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Revision 1865 - Directory Listing
Modified Mon Jun 4 13:37:53 2007 UTC (12 years, 1 month ago) by bates


Revision 1864 - Directory Listing
Modified Sun Jun 3 19:16:42 2007 UTC (12 years, 1 month ago) by bates
More modifications to nlmer

Revision 1861 - Directory Listing
Modified Sat Jun 2 20:30:05 2007 UTC (12 years, 1 month ago) by bates
More description of nlmer theory

Revision 1860 - Directory Listing
Modified Sat Jun 2 16:15:35 2007 UTC (12 years, 1 month ago) by bates
more work on nlmer

Revision 1859 - Directory Listing
Modified Sat Jun 2 14:26:38 2007 UTC (12 years, 1 month ago) by bates
More explanation

Revision 1858 - Directory Listing
Modified Wed May 30 15:30:34 2007 UTC (12 years, 1 month ago) by bates
Corrected syntax errors caught by R CMD build

Revision 1857 - Directory Listing
Modified Tue May 29 20:08:00 2007 UTC (12 years, 1 month ago) by bates
Initial version of the theory vignette.

Revision 1856 - Directory Listing
Modified Fri May 25 18:17:40 2007 UTC (12 years, 2 months ago) by bates
Adding more nlmer capabilities

Revision 1843 - Directory Listing
Modified Tue May 15 13:47:53 2007 UTC (12 years, 2 months ago) by bates
Beginning an nlmer class and constructor

Revision 1842 - Directory Listing
Modified Tue May 15 13:47:30 2007 UTC (12 years, 2 months ago) by bates
Beginning an nlmer class and constructor

Revision 1841 - Directory Listing
Modified Tue May 15 13:46:58 2007 UTC (12 years, 2 months ago) by bates
New release to coordinate with Matrix release

Revision 1840 - Directory Listing
Modified Tue May 15 13:46:34 2007 UTC (12 years, 2 months ago) by bates
Yet another attempt to explain the theory - to be changed

Revision 1839 - Directory Listing
Modified Tue May 15 13:25:58 2007 UTC (12 years, 2 months ago) by maechler
update Date (to last svn change date), ready for release

Revision 1831 - Directory Listing
Modified Fri Apr 27 13:38:19 2007 UTC (12 years, 2 months ago) by bates
name of included file changed for R-2.5.0

Revision 1823 - Directory Listing
Modified Tue Apr 10 23:12:04 2007 UTC (12 years, 3 months ago) by bates
Add more material to the Implementation vignette, more work on lmer2

Revision 1815 - Directory Listing
Modified Mon Apr 2 21:30:16 2007 UTC (12 years, 3 months ago) by bates
More on lmer2 version of glmm models

Revision 1814 - Directory Listing
Modified Mon Apr 2 14:38:36 2007 UTC (12 years, 3 months ago) by bates
glmm under lmer2 improvements

Revision 1813 - Directory Listing
Modified Fri Mar 30 23:09:39 2007 UTC (12 years, 3 months ago) by bates
More work on glmer2 representation

Revision 1812 - Directory Listing
Modified Fri Mar 30 12:49:30 2007 UTC (12 years, 3 months ago) by bates
Update man pages for mer2 -> lmer2 switch

Revision 1811 - Directory Listing
Modified Fri Mar 30 12:48:32 2007 UTC (12 years, 3 months ago) by bates
replace rbind by rBind; change version of Matrix in dependencies

Revision 1810 - Directory Listing
Modified Thu Mar 29 23:07:20 2007 UTC (12 years, 3 months ago) by bates
Extend the Implementation vignette

Revision 1809 - Directory Listing
Modified Thu Mar 29 23:04:49 2007 UTC (12 years, 3 months ago) by bates
Add simulate method for lmer2 objects

Revision 1807 - Directory Listing
Modified Thu Mar 29 00:10:43 2007 UTC (12 years, 3 months ago) by bates
Add lmer2_update_y

Revision 1802 - Directory Listing
Modified Tue Mar 27 16:28:44 2007 UTC (12 years, 3 months ago) by bates
Use of offset, allow glmer_linkinv

Revision 1801 - Directory Listing
Modified Mon Mar 26 13:31:40 2007 UTC (12 years, 4 months ago) by bates
Add ChangeLog entry - small update

Revision 1800 - Directory Listing
Modified Sun Mar 25 19:35:56 2007 UTC (12 years, 4 months ago) by bates
Modified and simplified lmer2

Revision 1797 - Directory Listing
Modified Wed Mar 21 22:04:27 2007 UTC (12 years, 4 months ago) by bates
More development on glmer in the mer2 formulation

Revision 1796 - Directory Listing
Modified Tue Mar 20 22:45:52 2007 UTC (12 years, 4 months ago) by bates
Begin moving glmm fitting to mer2 representation

Revision 1795 - Directory Listing
Modified Mon Mar 19 13:11:56 2007 UTC (12 years, 4 months ago) by bates
Clean up lmer2 by moving checks to auxillary functions

Revision 1794 - Directory Listing
Modified Fri Mar 16 22:16:41 2007 UTC (12 years, 4 months ago) by bates
Use renamed header and stubs files; Use lmer2_create

Revision 1793 - Directory Listing
Modified Tue Mar 13 17:00:22 2007 UTC (12 years, 4 months ago) by bates
by-pass storing weights and offset in lmer2 if not used

Revision 1792 - Directory Listing
Modified Mon Mar 12 13:29:16 2007 UTC (12 years, 4 months ago) by bates
Call port optimization code from with the C code.

Revision 1790 - Directory Listing
Modified Sat Feb 17 15:59:50 2007 UTC (12 years, 5 months ago) by bates
More changes in ST_update and reformating

Revision 1789 - Directory Listing
Modified Fri Feb 16 22:37:09 2007 UTC (12 years, 5 months ago) by bates
Split lmer.c into lmer.c and lmer2.c

Revision 1788 - Directory Listing
Modified Fri Feb 16 22:36:41 2007 UTC (12 years, 5 months ago) by bates
Split lmer.c into lmer.c and lmer2.c

Revision 1785 - Directory Listing
Modified Fri Feb 16 17:26:40 2007 UTC (12 years, 5 months ago) by bates
Allow lower triangular Wishart factor, fast ST update

Revision 1784 - Directory Listing
Modified Tue Feb 13 00:37:23 2007 UTC (12 years, 5 months ago) by bates
First complete cut at mcmcsamp for mer2 objects

Revision 1783 - Directory Listing
Modified Mon Feb 12 23:59:58 2007 UTC (12 years, 5 months ago) by bates
More work on mcmcsamp for mer2

Revision 1782 - Directory Listing
Modified Mon Feb 12 23:58:47 2007 UTC (12 years, 5 months ago) by bates
Remove nc slot from mer2

Revision 1781 - Directory Listing
Modified Mon Feb 12 15:14:39 2007 UTC (12 years, 5 months ago) by bates
Prepare for new release

Revision 1780 - Directory Listing
Modified Mon Feb 12 15:03:15 2007 UTC (12 years, 5 months ago) by bates
More checks in mer2_validate

Revision 1779 - Directory Listing
Modified Mon Feb 12 15:02:52 2007 UTC (12 years, 5 months ago) by bates
Enhancements from Andrew Robinson

Revision 1778 - Directory Listing
Modified Mon Feb 12 01:38:05 2007 UTC (12 years, 5 months ago) by bates
Clean up representation, add internal_update_A, add validity check

Revision 1777 - Directory Listing
Modified Sun Feb 11 00:41:18 2007 UTC (12 years, 5 months ago) by bates
Change to enum from defines - fix some -Wall warnings

Revision 1775 - Directory Listing
Modified Sat Feb 10 00:38:02 2007 UTC (12 years, 5 months ago) by bates
more development on mer2_MCMCsamp

Revision 1774 - Directory Listing
Modified Sat Feb 10 00:37:11 2007 UTC (12 years, 5 months ago) by bates
Add doc for method

Revision 1773 - Directory Listing
Modified Fri Feb 9 16:10:33 2007 UTC (12 years, 5 months ago) by bates
More modifications for mer2_MCMCsamp

Revision 1772 - Directory Listing
Modified Thu Feb 8 23:46:07 2007 UTC (12 years, 5 months ago) by bates
Preparing for mer2_MCMCsamp

Revision 1770 - Directory Listing
Modified Mon Feb 5 20:36:16 2007 UTC (12 years, 5 months ago) by bates
Add cake manual page

Revision 1769 - Directory Listing
Modified Mon Feb 5 20:27:54 2007 UTC (12 years, 5 months ago) by bates
Add cake data

Revision 1762 - Directory Listing
Modified Sun Feb 4 19:40:11 2007 UTC (12 years, 5 months ago) by bates
Added ranef for mer2 representation (including posterior variances)

Revision 1757 - Directory Listing
Modified Sat Feb 3 00:21:11 2007 UTC (12 years, 5 months ago) by bates
C code for ranef method on mer2 objects

Revision 1756 - Directory Listing
Modified Wed Jan 31 00:33:28 2007 UTC (12 years, 5 months ago) by bates
Cleaning up

Revision 1755 - Directory Listing
Modified Tue Jan 30 22:54:44 2007 UTC (12 years, 5 months ago) by bates
Remove unused references

Revision 1754 - Directory Listing
Modified Tue Jan 30 22:51:00 2007 UTC (12 years, 5 months ago) by bates
Not used

Revision 1753 - Directory Listing
Modified Tue Jan 30 22:40:19 2007 UTC (12 years, 5 months ago) by bates
Directory not used

