months ago) by bates
Add a call to ldl_numeric to obtain row indices of diagonal blocks of L

Revision 358 - Directory Listing
Modified Sat Nov 27 17:57:19 2004 UTC (14 years, 10 months ago) by bates
separate suboperations from Parent_inverse

Revision 357 - Directory Listing
Modified Sat Nov 27 17:56:13 2004 UTC (14 years, 10 months ago) by bates
silly typo

Revision 356 - Directory Listing
Modified Sat Nov 27 01:45:39 2004 UTC (14 years, 10 months ago) by bates
Add block updates in bCrosstab_convert

Revision 355 - Directory Listing
Modified Sat Nov 27 01:45:01 2004 UTC (14 years, 10 months ago) by bates
Make Parent_inverse visible in include file

Revision 354 - Directory Listing
Modified Sat Nov 27 01:44:15 2004 UTC (14 years, 10 months ago) by bates
Extract dependencies to an include file

Revision 351 - Directory Listing
Modified Tue Nov 23 15:40:28 2004 UTC (14 years, 11 months ago) by bates
Move include file to C sources so the .h file can be included without pulling in a bunch of other stuff

Revision 347 - Directory Listing
Modified Tue Nov 23 15:37:58 2004 UTC (14 years, 11 months ago) by bates
add blocked crosstabulations

Revision 345 - Directory Listing
Modified Tue Nov 23 15:35:55 2004 UTC (14 years, 11 months ago) by bates
keep valgrind happy

Revision 343 - Directory Listing
Modified Mon Nov 15 23:29:28 2004 UTC (14 years, 11 months ago) by bates
Fix on uninitialized value

Revision 342 - Directory Listing
Modified Mon Nov 15 13:55:52 2004 UTC (14 years, 11 months ago) by bates
Updates for factorization name and default value

Revision 341 - Directory Listing
Modified Fri Nov 12 21:20:14 2004 UTC (14 years, 11 months ago) by bates
Use Matrix_rcondSym

Revision 340 - Directory Listing
Modified Fri Nov 12 21:19:39 2004 UTC (14 years, 11 months ago) by bates
Add syrk code

Revision 339 - Directory Listing
Modified Fri Nov 12 21:19:19 2004 UTC (14 years, 11 months ago) by bates
Add syrk code

Revision 338 - Directory Listing
Modified Fri Nov 12 21:17:36 2004 UTC (14 years, 11 months ago) by bates
Initialize all slots

Revision 332 - Directory Listing
Modified Fri Nov 12 21:04:36 2004 UTC (14 years, 11 months ago) by bates
initialize all slots in a NEW_OBJECT

Revision 329 - Directory Listing
Modified Fri Nov 12 21:01:19 2004 UTC (14 years, 11 months ago) by bates
Keep symbols and filenames consistent

Revision 328 - Directory Listing
Modified Sat Nov 6 18:05:00 2004 UTC (14 years, 11 months ago) by bates
Keep Makefile.win in sync with Makefile

Revision 311 - Directory Listing
Modified Wed Oct 27 21:41:02 2004 UTC (14 years, 11 months ago) by bates
Keep -Wall happy

Revision 310 - Directory Listing
Modified Wed Oct 27 21:40:08 2004 UTC (14 years, 11 months ago) by bates
add a blas-like routine

Revision 309 - Directory Listing
Modified Wed Oct 27 21:40:02 2004 UTC (14 years, 11 months ago) by bates
add a blas-like routine

Revision 308 - Directory Listing
Modified Wed Oct 27 21:39:44 2004 UTC (14 years, 11 months ago) by bates
cosmetic changes

Revision 307 - Directory Listing
Modified Wed Oct 27 21:38:58 2004 UTC (14 years, 11 months ago) by bates
Changes for check on Debian dgesdd

Revision 306 - Directory Listing
Modified Wed Oct 27 21:38:33 2004 UTC (14 years, 11 months ago) by bates
Changes for check on Debian dgesdd

Revision 305 - Directory Listing
Modified Wed Oct 27 21:36:19 2004 UTC (14 years, 11 months ago) by bates
updates and downdates

Revision 304 - Directory Listing
Modified Wed Oct 27 21:35:13 2004 UTC (14 years, 11 months ago) by bates
lmeRep_invert now applies to multiple, nested grouping factors

Revision 301 - Directory Listing
Modified Sun Oct 17 05:06:04 2004 UTC (15 years ago) by bates
transfer to another computer

