openmx:openmx.git
4 years agoReorg latent distribution algebra
jpritikin [Tue, 20 Aug 2013 12:23:13 +0000 (12:23 +0000)]
Reorg latent distribution algebra

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2864 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdating twinData.Rd to document the reuse of zyg 6:10. Also added Nick Martin reference
tbates [Mon, 19 Aug 2013 08:48:59 +0000 (08:48 +0000)]
Updating twinData.Rd to document the reuse of zyg 6:10. Also added Nick Martin reference

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2863 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out multiply by quadrature area
jpritikin [Mon, 19 Aug 2013 05:53:26 +0000 (05:53 +0000)]
Factor out multiply by quadrature area

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2862 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTweak two-tier inner loop
jpritikin [Mon, 19 Aug 2013 05:53:16 +0000 (05:53 +0000)]
Tweak two-tier inner loop

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2861 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoNo need to take extra care to calculate EAP scores in Estep
jpritikin [Mon, 19 Aug 2013 05:53:06 +0000 (05:53 +0000)]
No need to take extra care to calculate EAP scores in Estep

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2860 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMerge Csolnp up to 2826
jpritikin [Sat, 17 Aug 2013 09:09:00 +0000 (09:09 +0000)]
Merge Csolnp up to 2826

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2859 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDocument how to find & adjust R's default compiler flags
jpritikin [Sat, 17 Aug 2013 04:19:18 +0000 (04:19 +0000)]
Document how to find & adjust R's default compiler flags

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2858 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAllow estimation to continue as long as at least 1 item is positive definite
jpritikin [Sat, 17 Aug 2013 04:15:00 +0000 (04:15 +0000)]
Allow estimation to continue as long as at least 1 item is positive definite

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2857 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReport free variable name in N-R diagnostics instead of just #
jpritikin [Sat, 17 Aug 2013 04:14:53 +0000 (04:14 +0000)]
Report free variable name in N-R diagnostics instead of just #

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2856 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSparse matrix vector product
jpritikin [Sat, 17 Aug 2013 04:14:44 +0000 (04:14 +0000)]
Sparse matrix vector product

There are two benefits: (1) With many parameters, drastically fewer
multiplies and adds. (2) Since the terms are sorted by offset into the
inverse Hessian, more cache friendly. The improvement in performance
small but measurable.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2855 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPrecompute quadrature locations
jpritikin [Sat, 17 Aug 2013 04:14:31 +0000 (04:14 +0000)]
Precompute quadrature locations

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2854 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove excessive caching
jpritikin [Sat, 17 Aug 2013 04:14:22 +0000 (04:14 +0000)]
Remove excessive caching

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2853 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCombine calculations into the E-step (helps two-tier more)
jpritikin [Sat, 17 Aug 2013 04:14:07 +0000 (04:14 +0000)]
Combine calculations into the E-step (helps two-tier more)

If you want to explore the estimation options, such as comparing
speed with/without caching, this snapshot has everything working
and selectable at runtime. Since two-tier gains so much by not
caching and regular BA81 is not slower, the next change set will
remove the cache option and a bunch of code.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2852 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAllow ComputeIterate to test maximum absolute change
jpritikin [Sat, 17 Aug 2013 04:13:51 +0000 (04:13 +0000)]
Allow ComputeIterate to test maximum absolute change

+ The adjustStart flag is gone. There is no longer a reason to request
adjustStart=FALSE. It might do something else besides adjust starting
values so the name isn't accurate either.

+ mxComputeOnce no longer has a fit=TRUE default action. By default it
does nothing.

+ Not evaluating the fit helps estimate IFA models. The performance is
about the same. The main advantage is that some bulky caching can be
turned off with no penalty. Here is page fault data for ifa-cai2009.R.
Ignore the difference in runtime because the EM cycle tolerance was not
equated between runs.

With cache:

55.60user 0.07system 0:08.41elapsed 661%CPU (0avgtext+0avgdata 83788maxresident)k
0inputs+0outputs (0major+72249minor)pagefaults 0swaps

Without cache:

60.64user 0.10system 0:09.01elapsed 673%CPU (0avgtext+0avgdata 71276maxresident)k
0inputs+0outputs (0major+61669minor)pagefaults 0swaps

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2851 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdated citation per M Neale request. And note in WLS prep for future work.
mhunter [Fri, 16 Aug 2013 17:06:41 +0000 (17:06 +0000)]
Updated citation per M Neale request.  And note in WLS prep for future work.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2850 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove obsolete variables
jpritikin [Fri, 16 Aug 2013 15:19:50 +0000 (15:19 +0000)]
Remove obsolete variables