Revision 1752 - Directory Listing
Modified Tue Jan 30 21:38:45 2007 UTC (12 years, 5 months ago) by bates
Bug fix in mer2_getPars and documentation fixes, new release

Revision 1745 - Directory Listing
Modified Mon Jan 29 14:05:29 2007 UTC (12 years, 5 months ago) by bates
allow for specification of a start argument and go with the default rel.tol

Revision 1744 - Directory Listing
Modified Thu Jan 25 20:22:51 2007 UTC (12 years, 5 months ago) by bates
Release 0.9975-11

Revision 1743 - Directory Listing
Modified Thu Jan 25 20:19:13 2007 UTC (12 years, 5 months ago) by bates
Incorporate "deviance" argument in mcmcsamp method for glmer objects

Revision 1742 - Directory Listing
Modified Thu Jan 25 20:17:49 2007 UTC (12 years, 5 months ago) by bates
Incorporate mer2 and lmer2 descriptions

Revision 1741 - Directory Listing
Modified Thu Jan 25 00:14:59 2007 UTC (12 years, 6 months ago) by bates


Revision 1740 - Directory Listing
Modified Wed Jan 24 23:59:11 2007 UTC (12 years, 6 months ago) by bates
cleanup

Revision 1739 - Directory Listing
Modified Wed Jan 24 23:58:35 2007 UTC (12 years, 6 months ago) by bates
reweight before calculating random effects in internal_bhat

Revision 1733 - Directory Listing
Modified Sat Jan 20 15:24:54 2007 UTC (12 years, 6 months ago) by bates
more on the simple example

Revision 1732 - Directory Listing
Modified Sat Jan 20 15:24:28 2007 UTC (12 years, 6 months ago) by bates
Remove bstar element of dims slot in mer2

Revision 1730 - Directory Listing
Modified Thu Jan 18 09:32:34 2007 UTC (12 years, 6 months ago) by maechler
first part to fix use of new 'deviance' argument..

Revision 1729 - Directory Listing
Modified Thu Jan 18 08:20:03 2007 UTC (12 years, 6 months ago) by maechler
use new 'deviance' argument where needed

Revision 1728 - Directory Listing
Modified Thu Jan 18 08:19:34 2007 UTC (12 years, 6 months ago) by maechler
+ 2 words for readability (of *produced* text)

Revision 1727 - Directory Listing
Modified Wed Jan 17 13:49:23 2007 UTC (12 years, 6 months ago) by bates
More detail on Rail example

Revision 1726 - Directory Listing
Modified Wed Jan 17 13:48:56 2007 UTC (12 years, 6 months ago) by bates
Added ST2Omega

Revision 1723 - Directory Listing
Modified Sat Jan 13 16:29:29 2007 UTC (12 years, 6 months ago) by bates
Modify anova method for mer2 objects

Revision 1722 - Directory Listing
Modified Sat Jan 13 16:00:29 2007 UTC (12 years, 6 months ago) by bates
Add an anova method for mer2 objects

Revision 1721 - Directory Listing
Modified Fri Jan 12 08:52:45 2007 UTC (12 years, 6 months ago) by bates
Introduce example

Revision 1720 - Directory Listing
Modified Wed Jan 10 13:10:45 2007 UTC (12 years, 6 months ago) by bates
Add deviance argument to mcmcsamp method for lmer models

Revision 1719 - Directory Listing
Modified Mon Jan 8 08:35:54 2007 UTC (12 years, 6 months ago) by bates
Back to LDL representation for \tilde{\bm{\Sigma}}

Revision 1717 - Directory Listing
Modified Sat Jan 6 03:09:58 2007 UTC (12 years, 6 months ago) by bates
Renaming and reformulating mer2 slots and methods

Revision 1715 - Directory Listing
Modified Fri Jan 5 21:16:50 2007 UTC (12 years, 6 months ago) by bates
Rename slots in mer2 objects; add to vignette

Revision 1709 - Directory Listing
Modified Sat Dec 23 06:22:50 2006 UTC (12 years, 7 months ago) by bates
Changed representation of \bm{\Sigma} to outer diag and standard deviation

Revision 1704 - Directory Listing
Modified Fri Dec 15 23:19:41 2006 UTC (12 years, 7 months ago) by bates
print, show and other methods for mer2 objects

Revision 1702 - Directory Listing
Modified Thu Dec 14 15:45:26 2006 UTC (12 years, 7 months ago) by bates
correct determinant calculation for supernodal decomposition

Revision 1701 - Directory Listing
Modified Thu Dec 14 15:44:30 2006 UTC (12 years, 7 months ago) by bates
reverse sense of convergence indicator; back out rel.tol change while doing comparisons against existing code

Revision 1700 - Directory Listing
Modified Thu Dec 14 15:42:35 2006 UTC (12 years, 7 months ago) by bates
Catch up on change in lmerFactorList

Revision 1699 - Directory Listing
Modified Thu Dec 14 15:39:30 2006 UTC (12 years, 7 months ago) by bates
Change dependence on Matrix to newer version

Revision 1698 - Directory Listing
Modified Wed Dec 13 23:47:12 2006 UTC (12 years, 7 months ago) by bates
Optimization for mer2 objects

Revision 1697 - Directory Listing
Modified Wed Dec 13 19:45:23 2006 UTC (12 years, 7 months ago) by bates
Added mer2 extractor functions

Revision 1695 - Directory Listing
Modified Mon Dec 11 14:52:57 2006 UTC (12 years, 7 months ago) by bates
Force user-specified ordering in analysis to produce K

Revision 1694 - Directory Listing
Modified Mon Dec 11 04:03:58 2006 UTC (12 years, 7 months ago) by bates
Correct the symmetrization

Revision 1693 - Directory Listing
Modified Mon Dec 11 00:18:04 2006 UTC (12 years, 7 months ago) by bates
Force LDL simplicial factorization

Revision 1692 - Directory Listing
Modified Sun Dec 10 13:57:19 2006 UTC (12 years, 7 months ago) by bates
Allow simplicial LDL factorization for K; Fix calculation of effects for LDL - turns out it is trivial

Revision 1690 - Directory Listing
Modified Sun Dec 10 03:21:05 2006 UTC (12 years, 7 months ago) by bates
Revisions and extensions of mer2 methods

Revision 1689 - Directory Listing
Modified Sat Dec 9 00:31:04 2006 UTC (12 years, 7 months ago) by bates
Switching internal representations - for the last time!

Revision 1685 - Directory Listing
Modified Sat Dec 2 19:14:17 2006 UTC (12 years, 7 months ago) by bates
Beginning new formulation

Revision 1684 - Directory Listing
Modified Sat Dec 2 15:59:45 2006 UTC (12 years, 7 months ago) by maechler
add print() example

Revision 1683 - Directory Listing
Modified Fri Dec 1 19:40:46 2006 UTC (12 years, 7 months ago) by bates
Release 0.9975-10

Revision 1680 - Directory Listing
Modified Tue Nov 14 20:31:54 2006 UTC (12 years, 8 months ago) by bates
Reformatting

Revision 1679 - Directory Listing
Modified Tue Nov 14 20:31:08 2006 UTC (12 years, 8 months ago) by bates
New version

Revision 1678 - Directory Listing
Modified Tue Nov 14 20:30:35 2006 UTC (12 years, 8 months ago) by bates
Allow factor on LHS of carry

Revision 1677 - Directory Listing
Modified Mon Nov 13 16:34:59 2006 UTC (12 years, 8 months ago) by maechler
simulate() fix

Revision 1676 - Directory Listing
Modified Mon Nov 13 15:42:37 2006 UTC (12 years, 8 months ago) by maechler
cosmetic

Revision 1672 - Directory Listing
Modified Mon Nov 6 20:25:10 2006 UTC (12 years, 8 months ago) by bates
fix (again) multiple definitions of lme4_iSym, etc.

Revision 1671 - Directory Listing
Modified Mon Nov 6 19:30:49 2006 UTC (12 years, 8 months ago) by bates
extern the symbols

Revision 1670 - Directory Listing
Modified Mon Nov 6 16:27:02 2006 UTC (12 years, 8 months ago) by bates
use extern before Syms.h except where they are defined

Revision 1669 - Directory Listing
Modified Mon Nov 6 16:17:57 2006 UTC (12 years, 8 months ago) by bates
Preparing for release 0.9975-9

Revision 1668 - Directory Listing
Modified Mon Nov 6 16:16:38 2006 UTC (12 years, 8 months ago) by bates
move mlirt to mlirt.R, set relative tolerance

Revision 1667 - Directory Listing
Modified Mon Nov 6 16:13:53 2006 UTC (12 years, 8 months ago) by bates
Added (hidden) mlirt function - but probably will remove it later

Revision 1653 - Directory Listing
Modified Tue Oct 24 21:45:22 2006 UTC (12 years, 9 months ago) by bates
New release

Revision 1652 - Directory Listing
Modified Tue Oct 24 21:44:38 2006 UTC (12 years, 9 months ago) by bates
Modifications to the carryOver model

Revision 1651 - Directory Listing
Modified Mon Oct 23 23:02:07 2006 UTC (12 years, 9 months ago) by bates
Discounting in carryOver

Revision 1650 - Directory Listing
Modified Mon Oct 23 23:01:21 2006 UTC (12 years, 9 months ago) by bates
Remove redundant calls to REAL