Revision 300 - Directory Listing
Modified Tue Oct 12 15:44:15 2004 UTC (15 years ago) by bates
Adding lmeRep_L_sm and support routines

Revision 299 - Directory Listing
Modified Fri Oct 8 14:48:06 2004 UTC (15 years ago) by bates
Only positions, not counts, from crossproduct

Revision 298 - Directory Listing
Modified Fri Oct 8 13:47:20 2004 UTC (15 years ago) by bates
added validate functions

Revision 297 - Directory Listing
Modified Mon Oct 4 17:13:42 2004 UTC (15 years ago) by bates
Add registration of .Call functions

Revision 296 - Directory Listing
Modified Mon Oct 4 17:13:29 2004 UTC (15 years ago) by bates
Add registration of .Call functions

Revision 291 - Directory Listing
Modified Sun Oct 3 21:51:33 2004 UTC (15 years ago) by bates
Release 0.8-15

Revision 282 - Directory Listing
Modified Sat Oct 2 15:03:47 2004 UTC (15 years ago) by bates
Bug fixes in 0.8-14

Revision 280 - Directory Listing
Modified Mon Sep 13 12:32:23 2004 UTC (15 years, 1 month ago) by bates
minor format change

Revision 275 - Directory Listing
Modified Fri Sep 3 18:55:14 2004 UTC (15 years, 1 month ago) by bates
New storage format - currently works for single grouping factor

Revision 274 - Directory Listing
Modified Thu Sep 2 23:14:51 2004 UTC (15 years, 1 month ago) by bates
Interim version of lmeRep - not yet complete

Revision 272 - Directory Listing
Modified Thu Sep 2 23:14:00 2004 UTC (15 years, 1 month ago) by bates
Add cscBlocked, tweak lmeRep

Revision 268 - Directory Listing
Modified Tue Aug 31 19:13:33 2004 UTC (15 years, 1 month ago) by bates
New version

Revision 264 - Directory Listing
Modified Mon Aug 30 13:24:53 2004 UTC (15 years, 1 month ago) by bates
Initial lmeRep_update_mm modifications for multiple grouping factors

Revision 263 - Directory Listing
Modified Thu Aug 26 16:01:35 2004 UTC (15 years, 1 month ago) by bates
extending lmeRep to multiple nested grouping factors

Revision 257 - Directory Listing
Modified Tue Aug 24 02:08:08 2004 UTC (15 years, 2 months ago) by bates
Remove taucs, add lmeRep, new release

Revision 255 - Directory Listing
Modified Fri Aug 20 16:27:15 2004 UTC (15 years, 2 months ago) by bates
Add the lmeRep class

Revision 250 - Directory Listing
Modified Tue Aug 17 16:50:27 2004 UTC (15 years, 2 months ago) by bates
cleanup in EMsteps_verbose_print

Revision 247 - Directory Listing
Modified Mon Jul 12 17:41:57 2004 UTC (15 years, 3 months ago) by bates
Combine ssclme_coef and ssclme_coefUnc, ssclme_coefGets and ssclme_coefGetsUnc.  Reorganize gradient code in preparation for Hessian calculations.

Revision 245 - Directory Listing
Modified Mon Jul 12 12:46:54 2004 UTC (15 years, 3 months ago) by bates
Remove warnings, new release, change gradient calculation method

Revision 241 - Directory Listing
Modified Wed Jul 7 18:23:11 2004 UTC (15 years, 3 months ago) by bates
Remove pdMat classes

Revision 238 - Directory Listing
Modified Fri Jul 2 14:36:08 2004 UTC (15 years, 3 months ago) by bates
Updated Hessian method to symmetrize the result

Revision 237 - Directory Listing
Modified Thu Jul 1 03:20:33 2004 UTC (15 years, 3 months ago) by bates
Added stub of a Hessian generic and methods.