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2849 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoBoth enable and disable use of gradients
jpritikin [Fri, 16 Aug 2013 15:19:34 +0000 (15:19 +0000)]
Both enable and disable use of gradients

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2848 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRestore ability to verify EM derivs; add test
jpritikin [Fri, 16 Aug 2013 15:19:15 +0000 (15:19 +0000)]
Restore ability to verify EM derivs; add test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2847 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPrint backend time
jpritikin [Fri, 16 Aug 2013 15:18:55 +0000 (15:18 +0000)]
Print backend time

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2846 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd back some UNPROTECTs
jpritikin [Fri, 16 Aug 2013 14:17:56 +0000 (14:17 +0000)]
Add back some UNPROTECTs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2845 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSync librpf
jpritikin [Fri, 16 Aug 2013 14:17:43 +0000 (14:17 +0000)]
Sync librpf

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2844 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorder two-tier loops
jpritikin [Mon, 12 Aug 2013 10:56:38 +0000 (10:56 +0000)]
Reorder two-tier loops

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2843 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRewrite EM fit for new loop order
jpritikin [Mon, 12 Aug 2013 10:56:29 +0000 (10:56 +0000)]
Rewrite EM fit for new loop order

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2842 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoOpenMP tweaks
jpritikin [Mon, 12 Aug 2013 10:56:19 +0000 (10:56 +0000)]
OpenMP tweaks

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2841 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPre-divide Eis for two-tier
jpritikin [Mon, 12 Aug 2013 10:56:10 +0000 (10:56 +0000)]
Pre-divide Eis for two-tier

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2840 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorganized the expected weights for cache friendliness
jpritikin [Mon, 12 Aug 2013 10:56:00 +0000 (10:56 +0000)]
Reorganized the expected weights for cache friendliness

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2839 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTranspose outcomeProb for better cache behavior
jpritikin [Sun, 11 Aug 2013 14:05:17 +0000 (14:05 +0000)]
Transpose outcomeProb for better cache behavior

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2838 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove unnecessary memory initialization
jpritikin [Sun, 11 Aug 2013 14:05:03 +0000 (14:05 +0000)]
Remove unnecessary memory initialization

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2837 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSync librpf
jpritikin [Sun, 11 Aug 2013 14:04:50 +0000 (14:04 +0000)]
Sync librpf

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2836 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd more tests
jpritikin [Sun, 11 Aug 2013 14:04:32 +0000 (14:04 +0000)]
Add more tests

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2835 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix bug with irregular number of outcomes
jpritikin [Sun, 11 Aug 2013 14:03:57 +0000 (14:03 +0000)]
Fix bug with irregular number of outcomes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2834 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTweak Newton-Raphson
jpritikin [Sun, 11 Aug 2013 14:03:46 +0000 (14:03 +0000)]
Tweak Newton-Raphson

+ Increase damping faster
+ Always allow 1 restart regardless of current iteration number
+ Try harder to return better estimates
+ Improve debugging output
+ Restart on NaN gradient

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2833 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoIgnore cachegrind logs
jpritikin [Sun, 11 Aug 2013 14:03:33 +0000 (14:03 +0000)]
Ignore cachegrind logs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2832 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTranspose cache to the optimal orientation
jpritikin [Sat, 10 Aug 2013 14:23:05 +0000 (14:23 +0000)]
Transpose cache to the optimal orientation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2831 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove estimation of the latent gradient
jpritikin [Sat, 10 Aug 2013 14:22:49 +0000 (14:22 +0000)]
Remove estimation of the latent gradient

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2830 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove EAP to the new loop nesting order
jpritikin [Sat, 10 Aug 2013 14:22:19 +0000 (14:22 +0000)]
Move EAP to the new loop nesting order

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2829 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAttempt to merge SVN 2824
jpritikin [Sat, 10 Aug 2013 05:27:45 +0000 (05:27 +0000)]
Attempt to merge SVN 2824

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2828 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTouch up fit execution path
jpritikin [Sat, 10 Aug 2013 05:27:34 +0000 (05:27 +0000)]
Touch up fit execution path

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2827 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdate warning for multiple groups
jpritikin [Thu, 8 Aug 2013 10:43:46 +0000 (10:43 +0000)]
Update warning for multiple groups