Revision 1649 - Directory Listing
Modified Mon Oct 23 14:02:47 2006 UTC (12 years, 9 months ago) by maechler
OOps! (sorry, Doug!) :  + 2 x ")" in example

Revision 1648 - Directory Listing
Modified Mon Oct 23 13:59:14 2006 UTC (12 years, 9 months ago) by maechler
a few left over  s/nc/nci/

Revision 1645 - Directory Listing
Modified Fri Oct 20 23:22:49 2006 UTC (12 years, 9 months ago) by bates
Less space use in bVar calculation

Revision 1644 - Directory Listing
Modified Fri Oct 20 23:20:59 2006 UTC (12 years, 9 months ago) by bates
Hide the symbols

Revision 1643 - Directory Listing
Modified Fri Oct 20 23:20:01 2006 UTC (12 years, 9 months ago) by bates
Remove redundant binomial examples.  Use cbpp examples instead

Revision 1640 - Directory Listing
Modified Fri Oct 20 07:37:22 2006 UTC (12 years, 9 months ago) by maechler
fix example; add equality check

Revision 1639 - Directory Listing
Modified Thu Oct 19 13:12:00 2006 UTC (12 years, 9 months ago) by maechler
new CBPP data from Renaut Lancelot - example still fails

Revision 1638 - Directory Listing
Modified Thu Oct 19 13:03:02 2006 UTC (12 years, 9 months ago) by maechler
revert "for (int i=.....)" to C90: declare first; then use in for()

Revision 1637 - Directory Listing
Modified Wed Oct 18 19:40:28 2006 UTC (12 years, 9 months ago) by bates
Fix weights problem reported by Renaud Lancelot

Revision 1636 - Directory Listing
Modified Tue Oct 17 22:02:19 2006 UTC (12 years, 9 months ago) by bates
install special methods for common family/link combinations; update weighting

Revision 1633 - Directory Listing
Modified Mon Oct 16 13:28:09 2006 UTC (12 years, 9 months ago) by bates


Revision 1632 - Directory Listing
Modified Mon Oct 16 12:49:57 2006 UTC (12 years, 9 months ago) by bates
New version

Revision 1631 - Directory Listing
Modified Mon Oct 16 00:17:24 2006 UTC (12 years, 9 months ago) by bates
Fix sorting problem in ZtZ; cleanup

Revision 1630 - Directory Listing
Modified Fri Oct 13 13:36:05 2006 UTC (12 years, 9 months ago) by bates
Internal code for predefined family types

Revision 1628 - Directory Listing
Modified Thu Oct 12 22:39:56 2006 UTC (12 years, 9 months ago) by bates
Internal evaluation of family functions

Revision 1627 - Directory Listing
Modified Thu Oct 12 22:39:25 2006 UTC (12 years, 9 months ago) by bates
Internal evaluation of family functions

Revision 1626 - Directory Listing
Modified Thu Oct 12 19:21:50 2006 UTC (12 years, 9 months ago) by bates
Divide source code to make navigation easier - new version number

Revision 1623 - Directory Listing
Modified Tue Oct 10 18:29:20 2006 UTC (12 years, 9 months ago) by bates
Release 0.9975-3

Revision 1622 - Directory Listing
Modified Tue Oct 10 18:26:57 2006 UTC (12 years, 9 months ago) by bates
Move to a safe name

Revision 1621 - Directory Listing
Modified Tue Oct 10 17:15:09 2006 UTC (12 years, 9 months ago) by bates
Calculate nnz correctly in Zt_carryOver

Revision 1614 - Directory Listing
Modified Wed Oct 4 22:43:11 2006 UTC (12 years, 9 months ago) by bates
New release with extensions carryOver and mlirt to lmer

Revision 1610 - Directory Listing
Modified Mon Oct 2 13:51:42 2006 UTC (12 years, 9 months ago) by bates
patch up carryOver function

Revision 1609 - Directory Listing
Modified Mon Oct 2 13:47:34 2006 UTC (12 years, 9 months ago) by bates
More on mlirt

Revision 1608 - Directory Listing
Modified Sun Oct 1 22:49:31 2006 UTC (12 years, 9 months ago) by bates
Initial version of a carryOver function

Revision 1607 - Directory Listing
Modified Sun Oct 1 22:44:02 2006 UTC (12 years, 9 months ago) by bates
Added initial (Rasch) version of mlirt

Revision 1606 - Directory Listing
Modified Fri Sep 29 22:52:49 2006 UTC (12 years, 9 months ago) by bates
Allow creation of a list of sparse model matrices corresponding to the grouping factors in lmer

Revision 1605 - Directory Listing
Modified Fri Sep 29 21:19:54 2006 UTC (12 years, 9 months ago) by bates
Simplify lmer, fix checks

Revision 1603 - Directory Listing
Modified Fri Sep 29 13:42:54 2006 UTC (12 years, 9 months ago) by bates
Create a valid cholmod_sparse object

Revision 1602 - Directory Listing
Modified Fri Sep 29 13:39:20 2006 UTC (12 years, 9 months ago) by maechler
one more item moved from "Matrix"

Revision 1597 - Directory Listing
Modified Thu Sep 28 23:24:28 2006 UTC (12 years, 9 months ago) by bates
Add functions for the carry-over model.  Not yet correct

Revision 1590 - Directory Listing
Modified Wed Sep 27 18:30:43 2006 UTC (12 years, 9 months ago) by bates
Move lmer argument checking and construction of model matrices to auxillary functions.  Change default method for GLMMs

Revision 1588 - Directory Listing
Modified Fri Sep 22 23:24:18 2006 UTC (12 years, 10 months ago) by bates
Change nature of status vector, eliminate method slot

Revision 1587 - Directory Listing
Modified Fri Sep 22 17:04:19 2006 UTC (12 years, 10 months ago) by bates
Remove useScale slot from mer objects keeping the scale in the devComp slot.  Negative values are fixed scales

Revision 1586 - Directory Listing
Modified Thu Sep 21 22:42:58 2006 UTC (12 years, 10 months ago) by bates
Move family slot to glmer class; create a summary.glmer

Revision 1585 - Directory Listing
Modified Wed Sep 20 22:17:55 2006 UTC (12 years, 10 months ago) by bates
Move unused functions to backup file - trying to straighten out MCMC for glmms

Revision 1581 - Directory Listing
Modified Tue Sep 19 07:53:50 2006 UTC (12 years, 10 months ago) by maechler
Martin's 

Revision 1580 - Directory Listing
Modified Mon Sep 18 21:16:47 2006 UTC (12 years, 10 months ago) by bates
Move TODOs related to lmer from Matrix

Revision 1579 - Directory Listing
Modified Mon Sep 18 21:15:20 2006 UTC (12 years, 10 months ago) by bates
Remove no-longer-needed calls to data(sleepstudy); modify mcmcsamp example

Revision 1561 - Directory Listing
Modified Thu Sep 14 12:11:49 2006 UTC (12 years, 10 months ago) by bates
Fix expansion of formula when no fixed effects terms are specified

Revision 1547 - Directory Listing
Modified Mon Sep 11 14:49:39 2006 UTC (12 years, 10 months ago) by bates
Move the alloc_d**Matrix utility functions from the Matrix package to the lme4 package

Revision 1539 - Directory Listing
Modified Fri Sep 8 14:32:49 2006 UTC (12 years, 10 months ago) by bates
Update description and add an alias for the print method

Revision 1530 - Directory Listing
Modified Thu Sep 7 09:11:57 2006 UTC (12 years, 10 months ago) by maechler
S4 print() method for "mer"

Revision 1529 - Directory Listing
Modified Thu Sep 7 09:11:19 2006 UTC (12 years, 10 months ago) by maechler
Imports latticeExtra (detected by new QA checks)

Revision 1527 - Directory Listing
Modified Wed Sep 6 22:38:12 2006 UTC (12 years, 10 months ago) by bates
Use LinkingTo in DESCRIPTION and headers and stubs from the Matrix package

Revision 1526 - Directory Listing
Modified Wed Sep 6 22:37:00 2006 UTC (12 years, 10 months ago) by bates
Remove import of functions already in Matrix

Revision 1522 - Directory Listing
Modified Wed Sep 6 15:44:06 2006 UTC (12 years, 10 months ago) by bates
Add the local_stubs.c file that simply includes Matrix_stubs.c

Revision 1521 - Directory Listing
Modified Wed Sep 6 15:41:43 2006 UTC (12 years, 10 months ago) by bates
Move the calls to R_GetCCallable to Matrix/inst/include/Matrix_stubs.c

Revision 1520 - Directory Listing
Modified Wed Sep 6 15:38:38 2006 UTC (12 years, 10 months ago) by bates
Use LinkingTo in DESCRIPTION so headers go back to the Matrix package

Revision 1519 - Directory Listing
Modified Wed Sep 6 15:37:50 2006 UTC (12 years, 10 months ago) by bates
Use LinkingTo in DESCRIPTION so headers go back to the Matrix package

Revision 1516 - Directory Listing
Modified Wed Sep 6 11:54:38 2006 UTC (12 years, 10 months ago) by bates
Updates for CHOLMOD version 1.2

Revision 1506 - Directory Listing
Modified Mon Sep 4 16:40:57 2006 UTC (12 years, 10 months ago) by bates
Merge changes from lme4-lmer branch

Revision 1221 - Directory Listing
Modified Sat Mar 4 00:03:56 2006 UTC (13 years, 4 months ago) by bates
More grist

Revision 1212 - Directory Listing
Modified Tue Jan 31 23:55:32 2006 UTC (13 years, 5 months ago) by bates
More on the implementation