Revision 209 - Directory Listing
Modified Thu Jun 3 18:22:56 2004 UTC (15 years, 4 months ago) by bates
Combine the two ldl_symbolic routines

Revision 184 - Directory Listing
Modified Sun May 30 22:38:37 2004 UTC (15 years, 4 months ago) by bates
Experiments with projecting

Revision 176 - Directory Listing
Modified Fri May 28 13:23:44 2004 UTC (15 years, 4 months ago) by bates
Adding documentation - cleaning up code

Revision 174 - Directory Listing
Modified Wed May 19 16:45:00 2004 UTC (15 years, 5 months ago) by bates
remove unused variable

Revision 168 - Directory Listing
Modified Wed May 19 16:18:48 2004 UTC (15 years, 5 months ago) by bates
Multiple factors with some ni > 1

Revision 166 - Directory Listing
Modified Sat May 15 12:59:43 2004 UTC (15 years, 5 months ago) by bates
Accurate EM iteration count

Revision 164 - Directory Listing
Modified Fri May 14 21:00:04 2004 UTC (15 years, 5 months ago) by bates
Moving utilities to Matrix package

Revision 159 - Directory Listing
Modified Sun May 9 22:06:53 2004 UTC (15 years, 5 months ago) by bates
Remove storage of L-inverse

Revision 158 - Directory Listing
Modified Sun May 9 17:06:12 2004 UTC (15 years, 5 months ago) by bates
maxLI=0 option works

Revision 157 - Directory Listing
Modified Sun May 9 14:26:36 2004 UTC (15 years, 5 months ago) by bates
More attempts at the bVar calculation

Revision 153 - Directory Listing
Modified Fri May 7 19:35:35 2004 UTC (15 years, 5 months ago) by bates
Add routines to project and ldl_symbolic the ctab

Revision 150 - Directory Listing
Modified Tue May 4 22:52:19 2004 UTC (15 years, 5 months ago) by bates
Confused conflicts in checkins

Revision 149 - Directory Listing
Modified Tue May 4 22:30:39 2004 UTC (15 years, 5 months ago) by bates
Previous to changing permutation method

Revision 148 - Directory Listing
Modified Mon May 3 12:49:17 2004 UTC (15 years, 5 months ago) by bates
Rearranging code to isolate Metis includes

Revision 146 - Directory Listing
Modified Sat May 1 20:27:04 2004 UTC (15 years, 5 months ago) by bates
Yet another permutation calculation method

Revision 143 - Directory Listing
Modified Fri Apr 30 20:33:01 2004 UTC (15 years, 5 months ago) by bates
Permutations and update_mm

Revision 127 - Directory Listing
Modified Sun Apr 25 18:06:27 2004 UTC (15 years, 5 months ago) by bates
Remove useLast argument

Revision 125 - Directory Listing
Modified Sun Apr 25 11:59:37 2004 UTC (15 years, 5 months ago) by bates
gradients missing when deviance missing

Revision 122 - Directory Listing
Modified Fri Apr 23 22:06:08 2004 UTC (15 years, 6 months ago) by bates
Change ssclme_variances call

Revision 115 - Directory Listing
Modified Wed Apr 21 22:37:28 2004 UTC (15 years, 6 months ago) by bates
updated ssclme_collapse

Revision 114 - Directory Listing
Modified Wed Apr 21 20:45:22 2004 UTC (15 years, 6 months ago) by bates
Added ssclme_collapse

Revision 113 - Directory Listing
Modified Tue Apr 20 17:34:49 2004 UTC (15 years, 6 months ago) by bates
Correction for gradient and EMsteps

Revision 111 - Directory Listing
Modified Tue Apr 20 15:46:04 2004 UTC (15 years, 6 months ago) by bates
Release 0.8-5

Revision 108 - Directory Listing
Modified Mon Apr 19 17:44:22 2004 UTC (15 years, 6 months ago) by bates
Logic error in ssclme_update_mm

Revision 106 - Directory Listing
Modified Mon Apr 19 00:48:02 2004 UTC (15 years, 6 months ago) by bates
More work on gradient (still not correct)

Revision 105 - Directory Listing
Modified Sun Apr 18 22:12:10 2004 UTC (15 years, 6 months ago) by bates
Added gradient, consistent order of parameters

Revision 104 - Directory Listing
Modified Sun Apr 18 19:21:57 2004 UTC (15 years, 6 months ago) by bates
analytic gradient except for unconstrained, multidimensional case

Revision 101 - Directory Listing
Modified Sun Apr 18 14:59:53 2004 UTC (15 years, 6 months ago) by bates
Add gradient calculation

Revision 100 - Directory Listing
Modified Sat Apr 17 17:03:59 2004 UTC (15 years, 6 months ago) by bates
First cut at gradient

Revision 97 - Directory Listing
Modified Sat Apr 17 16:57:42 2004 UTC (15 years, 6 months ago) by bates
Cleanup of header file