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2823 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoOptimize E step (helps two-tier more)
jpritikin [Thu, 8 Aug 2013 10:43:38 +0000 (10:43 +0000)]
Optimize E step (helps two-tier more)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2822 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMake summary work for IFA models
jpritikin [Mon, 5 Aug 2013 09:59:39 +0000 (09:59 +0000)]
Make summary work for IFA models

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2821 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFurther document Ramsay 1975 choices
jpritikin [Mon, 5 Aug 2013 09:59:27 +0000 (09:59 +0000)]
Further document Ramsay 1975 choices

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2820 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSlightly optimize vector matrix product
jpritikin [Mon, 5 Aug 2013 09:59:19 +0000 (09:59 +0000)]
Slightly optimize vector matrix product

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2819 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDon't copy derivs between FitContext instances (by default)
jpritikin [Mon, 5 Aug 2013 09:59:11 +0000 (09:59 +0000)]
Don't copy derivs between FitContext instances (by default)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2818 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove EItemParam
jpritikin [Mon, 5 Aug 2013 09:59:03 +0000 (09:59 +0000)]
Remove EItemParam

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2817 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUse full range of double
jpritikin [Mon, 5 Aug 2013 09:58:45 +0000 (09:58 +0000)]
Use full range of double

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2816 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoBe more paranoid about importing mxData to backend
jpritikin [Sun, 4 Aug 2013 14:25:05 +0000 (14:25 +0000)]
Be more paranoid about importing mxData to backend

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2815 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdate state space documentation and adjust data sorting to the nuclear option.
mhunter [Sun, 4 Aug 2013 05:34:28 +0000 (05:34 +0000)]
Update state space documentation and adjust data sorting to the nuclear option.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2814 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoIgnore non-positive definite Hessian if less than half the items are afflicted
jpritikin [Sun, 4 Aug 2013 05:31:24 +0000 (05:31 +0000)]
Ignore non-positive definite Hessian if less than half the items are afflicted

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2813 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAuto-tune Newton-Raphson
jpritikin [Sun, 4 Aug 2013 04:20:53 +0000 (04:20 +0000)]
Auto-tune Newton-Raphson

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2812 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove Schilling & Bock (2005) adjustment
jpritikin [Sun, 4 Aug 2013 04:20:25 +0000 (04:20 +0000)]
Remove Schilling & Bock (2005) adjustment

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2811 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFlip sign of derivatives
jpritikin [Sun, 4 Aug 2013 04:20:16 +0000 (04:20 +0000)]
Flip sign of derivatives

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2810 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoInvert Hessian piecewise
jpritikin [Sun, 4 Aug 2013 04:20:07 +0000 (04:20 +0000)]
Invert Hessian piecewise

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2809 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCheck expectation@patternLikelihood in log units
jpritikin [Fri, 2 Aug 2013 08:45:04 +0000 (08:45 +0000)]
Check expectation@patternLikelihood in log units

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2808 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove autoconf remnant
jpritikin [Fri, 2 Aug 2013 08:44:55 +0000 (08:44 +0000)]
Remove autoconf remnant

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2807 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out density multiplication
jpritikin [Thu, 1 Aug 2013 13:58:25 +0000 (13:58 +0000)]
Factor out density multiplication

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2806 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 9/9
jpritikin [Thu, 1 Aug 2013 13:58:11 +0000 (13:58 +0000)]
Reorg E step 9/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2805 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 8/9
jpritikin [Thu, 1 Aug 2013 13:57:59 +0000 (13:57 +0000)]
Reorg E step 8/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2804 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 7/9
jpritikin [Thu, 1 Aug 2013 13:57:51 +0000 (13:57 +0000)]
Reorg E step 7/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2803 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 6/9
jpritikin [Thu, 1 Aug 2013 13:57:37 +0000 (13:57 +0000)]
Reorg E step 6/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2802 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 5/9
jpritikin [Thu, 1 Aug 2013 13:57:26 +0000 (13:57 +0000)]
Reorg E step 5/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2801 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 4/9
jpritikin [Thu, 1 Aug 2013 13:57:18 +0000 (13:57 +0000)]
Reorg E step 4/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2800 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 3/9
jpritikin [Thu, 1 Aug 2013 13:57:07 +0000 (13:57 +0000)]
Reorg E step 3/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2799 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 2/9
jpritikin [Thu, 1 Aug 2013 13:56:59 +0000 (13:56 +0000)]
Reorg E step 2/9

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2798 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorg E step 1/9
jpritikin [Thu, 1 Aug 2013 13:56:49 +0000 (13:56 +0000)]
Reorg E step 1/9