Revision 1211 - Directory Listing
Modified Tue Jan 31 00:25:18 2006 UTC (13 years, 5 months ago) by bates
More on implementation

Revision 1203 - Directory Listing
Modified Mon Jan 23 23:16:48 2006 UTC (13 years, 6 months ago) by bates


Revision 1184 - Directory Listing
Modified Thu Jan 19 15:08:31 2006 UTC (13 years, 6 months ago) by bates
Remove import of plot function

Revision 1179 - Directory Listing
Modified Thu Jan 19 00:43:10 2006 UTC (13 years, 6 months ago) by bates
Release 0.995-2

Revision 1172 - Directory Listing
Modified Mon Jan 16 17:49:19 2006 UTC (13 years, 6 months ago) by bates
Release 0.995-1

Revision 821 - Directory Listing
Modified Wed Jul 27 23:07:15 2005 UTC (13 years, 11 months ago) by bates
Version 0.98-1

Revision 819 - Directory Listing
Modified Tue Jul 26 22:46:58 2005 UTC (14 years ago) by bates
Removed formula manipulation functions

Revision 817 - Directory Listing
Modified Tue Jul 26 12:39:34 2005 UTC (14 years ago) by bates
Evaluate model frame for lmList to get options

Revision 771 - Directory Listing
Modified Thu Jun 9 16:56:33 2005 UTC (14 years, 1 month ago) by bates
Package now works with Matrix_0.96-1

Revision 770 - Directory Listing
Modified Wed Jun 8 23:48:02 2005 UTC (14 years, 1 month ago) by bates
Moving lmer to the Matrix package

Revision 767 - Directory Listing
Modified Tue Jun 7 23:05:00 2005 UTC (14 years, 1 month ago) by bates
Move more of glmm calculations to C code

Revision 755 - Directory Listing
Modified Mon Jun 6 15:37:45 2005 UTC (14 years, 1 month ago) by bates
Use the mer class explicitly and combine code for lmer and glmer creation

Revision 754 - Directory Listing
Modified Mon May 30 18:40:45 2005 UTC (14 years, 1 month ago) by bates
Release 0.95-10

Revision 752 - Directory Listing
Modified Sun May 29 02:14:58 2005 UTC (14 years, 1 month ago) by bates
Release 0.95-9

Revision 751 - Directory Listing
Modified Tue May 24 17:49:33 2005 UTC (14 years, 2 months ago) by bates
Add optimization through port

Revision 750 - Directory Listing
Modified Fri May 20 13:15:58 2005 UTC (14 years, 2 months ago) by bates
Release 0.95-8

Revision 727 - Directory Listing
Modified Fri May 13 15:14:14 2005 UTC (14 years, 2 months ago) by bates
Release 0.95-7

Revision 724 - Directory Listing
Modified Tue May 10 01:42:58 2005 UTC (14 years, 2 months ago) by bates
Add glmer method documentation

Revision 721 - Directory Listing
Modified Mon May 9 02:13:25 2005 UTC (14 years, 2 months ago) by deepayan
added glmer class

Revision 719 - Directory Listing
Modified Mon May 9 01:24:44 2005 UTC (14 years, 2 months ago) by bates
Getting ready for a release

Revision 717 - Directory Listing
Modified Sun May 8 18:58:05 2005 UTC (14 years, 2 months ago) by deepayan
commented out code for Laplace approx in R

Revision 716 - Directory Listing
Modified Sun May 8 13:26:43 2005 UTC (14 years, 2 months ago) by bates


Revision 713 - Directory Listing
Modified Fri May 6 22:21:46 2005 UTC (14 years, 2 months ago) by bates
Conditionalize use of latticeExtra

Revision 711 - Directory Listing
Modified Thu May 5 04:12:44 2005 UTC (14 years, 2 months ago) by deepayan
Updates related to Laplace approximation

Revision 710 - Directory Listing
Modified Tue May 3 16:10:17 2005 UTC (14 years, 2 months ago) by deepayan
added option to calculate parts of Laplace approximation in C code. Currently doesn't work

Revision 708 - Directory Listing
Modified Mon May 2 21:29:55 2005 UTC (14 years, 2 months ago) by deepayan
to reduce overhead of calling as.matrix on ranef()'s, now using
.Call("lmer_ranef") directly

Revision 707 - Directory Listing
Modified Mon May 2 17:27:53 2005 UTC (14 years, 2 months ago) by deepayan
updated Laplace calculations

Revision 706 - Directory Listing
Modified Fri Apr 29 15:42:12 2005 UTC (14 years, 2 months ago) by deepayan
added code for Laplace approximation, essentially porting the ssclme version

Revision 704 - Directory Listing
Modified Thu Apr 21 22:01:09 2005 UTC (14 years, 3 months ago) by bates
Release 0.95-6

Revision 691 - Directory Listing
Modified Fri Apr 15 14:37:38 2005 UTC (14 years, 3 months ago) by bates
Release 0.95-5

Revision 690 - Directory Listing
Modified Tue Apr 5 22:17:04 2005 UTC (14 years, 3 months ago) by bates
Release 0.95-2

Revision 689 - Directory Listing
Modified Sat Apr 2 14:41:46 2005 UTC (14 years, 3 months ago) by bates
Release of lme_0.95-1

Revision 674 - Directory Listing
Modified Fri Mar 25 15:48:36 2005 UTC (14 years, 4 months ago) by bates
Moving random.effects to ranef

Revision 673 - Directory Listing
Modified Fri Mar 25 15:45:38 2005 UTC (14 years, 4 months ago) by bates
Moving fixed.effects to fixef

Revision 672 - Directory Listing
Modified Fri Mar 25 15:45:25 2005 UTC (14 years, 4 months ago) by bates
Moving fixed.effects to fixef

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Modified Fri Mar 25 15:45:13 2005 UTC (14 years, 4 months ago) by bates
Moving fixed.effects to fixef

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Modified Thu Mar 24 17:05:28 2005 UTC (14 years, 4 months ago) by bates


Revision 669 - Directory Listing
Modified Thu Mar 24 17:03:57 2005 UTC (14 years, 4 months ago) by bates
Change to lmerControl

Revision 668 - Directory Listing
Modified Thu Mar 24 16:49:28 2005 UTC (14 years, 4 months ago) by bates
Eliminating warnings

Revision 667 - Directory Listing
Modified Thu Mar 24 13:57:38 2005 UTC (14 years, 4 months ago) by bates
Archive copy before splitting the ssclme parts out

Revision 625 - Directory Listing
Modified Mon Mar 7 13:03:21 2005 UTC (14 years, 4 months ago) by bates


Revision 624 - Directory Listing
Modified Mon Mar 7 12:48:25 2005 UTC (14 years, 4 months ago) by bates
PQL iterations now work

Revision 623 - Directory Listing
Modified Mon Mar 7 12:47:53 2005 UTC (14 years, 4 months ago) by bates


Revision 601 - Directory Listing
Modified Fri Mar 4 03:52:38 2005 UTC (14 years, 4 months ago) by bates
C function lmer_fitted added

Revision 600 - Directory Listing
Modified Fri Mar 4 03:51:25 2005 UTC (14 years, 4 months ago) by bates
Temporary GLMM1 function for development

Revision 581 - Directory Listing
Modified Mon Feb 28 15:13:13 2005 UTC (14 years, 4 months ago) by bates
Release 0.9-2

Revision 580 - Directory Listing
Modified Mon Feb 28 15:12:43 2005 UTC (14 years, 4 months ago) by bates
Remove stubs of plot methods

Revision 571 - Directory Listing
Modified Fri Feb 25 13:30:34 2005 UTC (14 years, 4 months ago) by bates
Release 0.9-1

Revision 568 - Directory Listing
Modified Thu Feb 24 19:48:51 2005 UTC (14 years, 5 months ago) by bates
Moving tests to data packages

Revision 567 - Directory Listing
Modified Wed Feb 23 23:54:42 2005 UTC (14 years, 5 months ago) by bates
Move data sets to mlmRev and MEMSS

Revision 562 - Directory Listing
Modified Fri Feb 18 19:25:47 2005 UTC (14 years, 5 months ago) by bates
Release 0.8-3

Revision 550 - Directory Listing
Modified Tue Feb 15 22:15:11 2005 UTC (14 years, 5 months ago) by bates
Use coercion to extract L from an lmer object

Revision 549 - Directory Listing
Modified Tue Feb 15 22:14:07 2005 UTC (14 years, 5 months ago) by bates
New format in output

Revision 545 - Directory Listing
Modified Tue Feb 15 16:06:25 2005 UTC (14 years, 5 months ago) by bates
Updates to extract pieces of lmer objects for debugging

Revision 535 - Directory Listing
Modified Wed Feb 9 08:51:08 2005 UTC (14 years, 5 months ago) by bates
Change use of = for assignment to <-

Revision 469 - Directory Listing
Modified Sat Jan 29 14:19:26 2005 UTC (14 years, 5 months ago) by bates
Preparing for new release

Revision 468 - Directory Listing
Modified Sat Jan 29 14:18:34 2005 UTC (14 years, 5 months ago) by bates
Result of all.equal is not necessarily a logical value

Revision 467 - Directory Listing
Modified Sat Jan 29 14:17:10 2005 UTC (14 years, 5 months ago) by bates
add encoding declaration

Revision 457 - Directory Listing
Modified Mon Jan 24 09:12:53 2005 UTC (14 years, 6 months ago) by bates
Check parameter values before assigning them in the gradient
calculation.  This may save unnecessary decompositions (although it
turns out that the decomposition is fast and the inversion is slow).