Revision 93 - Directory Listing
Modified Fri Apr 16 21:19:40 2004 UTC (15 years, 6 months ago) by bates
New method of choosing between ties

Revision 86 - Directory Listing
Modified Thu Apr 15 21:40:17 2004 UTC (15 years, 6 months ago) by bates
Allow useLast option in sscCrosstab_groupedPerm

Revision 85 - Directory Listing
Modified Thu Apr 15 20:50:57 2004 UTC (15 years, 6 months ago) by bates
Working version of sscCrosstab_groupedPerm but about to do surgery on it

Revision 83 - Directory Listing
Modified Thu Apr 15 02:51:07 2004 UTC (15 years, 6 months ago) by bates
Working version of sscCrosstab_groupedPerm - still needs work

Revision 82 - Directory Listing
Modified Wed Apr 14 23:20:06 2004 UTC (15 years, 6 months ago) by bates
Updates to sscCrosstab_groupedPerm

Revision 77 - Directory Listing
Modified Wed Apr 14 20:44:19 2004 UTC (15 years, 6 months ago) by bates
New (experimental) groupedPerm

Revision 76 - Directory Listing
Modified Wed Apr 14 20:43:40 2004 UTC (15 years, 6 months ago) by bates
ssclme_EMsteps miscalculation

Revision 75 - Directory Listing
Modified Wed Apr 14 20:43:06 2004 UTC (15 years, 6 months ago) by bates
Fix Makefile.win

Revision 74 - Directory Listing
Modified Wed Apr 14 16:37:24 2004 UTC (15 years, 6 months ago) by bates
Original version of sscCrosstab_groupedPerm is about to be dismembered

Revision 73 - Directory Listing
Modified Tue Apr 13 15:53:38 2004 UTC (15 years, 6 months ago) by bates
R version of fill-reducing permutation

Revision 71 - Directory Listing
Modified Mon Apr 12 22:08:52 2004 UTC (15 years, 6 months ago) by bates
Release 0.8-3 to fix Makefile.win

Revision 70 - Directory Listing
Modified Mon Apr 12 12:10:01 2004 UTC (15 years, 6 months ago) by bates
Adding coercions - fixing bugs

Revision 57 - Directory Listing
Modified Tue Apr 6 22:09:52 2004 UTC (15 years, 6 months ago) by bates
Minor change for VarCorr

Revision 52 - Directory Listing
Modified Tue Apr 6 02:54:14 2004 UTC (15 years, 6 months ago) by bates
Lack of inclusion picked up by -Wall

Revision 50 - Directory Listing
Modified Tue Apr 6 02:27:37 2004 UTC (15 years, 6 months ago) by bates
Removing explicit umfpack code

Revision 47 - Directory Listing
Modified Tue Apr 6 02:25:00 2004 UTC (15 years, 6 months ago) by bates
Move triplet_to_col from umfpack

Revision 45 - Directory Listing
Modified Mon Apr 5 01:06:55 2004 UTC (15 years, 6 months ago) by bates
Added ssclme_variances

Revision 43 - Directory Listing
Modified Tue Mar 30 23:26:33 2004 UTC (15 years, 6 months ago) by bates
remove unnecessarily complicated C code for coercion (better done in R code)

Revision 34 - Directory Listing
Modified Mon Mar 29 01:49:38 2004 UTC (15 years, 6 months ago) by bates
Correct column of b[[i]] in _fitted

Revision 28 - Directory Listing
Modified Sun Mar 28 17:06:05 2004 UTC (15 years, 6 months ago) by bates
Added ssclme_fitted function

Revision 22 - Directory Listing
Modified Sat Mar 27 18:17:00 2004 UTC (15 years, 6 months ago) by bates
Dimensions of b-related values, dimnames

Revision 21 - Directory Listing
Modified Sat Mar 27 00:06:02 2004 UTC (15 years, 6 months ago) by bates
Changing dimensions in bVar and returned value from _ranef

Revision 19 - Directory Listing
Modified Tue Mar 23 23:29:55 2004 UTC (15 years, 7 months ago) by bates
Allow unconstrained coefficients

Revision 11 - Directory Listing
Modified Tue Mar 23 13:15:04 2004 UTC (15 years, 7 months ago) by bates
Change name of C function ssclme_EMsteps

Revision 10 - Directory Listing
Added Mon Mar 22 20:20:05 2004 UTC (15 years, 7 months ago) by bates
Initial import

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