Revision 456 - Directory Listing
Modified Mon Jan 24 09:10:50 2005 UTC (14 years, 6 months ago) by bates
New release

Revision 455 - Directory Listing
Modified Mon Jan 24 09:10:23 2005 UTC (14 years, 6 months ago) by bates
New release

Revision 454 - Directory Listing
Modified Sun Jan 23 10:10:01 2005 UTC (14 years, 6 months ago) by bates
New version

Revision 453 - Directory Listing
Modified Sun Jan 23 10:09:18 2005 UTC (14 years, 6 months ago) by bates
New version

Revision 452 - Directory Listing
Modified Sun Jan 23 10:09:03 2005 UTC (14 years, 6 months ago) by bates
Allow constant fixed part of formula

Revision 449 - Directory Listing
Modified Fri Jan 21 22:01:21 2005 UTC (14 years, 6 months ago) by bates
Release 0.6-12

Revision 446 - Directory Listing
Modified Wed Jan 19 19:08:01 2005 UTC (14 years, 6 months ago) by bates
Add slots and methods

Revision 435 - Directory Listing
Modified Thu Jan 13 19:37:26 2005 UTC (14 years, 6 months ago) by bates
Add the lmer generic and methods

Revision 428 - Directory Listing
Modified Fri Jan 7 16:42:23 2005 UTC (14 years, 6 months ago) by bates
Added documentation

Revision 427 - Directory Listing
Modified Wed Jan 5 16:28:40 2005 UTC (14 years, 6 months ago) by bates
Add the Exam data set

Revision 426 - Directory Listing
Modified Wed Jan 5 16:20:06 2005 UTC (14 years, 6 months ago) by bates
school factor levels in numeric order

Revision 423 - Directory Listing
Modified Tue Jan 4 23:45:49 2005 UTC (14 years, 6 months ago) by bates
Check in prior to leaving for Zuerich

Revision 421 - Directory Listing
Modified Mon Jan 3 20:10:42 2005 UTC (14 years, 6 months ago) by bates
Updating the Pixel example

Revision 416 - Directory Listing
Modified Mon Jan 3 19:13:56 2005 UTC (14 years, 6 months ago) by bates
Change to the lmer representation

Revision 414 - Directory Listing
Modified Mon Jan 3 18:55:11 2005 UTC (14 years, 6 months ago) by bates
New release

Revision 413 - Directory Listing
Modified Mon Jan 3 18:51:30 2005 UTC (14 years, 6 months ago) by bates
Switch from lmeRep to lmer

Revision 411 - Directory Listing
Modified Tue Dec 28 14:52:19 2004 UTC (14 years, 6 months ago) by bates
Updates to GLMM

Revision 409 - Directory Listing
Modified Sun Dec 19 02:19:58 2004 UTC (14 years, 7 months ago) by bates
Add anova method

Revision 408 - Directory Listing
Modified Sun Dec 19 02:19:38 2004 UTC (14 years, 7 months ago) by bates
Correct bug for order > 2

Revision 407 - Directory Listing
Modified Sun Dec 19 02:18:46 2004 UTC (14 years, 7 months ago) by bates
Begin revision of GLMM function

Revision 406 - Directory Listing
Modified Sun Dec 19 02:18:13 2004 UTC (14 years, 7 months ago) by bates
Add terms and assign to lme class for anova methods

Revision 405 - Directory Listing
Modified Sun Dec 19 02:18:04 2004 UTC (14 years, 7 months ago) by bates
Add terms and assign to lme class for anova methods

Revision 404 - Directory Listing
Modified Sun Dec 19 02:17:24 2004 UTC (14 years, 7 months ago) by bates
Update

Revision 403 - Directory Listing
Modified Sun Dec 19 02:17:07 2004 UTC (14 years, 7 months ago) by bates
Preparing for new release

Revision 402 - Directory Listing
Modified Sun Dec 19 02:16:59 2004 UTC (14 years, 7 months ago) by bates
Preparing for new release

Revision 401 - Directory Listing
Modified Sun Dec 19 02:16:40 2004 UTC (14 years, 7 months ago) by bates
New man page

Revision 400 - Directory Listing
Modified Sun Dec 19 02:16:14 2004 UTC (14 years, 7 months ago) by bates
no longer allow choice of optimizer

Revision 399 - Directory Listing
Modified Sun Dec 19 02:15:27 2004 UTC (14 years, 7 months ago) by bates
New man page

Revision 395 - Directory Listing
Modified Tue Dec 14 20:15:41 2004 UTC (14 years, 7 months ago) by bates
showing the strange optim result

Revision 394 - Directory Listing
Modified Tue Dec 14 20:07:56 2004 UTC (14 years, 7 months ago) by bates


Revision 393 - Directory Listing
Modified Tue Dec 14 20:02:06 2004 UTC (14 years, 7 months ago) by bates
Add the contr.SAS function

Revision 385 - Directory Listing
Modified Mon Dec 13 15:50:44 2004 UTC (14 years, 7 months ago) by bates
New release

Revision 384 - Directory Listing
Modified Mon Dec 13 15:50:21 2004 UTC (14 years, 7 months ago) by bates
change to integer value for msVerbose

Revision 383 - Directory Listing
Modified Mon Dec 13 15:49:02 2004 UTC (14 years, 7 months ago) by bates
Change to constrained optimization

Revision 382 - Directory Listing
Modified Sun Dec 12 17:30:29 2004 UTC (14 years, 7 months ago) by bates
Use constrained optimization for the ssclme representation as well as for the lmeRep

Revision 381 - Directory Listing
Modified Sat Dec 11 13:51:13 2004 UTC (14 years, 7 months ago) by bates
re conversation with JMC

Revision 380 - Directory Listing
Modified Sat Dec 11 13:50:17 2004 UTC (14 years, 7 months ago) by bates
conditionalize use of analytic gradient in lme1

Revision 365 - Directory Listing
Modified Sun Dec 5 13:48:20 2004 UTC (14 years, 7 months ago) by bates


Revision 364 - Directory Listing
Modified Sun Dec 5 13:47:55 2004 UTC (14 years, 7 months ago) by bates
cosmetic edit

Revision 363 - Directory Listing
Modified Sun Dec 5 13:47:21 2004 UTC (14 years, 7 months ago) by bates
latticeExtra not lattice

Revision 362 - Directory Listing
Modified Sun Dec 5 13:46:51 2004 UTC (14 years, 7 months ago) by bates
Make verbose really verbose for lme1

Revision 361 - Directory Listing
Modified Sun Dec 5 13:45:31 2004 UTC (14 years, 7 months ago) by bates
No need to require packages that are imported in the NAMESPACE

Revision 360 - Directory Listing
Modified Thu Dec 2 17:11:00 2004 UTC (14 years, 7 months ago) by bates
trim trailing blanks in levels of schoolid and childid

Revision 323 - Directory Listing
Modified Thu Nov 4 03:03:53 2004 UTC (14 years, 8 months ago) by deepayan
exported convertFromS3groupedData

Revision 322 - Directory Listing
Modified Thu Nov 4 01:54:25 2004 UTC (14 years, 8 months ago) by deepayan
added latticeExtra to Depends field

Revision 321 - Directory Listing
Modified Wed Nov 3 22:18:23 2004 UTC (14 years, 8 months ago) by bates
starting mlmRev package

Revision 320 - Directory Listing
Modified Wed Nov 3 14:14:59 2004 UTC (14 years, 8 months ago) by bates
Dependency on current Matrix package

Revision 319 - Directory Listing
Modified Tue Nov 2 21:38:27 2004 UTC (14 years, 8 months ago) by bates
Remove Packaged: line

Revision 318 - Directory Listing
Modified Tue Nov 2 21:30:03 2004 UTC (14 years, 8 months ago) by bates
add lme1 calls; update results

Revision 317 - Directory Listing
Modified Tue Nov 2 21:29:10 2004 UTC (14 years, 8 months ago) by bates
skeleton documentation

Revision 316 - Directory Listing
Modified Tue Nov 2 21:28:48 2004 UTC (14 years, 8 months ago) by bates
Adding lme1 and the lmeRep methods

Revision 315 - Directory Listing
Modified Tue Nov 2 17:51:44 2004 UTC (14 years, 8 months ago) by deepayan
modified DESCRIPTION to depend on latticeExtra rather than lattice

Revision 314 - Directory Listing
Modified Mon Nov 1 17:59:20 2004 UTC (14 years, 8 months ago) by bates
Remove redundant data() calls.  Add calls to lme1

Revision 313 - Directory Listing
Modified Mon Nov 1 17:58:20 2004 UTC (14 years, 8 months ago) by bates
Add correct call component

Revision 312 - Directory Listing
Modified Mon Nov 1 15:35:18 2004 UTC (14 years, 8 months ago) by deepayan
removed groupedData class, plots now using gplot in lattice

Revision 295 - Directory Listing
Modified Mon Oct 4 17:08:54 2004 UTC (14 years, 9 months ago) by bates
New release

Revision 294 - Directory Listing
Modified Mon Oct 4 17:08:24 2004 UTC (14 years, 9 months ago) by bates
Reconciling number of args in .Call

Revision 293 - Directory Listing
Modified Sun Oct 3 21:54:13 2004 UTC (14 years, 9 months ago) by bates
Remove PDF file that will be regenerated

Revision 292 - Directory Listing
Modified Sun Oct 3 21:53:46 2004 UTC (14 years, 9 months ago) by bates
Release 0.6-8

Revision 289 - Directory Listing
Modified Sat Oct 2 17:11:44 2004 UTC (14 years, 9 months ago) by bates
Clean up tests

Revision 288 - Directory Listing
Modified Sat Oct 2 17:11:20 2004 UTC (14 years, 9 months ago) by bates
Allow use of lme1

Revision 287 - Directory Listing
Modified Sat Oct 2 17:10:54 2004 UTC (14 years, 9 months ago) by bates
Allow use of lme1

Revision 286 - Directory Listing
Modified Sat Oct 2 17:10:13 2004 UTC (14 years, 9 months ago) by bates
Preparation for release

Revision 285 - Directory Listing
Modified Sat Oct 2 17:09:08 2004 UTC (14 years, 9 months ago) by bates
Add test for bug report #10

Revision 284 - Directory Listing
Modified Sat Oct 2 17:08:45 2004 UTC (14 years, 9 months ago) by bates
Close bug report #10

Revision 278 - Directory Listing
Modified Sat Sep 4 13:57:47 2004 UTC (14 years, 10 months ago) by bates
Prepare for next release

Revision 277 - Directory Listing
Modified Sat Sep 4 13:57:20 2004 UTC (14 years, 10 months ago) by bates
Restoring lme1 function for testing

Revision 276 - Directory Listing
Modified Sat Sep 4 13:57:00 2004 UTC (14 years, 10 months ago) by bates
Restoring lme1 function for testing

Revision 270 - Directory Listing
Modified Tue Aug 31 21:39:28 2004 UTC (14 years, 10 months ago) by bates
Temporarily suppress this test

Revision 269 - Directory Listing
Modified Tue Aug 31 19:14:30 2004 UTC (14 years, 10 months ago) by bates
New version

Revision 267 - Directory Listing
Modified Tue Aug 31 19:06:38 2004 UTC (14 years, 10 months ago) by bates
Suppress lme1 test

Revision 266 - Directory Listing
Modified Tue Aug 31 19:06:15 2004 UTC (14 years, 10 months ago) by bates
Suppress lme1 generic and methods

Revision 265 - Directory Listing
Modified Mon Aug 30 17:25:50 2004 UTC (14 years, 10 months ago) by bates
Incorrect arguments in call to "ssclme_sigma" as pointed out by John Chambers and others.

Revision 262 - Directory Listing
Modified Thu Aug 26 16:00:29 2004 UTC (14 years, 11 months ago) by bates
Use of <- instead of =

Revision 261 - Directory Listing
Modified Thu Aug 26 15:59:46 2004 UTC (14 years, 11 months ago) by bates
Remove vestigial pdMat classes

Revision 260 - Directory Listing
Modified Thu Aug 26 15:59:12 2004 UTC (14 years, 11 months ago) by bates
Add a test of lme1

Revision 259 - Directory Listing
Modified Thu Aug 26 15:58:42 2004 UTC (14 years, 11 months ago) by bates
Suitable for 1.9.1. or 2.0.0

Revision 256 - Directory Listing
Modified Fri Aug 20 16:27:56 2004 UTC (14 years, 11 months ago) by bates
Add an lme1 function for testing the lmeRep class

Revision 253 - Directory Listing
Modified Tue Aug 17 17:28:08 2004 UTC (14 years, 11 months ago) by bates
corrected use of |\bOmega| when \log|\bOmega| was meant

Revision 252 - Directory Listing
Modified Tue Aug 17 17:03:36 2004 UTC (14 years, 11 months ago) by bates
Added to Implementation vignette

Revision 251 - Directory Listing
Modified Tue Aug 17 17:02:02 2004 UTC (14 years, 11 months ago) by bates
Preparing for next release

Revision 249 - Directory Listing
Modified Thu Jul 15 03:06:39 2004 UTC (15 years ago) by bates
New vignette

Revision 246 - Directory Listing
Modified Mon Jul 12 17:39:11 2004 UTC (15 years ago) by bates
Moved saved output from tests to correct file names.  Modify example in gsummary for new form of Early data.  Modify calls to ssclme_coef and ssclme_coefGets.

Revision 244 - Directory Listing
Modified Mon Jul 12 12:45:17 2004 UTC (15 years ago) by bates
New release number, make Early data into a data frame

Revision 243 - Directory Listing
Modified Sat Jul 10 14:22:35 2004 UTC (15 years ago) by deepayan
fixed typo (variable name misspelled) causing summary to fail

Revision 242 - Directory Listing
Modified Wed Jul 7 18:26:33 2004 UTC (15 years ago) by bates
Change show methods to be more compact; add output of some tests

Revision 240 - Directory Listing
Modified Tue Jul 6 19:16:26 2004 UTC (15 years ago) by bates
New release.  Modified Exam data set, added gsummary and anova methods.

Revision 239 - Directory Listing
Modified Mon Jul 5 12:45:30 2004 UTC (15 years ago) by bates
Updates for book

Revision 236 - Directory Listing
Modified Thu Jul 1 03:18:40 2004 UTC (15 years ago) by bates
Documentation of the Early childhood intervention program data

Revision 235 - Directory Listing
Modified Thu Jul 1 03:17:19 2004 UTC (15 years ago) by bates
Added a Suggests: in the DESCRIPTION

Revision 234 - Directory Listing
Modified Fri Jun 25 23:53:34 2004 UTC (15 years, 1 month ago) by bates


Revision 233 - Directory Listing
Modified Fri Jun 25 23:51:52 2004 UTC (15 years, 1 month ago) by bates


Revision 232 - Directory Listing
Modified Fri Jun 25 23:50:44 2004 UTC (15 years, 1 month ago) by bates


Revision 231 - Directory Listing
Modified Sat Jun 19 11:47:32 2004 UTC (15 years, 1 month ago) by bates
Change affiliation

Revision 230 - Directory Listing
Modified Fri Jun 18 18:02:42 2004 UTC (15 years, 1 month ago) by bates
Ready to go

Revision 228 - Directory Listing
Modified Tue Jun 15 21:36:39 2004 UTC (15 years, 1 month ago) by bates
Summary section

Revision 227 - Directory Listing
Modified Mon Jun 14 00:26:41 2004 UTC (15 years, 1 month ago) by bates
Added cross-classified example

Revision 226 - Directory Listing
Modified Fri Jun 11 18:19:37 2004 UTC (15 years, 1 month ago) by bates
New vignette

Revision 225 - Directory Listing
Modified Fri Jun 11 18:19:21 2004 UTC (15 years, 1 month ago) by bates
Conditionalize verbose output

Revision 224 - Directory Listing
Modified Fri Jun 11 18:18:44 2004 UTC (15 years, 1 month ago) by bates
confint method

Revision 223 - Directory Listing
Modified Fri Jun 11 18:18:27 2004 UTC (15 years, 1 month ago) by bates
New version

Revision 222 - Directory Listing
Modified Fri Jun 11 18:18:10 2004 UTC (15 years, 1 month ago) by bates
Add confint dependency

Revision 221 - Directory Listing
Modified Fri Jun 11 00:01:42 2004 UTC (15 years, 1 month ago) by bates
Still incomplete

Revision 220 - Directory Listing
Modified Wed Jun 9 23:03:25 2004 UTC (15 years, 1 month ago) by bates
Revisions, revisions

Revision 219 - Directory Listing
Modified Wed Jun 9 23:02:56 2004 UTC (15 years, 1 month ago) by bates
Change name of control variable

Revision 218 - Directory Listing
Modified Wed Jun 9 23:02:30 2004 UTC (15 years, 1 month ago) by bates
Change name of control variable

Revision 217 - Directory Listing
Modified Wed Jun 9 23:01:58 2004 UTC (15 years, 1 month ago) by bates
Change name of control variable

Revision 216 - Directory Listing
Modified Wed Jun 9 23:01:37 2004 UTC (15 years, 1 month ago) by bates
Wrong order of options

Revision 215 - Directory Listing
Modified Wed Jun 9 15:36:02 2004 UTC (15 years, 1 month ago) by bates
Reorganization of the paper - clean up

Revision 214 - Directory Listing
Modified Wed Jun 9 15:35:16 2004 UTC (15 years, 1 month ago) by bates
Spelling correction

Revision 212 - Directory Listing
Modified Mon Jun 7 19:31:37 2004 UTC (15 years, 1 month ago) by bates
Ready for next release

Revision 211 - Directory Listing
Modified Fri Jun 4 18:49:07 2004 UTC (15 years, 1 month ago) by bates
Added four-panel plot of the projected matrix in the Scottish secondary example

Revision 210 - Directory Listing
Modified Fri Jun 4 04:12:56 2004 UTC (15 years, 1 month ago) by deepayan
added explanatory note

Revision 208 - Directory Listing
Modified Wed Jun 2 17:35:16 2004 UTC (15 years, 1 month ago) by bates
Add description of family in show and summary

Revision 207 - Directory Listing
Modified Wed Jun 2 17:34:05 2004 UTC (15 years, 1 month ago) by bates
Remove documentation that no longer applies

Revision 206 - Directory Listing
Modified Tue Jun 1 23:14:34 2004 UTC (15 years, 1 month ago) by deepayan
added drop=FALSE to ensure cm remains a matrix when nrow = 1

Revision 204 - Directory Listing
Modified Tue Jun 1 21:36:27 2004 UTC (15 years, 1 month ago) by bates
Prepare for next release

Revision 203 - Directory Listing
Modified Tue Jun 1 19:39:53 2004 UTC (15 years, 1 month ago) by bates
Clean up calls to require

Revision 201 - Directory Listing
Modified Tue Jun 1 19:29:43 2004 UTC (15 years, 1 month ago) by bates
Summary for GLMMs fit by Laplace method

Revision 200 - Directory Listing
Modified Tue Jun 1 19:29:02 2004 UTC (15 years, 1 month ago) by bates
Changed data set name

Revision 199 - Directory Listing
Modified Tue Jun 1 15:07:58 2004 UTC (15 years, 1 month ago) by bates
Change output object for Laplace method

Revision 198 - Directory Listing
Modified Tue Jun 1 15:06:17 2004 UTC (15 years, 1 month ago) by bates
Workarounds on useScale

Revision 197 - Directory Listing
Modified Tue Jun 1 15:05:17 2004 UTC (15 years, 1 month ago) by bates
Remove system.time calls in examples

Revision 196 - Directory Listing
Modified Tue Jun 1 15:04:25 2004 UTC (15 years, 1 month ago) by bates
Move Bang to Contraception

Revision 195 - Directory Listing
Modified Tue Jun 1 14:43:36 2004 UTC (15 years, 1 month ago) by bates
Prior to name change

Revision 194 - Directory Listing
Modified Mon May 31 21:59:12 2004 UTC (15 years, 1 month ago) by bates
Negative log-likelihood, I think

Revision 193 - Directory Listing
Modified Mon May 31 21:49:19 2004 UTC (15 years, 1 month ago) by bates
Remove redundant calls to library(lme4)

Revision 192 - Directory Listing
Modified Mon May 31 21:48:45 2004 UTC (15 years, 1 month ago) by bates
Getting ready for a release

Revision 191 - Directory Listing
Modified Mon May 31 21:48:22 2004 UTC (15 years, 1 month ago) by bates
New GLMM class and methods

Revision 187 - Directory Listing
Modified Mon May 31 18:49:54 2004 UTC (15 years, 1 month ago) by bates
Moving Doxyfile to the Matrix package

Revision 186 - Directory Listing
Modified Sun May 30 23:02:32 2004 UTC (15 years, 1 month ago) by bates
Major reorganization

Revision 183 - Directory Listing
Modified Sun May 30 07:36:30 2004 UTC (15 years, 1 month ago) by deepayan
minor cleanup

Revision 182 - Directory Listing
Modified Sun May 30 07:20:10 2004 UTC (15 years, 1 month ago) by deepayan
hopefully fixed (but not tested) problems with user specified offset

Revision 181 - Directory Listing
Modified Sat May 29 05:44:18 2004 UTC (15 years, 1 month ago) by deepayan
hopefully fixed offset problem for Laplace approx, plus removed debugging messages

Revision 180 - Directory Listing
Modified Fri May 28 15:16:47 2004 UTC (15 years, 1 month ago) by bates
Merging differences

Revision 179 - Directory Listing
Modified Fri May 28 14:21:08 2004 UTC (15 years, 1 month ago) by bates
Passing R CMD check

Revision 178 - Directory Listing
Modified Fri May 28 13:35:55 2004 UTC (15 years, 1 month ago) by bates
updates

Revision 177 - Directory Listing
Modified Fri May 28 13:35:05 2004 UTC (15 years, 1 month ago) by bates
do not require lattice unless used

Revision 175 - Directory Listing
Modified Fri May 28 00:28:19 2004 UTC (15 years, 1 month ago) by deepayan
use un-collapsed ssclme object for Laplace approximation - seems to work

Revision 173 - Directory Listing
Modified Wed May 19 16:31:02 2004 UTC (15 years, 2 months ago) by bates
New docs

Revision 172 - Directory Listing
Modified Wed May 19 16:30:23 2004 UTC (15 years, 2 months ago) by bates
New docs

Revision 171 - Directory Listing
Modified Wed May 19 16:29:17 2004 UTC (15 years, 2 months ago) by bates
Remove maxLIsize

Revision 170 - Directory Listing
Modified Wed May 19 16:27:38 2004 UTC (15 years, 2 months ago) by bates
Do not require lattice

Revision 169 - Directory Listing
Modified Wed May 19 16:25:12 2004 UTC (15 years, 2 months ago) by bates
Examples from the Multilevel software comparison

Revision 167 - Directory Listing
Modified Sat May 15 13:00:36 2004 UTC (15 years, 2 months ago) by bates
Use more general formula for random

Revision 165 - Directory Listing
Modified Fri May 14 21:00:35 2004 UTC (15 years, 2 months ago) by bates
Optional argument to ssclme_fitted

Revision 163 - Directory Listing
Modified Fri May 14 18:06:16 2004 UTC (15 years, 2 months ago) by bates
move utilities to the Matrix package

Revision 162 - Directory Listing
Modified Fri May 14 17:44:21 2004 UTC (15 years, 2 months ago) by bates
move utilities to the Matrix package

Revision 161 - Directory Listing
Modified Tue May 11 16:45:27 2004 UTC (15 years, 2 months ago) by deepayan
fixed errors, added some debugging statements

Revision 160 - Directory Listing
Modified Sun May 9 22:07:20 2004 UTC (15 years, 2 months ago) by bates
Save a bit of storage

Revision 156 - Directory Listing
Modified Fri May 7 20:47:29 2004 UTC (15 years, 2 months ago) by bates
Removing old documentation files

Revision 155 - Directory Listing
Modified Fri May 7 19:37:19 2004 UTC (15 years, 2 months ago) by bates
Add egsingle

Revision 154 - Directory Listing
Modified Fri May 7 19:36:10 2004 UTC (15 years, 2 months ago) by bates
Documentation updates

Revision 152 - Directory Listing
Modified Fri May 7 19:32:21 2004 UTC (15 years, 2 months ago) by deepayan
fixed wrong constants, added unconst = TRUE to coef

Revision 151 - Directory Listing
Modified Fri May 7 17:46:49 2004 UTC (15 years, 2 months ago) by deepayan
preliminary Laplace calculations

Revision 147 - Directory Listing
Modified Mon May 3 05:26:01 2004 UTC (15 years, 2 months ago) by deepayan
removed debugging code

Revision 145 - Directory Listing
Modified Sat May 1 20:16:04 2004 UTC (15 years, 2 months ago) by bates
Adding table

Revision 144 - Directory Listing
Modified Fri Apr 30 20:36:51 2004 UTC (15 years, 2 months ago) by bates
Changing calls

Revision 142 - Directory Listing
Modified Fri Apr 30 04:07:16 2004 UTC (15 years, 2 months ago) by deepayan
trying to debug

Revision 141 - Directory Listing
Modified Thu Apr 29 22:56:42 2004 UTC (15 years, 2 months ago) by bates
Change release number

Revision 139 - Directory Listing
Modified Thu Apr 29 15:30:56 2004 UTC (15 years, 2 months ago) by bates
Add summary.lme-class documentation

Revision 138 - Directory Listing
Modified Thu Apr 29 15:27:32 2004 UTC (15 years, 2 months ago) by deepayan
using glm call to initialize lots of stuff

Revision 137 - Directory Listing
Modified Thu Apr 29 14:26:04 2004 UTC (15 years, 2 months ago) by bates
Change memory limit to a setting

Revision 136 - Directory Listing
Modified Thu Apr 29 13:32:40 2004 UTC (15 years, 2 months ago) by bates


Revision 135 - Directory Listing
Modified Wed Apr 28 14:46:44 2004 UTC (15 years, 2 months ago) by deepayan
make example run

Revision 134 - Directory Listing
Modified Wed Apr 28 14:46:36 2004 UTC (15 years, 2 months ago) by deepayan
make example run

Revision 133 - Directory Listing
Modified Wed Apr 28 14:43:50 2004 UTC (15 years, 2 months ago) by deepayan
minor corrections, allow family to be character or function

Revision 132 - Directory Listing
Modified Wed Apr 28 12:27:24 2004 UTC (15 years, 2 months ago) by bates
Remove family oldClass

Revision 131 - Directory Listing
Modified Tue Apr 27 23:09:25 2004 UTC (15 years, 2 months ago) by bates
Preparations for rc1

Revision 130 - Directory Listing
Modified Tue Apr 27 20:39:13 2004 UTC (15 years, 2 months ago) by bates
Readying rc1

Revision 129 - Directory Listing
Modified Tue Apr 27 20:38:18 2004 UTC (15 years, 2 months ago) by bates
Prior to moving

Revision 128 - Directory Listing
Modified Mon Apr 26 04:38:37 2004 UTC (15 years, 3 months ago) by deepayan
cleanup and bhat function

Revision 126 - Directory Listing
Modified Sun Apr 25 18:00:15 2004 UTC (15 years, 3 months ago) by bates
Documentation changes for R CMD check

Revision 124 - Directory Listing
Modified Sat Apr 24 23:36:29 2004 UTC (15 years, 3 months ago) by bates
Factored out code to create model.frame

Revision 123 - Directory Listing
Modified Sat Apr 24 22:42:08 2004 UTC (15 years, 3 months ago) by bates
Fixing printing and summary methods

Revision 121 - Directory Listing
Modified Fri Apr 23 22:04:34 2004 UTC (15 years, 3 months ago) by bates
Adding show and summary methods

Revision 120 - Directory Listing
Modified Thu Apr 22 20:00:29 2004 UTC (15 years, 3 months ago) by deepayan
reorder random

Revision 119 - Directory Listing
Modified Thu Apr 22 19:53:46 2004 UTC (15 years, 3 months ago) by bates
declaration in wrong place

Revision 118 - Directory Listing
Modified Thu Apr 22 19:32:55 2004 UTC (15 years, 3 months ago) by bates
Changes

Revision 117 - Directory Listing
Modified Thu Apr 22 18:14:38 2004 UTC (15 years, 3 months ago) by deepayan
preliminary laplacian correction code

Revision 116 - Directory Listing
Modified Thu Apr 22 16:15:58 2004 UTC (15 years, 3 months ago) by bates
Add weighted matrices in C

Revision 110 - Directory Listing
Modified Mon Apr 19 18:40:16 2004 UTC (15 years, 3 months ago) by deepayan
removed some debugging code

Revision 107 - Directory Listing
Modified Mon Apr 19 05:10:32 2004 UTC (15 years, 3 months ago) by deepayan
still debugging

Revision 103 - Directory Listing
Modified Sun Apr 18 18:31:43 2004 UTC (15 years, 3 months ago) by bates
Fix mistake w.r.t. unconstrained args

Revision 102 - Directory Listing
Modified Sun Apr 18 15:54:27 2004 UTC (15 years, 3 months ago) by bates
Results on comparisons

Revision 99 - Directory Listing
Modified Sat Apr 17 16:58:38 2004 UTC (15 years, 3 months ago) by bates
Spell setMethod correctly

Revision 98 - Directory Listing
Modified Sat Apr 17 16:58:16 2004 UTC (15 years, 3 months ago) by bates
Cleanup of utilities

Revision 96 - Directory Listing
Modified Sat Apr 17 16:23:42 2004 UTC (15 years, 3 months ago) by bates
Adding gradient generic and methods

Revision 95 - Directory Listing
Modified Sat Apr 17 15:58:25 2004 UTC (15 years, 3 months ago) by bates
Remove unused routines from utilties

Revision 94 - Directory Listing
Modified Sat Apr 17 15:57:27 2004 UTC (15 years, 3 months ago) by bates
Remove this until we see if we really want ms code

Revision 91 - Directory Listing
Modified Fri Apr 16 21:18:32 2004 UTC (15 years, 3 months ago) by bates
Watch methods and exports

Revision 90 - Directory Listing
Modified Fri Apr 16 21:18:23 2004 UTC (15 years, 3 months ago) by bates
Watch methods and exports

Revision 89 - Directory Listing
Modified Fri Apr 16 18:30:57 2004 UTC (15 years, 3 months ago) by bates
export sparseGLMM

Revision 88 - Directory Listing
Modified Fri Apr 16 17:30:40 2004 UTC (15 years, 3 months ago) by deepayan
changes for debugging

Revision 87 - Directory Listing
Modified Fri Apr 16 17:29:25 2004 UTC (15 years, 3 months ago) by deepayan
sparseGLMM help file, essentially a placeholder for now

Revision 84 - Directory Listing
Modified Thu Apr 15 02:51:52 2004 UTC (15 years, 3 months ago) by bates
Add unconstr parameter to coef method

Revision 81 - Directory Listing
Modified Wed Apr 14 23:03:07 2004 UTC (15 years, 3 months ago) by bates
Adding results for new separated native permutation method

Revision 69 - Directory Listing
Modified Sun Apr 11 23:20:25 2004 UTC (15 years, 3 months ago) by bates
More of the table

Revision 68 - Directory Listing
Modified Sun Apr 11 19:41:45 2004 UTC (15 years, 3 months ago) by bates
More info on table

Revision 67 - Directory Listing
Modified Sun Apr 11 17:54:00 2004 UTC (15 years, 3 months ago) by bates
Data for table in comments

Revision 66 - Directory Listing
Modified Sun Apr 11 02:31:21 2004 UTC (15 years, 3 months ago) by bates
Tweaking figures

Revision 65 - Directory Listing
Modified Sun Apr 11 02:10:53 2004 UTC (15 years, 3 months ago) by bates
Revisions, more figures

Revision 64 - Directory Listing
Modified Sat Apr 10 17:33:06 2004 UTC (15 years, 3 months ago) by bates
Revisions, rearrangements

Revision 63 - Directory Listing
Modified Thu Apr 8 23:09:51 2004 UTC (15 years, 3 months ago) by bates
Re-writing, more re-writing, ...

Revision 62 - Directory Listing
Modified Thu Apr 8 16:51:06 2004 UTC (15 years, 3 months ago) by bates
Adding R reference

Revision 61 - Directory Listing
Modified Tue Apr 6 22:11:09 2004 UTC (15 years, 3 months ago) by bates
Minor cleanup

Revision 60 - Directory Listing
Modified Tue Apr 6 22:10:49 2004 UTC (15 years, 3 months ago) by bates
Minor change for VarCorr

Revision 59 - Directory Listing
Modified Tue Apr 6 22:10:37 2004 UTC (15 years, 3 months ago) by bates
New dependency

Revision 56 - Directory Listing
Modified Tue Apr 6 17:24:44 2004 UTC (15 years, 3 months ago) by bates
Moved MixedEffects vignette to lme4 package

Revision 54 - Directory Listing
Modified Tue Apr 6 17:20:52 2004 UTC (15 years, 3 months ago) by bates
add VarCorr methods

Revision 53 - Directory Listing
Modified Tue Apr 6 14:00:08 2004 UTC (15 years, 3 months ago) by bates


Revision 46 - Directory Listing
Modified Mon Apr 5 01:08:02 2004 UTC (15 years, 3 months ago) by bates
Added vcov method, rearranged source files

Revision 44 - Directory Listing
Modified Tue Mar 30 23:27:48 2004 UTC (15 years, 3 months ago) by bates
initial call to ssclme_initial not needed

Revision 39 - Directory Listing
Modified Tue Mar 30 15:58:19 2004 UTC (15 years, 3 months ago) by deepayan
misc updates

Revision 38 - Directory Listing
Modified Tue Mar 30 15:48:58 2004 UTC (15 years, 3 months ago) by deepayan
added a lmeControl option glmmMaxIter for sparseGLMM

Revision 37 - Directory Listing
Modified Mon Mar 29 23:16:49 2004 UTC (15 years, 3 months ago) by bates
propagate names to facs slot, transpose ranef result

Revision 36 - Directory Listing
Modified Mon Mar 29 23:15:58 2004 UTC (15 years, 3 months ago) by bates
experiments with sparseGLMM

Revision 35 - Directory Listing
Modified Mon Mar 29 01:50:46 2004 UTC (15 years, 3 months ago) by bates
Corrected dimnames in ranef method

Revision 33 - Directory Listing
Modified Sun Mar 28 20:06:50 2004 UTC (15 years, 3 months ago) by deepayan
minor adjustment

Revision 32 - Directory Listing
Modified Sun Mar 28 20:02:06 2004 UTC (15 years, 3 months ago) by deepayan
changed convergence check to use fitted values

Revision 31 - Directory Listing
Modified Sun Mar 28 19:03:54 2004 UTC (15 years, 3 months ago) by bates
Remove vestigial call to ssclme_factor

Revision 30 - Directory Listing
Modified Sun Mar 28 18:35:59 2004 UTC (15 years, 3 months ago) by deepayan
using ssclme_fitted instead of explicit calculations

Revision 29 - Directory Listing
Modified Sun Mar 28 17:11:26 2004 UTC (15 years, 3 months ago) by bates
fitted slot in lme class, new and improved fitted, fixef and ranef methods

Revision 27 - Directory Listing
Modified Sun Mar 28 16:40:05 2004 UTC (15 years, 3 months ago) by deepayan
added deviance based convergence check

Revision 26 - Directory Listing
Modified Sun Mar 28 16:20:26 2004 UTC (15 years, 3 months ago) by deepayan
updates to sparseGLMM

Revision 25 - Directory Listing
Modified Sun Mar 28 14:27:46 2004 UTC (15 years, 3 months ago) by bates
Remove redundant calls to _factor

Revision 24 - Directory Listing
Modified Sun Mar 28 14:21:06 2004 UTC (15 years, 3 months ago) by bates
Remove redundant calls to _factor

Revision 23 - Directory Listing
Modified Sat Mar 27 20:29:19 2004 UTC (15 years, 3 months ago) by deepayan
checking if I can commit

Revision 20 - Directory Listing
Modified Fri Mar 26 05:17:36 2004 UTC (15 years, 4 months ago) by deepayan
added sparseGLMM.R

Revision 16 - Directory Listing
Modified Tue Mar 23 23:28:12 2004 UTC (15 years, 4 months ago) by bates
Adding optimization step

Revision 15 - Directory Listing
Modified Tue Mar 23 23:27:51 2004 UTC (15 years, 4 months ago) by bates
initial version

Revision 12 - Directory Listing
Modified Tue Mar 23 13:15:22 2004 UTC (15 years, 4 months ago) by bates
Change name of C function ssclme_EMsteps

Revision 9 - Directory Listing
Modified Sun Mar 21 20:02:12 2004 UTC (15 years, 4 months ago) by bates
model and x arguments to lme

Revision 8 - Directory Listing
Modified Sun Mar 21 18:56:52 2004 UTC (15 years, 4 months ago) by bates
Use EMverbose flag

Revision 7 - Directory Listing
Modified Fri Mar 19 23:31:32 2004 UTC (15 years, 4 months ago) by bates
Change to ssclme representation

Revision 6 - Directory Listing
Added Fri Mar 19 20:16:29 2004 UTC (15 years, 4 months ago) by bates
Initial import

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