The purpose of this patch series is to reorder the loops in the E step
such that the unique pattern is the outermost loop instead of the
quadrature as the outermost loop. There are at least two reasons why
this is a good idea. The first reason is that this organization permits
us to skip the maximum amount of computation for missing data. Missing
data is detected in the outermost loop and the inner loops can be
skipped entirely. The second reason why this organization wins is
because most information is responses specific. By distributing threads
over responses, there is less need for expensive between thread
synchronization.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2797 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd cache for outcomeProb
jpritikin [Thu, 1 Aug 2013 13:56:41 +0000 (13:56 +0000)]
Add cache for outcomeProb

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2796 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMore tests
jpritikin [Thu, 1 Aug 2013 13:56:22 +0000 (13:56 +0000)]
More tests

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2795 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove allocation out of computeRPF
jpritikin [Thu, 1 Aug 2013 13:56:09 +0000 (13:56 +0000)]
Move allocation out of computeRPF

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2794 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoStore outcome probs more compactly
jpritikin [Thu, 1 Aug 2013 13:56:00 +0000 (13:56 +0000)]
Store outcome probs more compactly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2793 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoProper handling for an empty free.set
jpritikin [Thu, 1 Aug 2013 13:55:50 +0000 (13:55 +0000)]
Proper handling for an empty free.set

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2792 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd multigroup state space test (failing)
jpritikin [Thu, 1 Aug 2013 13:46:27 +0000 (13:46 +0000)]
Add multigroup state space test (failing)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2791 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoInitialize omxState.stale to keep valgrind happy
jpritikin [Wed, 31 Jul 2013 13:03:22 +0000 (13:03 +0000)]
Initialize omxState.stale to keep valgrind happy

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2790 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRecord Mike Neale's suggestion
jpritikin [Wed, 31 Jul 2013 13:02:13 +0000 (13:02 +0000)]
Record Mike Neale's suggestion

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2789 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename
jpritikin [Mon, 29 Jul 2013 09:04:19 +0000 (09:04 +0000)]
Rename

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2788 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAvoid final copyParamToModel when not needed
jpritikin [Mon, 29 Jul 2013 08:53:14 +0000 (08:53 +0000)]
Avoid final copyParamToModel when not needed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2787 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix diag
jpritikin [Mon, 29 Jul 2013 08:53:04 +0000 (08:53 +0000)]
Fix diag

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2786 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoProtect against parameter oscillation using Ramsay (1975)
jpritikin [Mon, 29 Jul 2013 08:52:57 +0000 (08:52 +0000)]
Protect against parameter oscillation using Ramsay (1975)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2785 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove artificial lower bound on patternLik
jpritikin [Mon, 29 Jul 2013 08:52:48 +0000 (08:52 +0000)]
Remove artificial lower bound on patternLik

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2784 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix incorrect handling of missing data
jpritikin [Mon, 29 Jul 2013 08:52:40 +0000 (08:52 +0000)]
Fix incorrect handling of missing data

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2783 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix Hessian to work with equality constraints
jpritikin [Mon, 29 Jul 2013 08:52:30 +0000 (08:52 +0000)]
Fix Hessian to work with equality constraints

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2782 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMake more internal data available from R
jpritikin [Mon, 29 Jul 2013 08:52:20 +0000 (08:52 +0000)]
Make more internal data available from R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2781 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPermit non-integral quadrature widths (oops)
jpritikin [Sun, 28 Jul 2013 12:26:36 +0000 (12:26 +0000)]
Permit non-integral quadrature widths (oops)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2780 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove diagnostics
jpritikin [Sun, 28 Jul 2013 12:26:28 +0000 (12:26 +0000)]
Improve diagnostics

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2779 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoConditionalize some debugging noise on the runtime verbose flag
jpritikin [Sat, 27 Jul 2013 13:45:56 +0000 (13:45 +0000)]
Conditionalize some debugging noise on the runtime verbose flag

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2778 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPermit vector indexing on row or col matrices
jpritikin [Sat, 27 Jul 2013 13:38:28 +0000 (13:38 +0000)]
Permit vector indexing on row or col matrices

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2777 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoBounds check matrix indices
jpritikin [Sat, 27 Jul 2013 09:20:11 +0000 (09:20 +0000)]
Bounds check matrix indices

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2776 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd sentinel to help detect memory corruption
jpritikin [Sat, 27 Jul 2013 09:17:33 +0000 (09:17 +0000)]
Add sentinel to help detect memory corruption

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2775 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSome printf -> mxLog
jpritikin [Sat, 27 Jul 2013 09:17:18 +0000 (09:17 +0000)]
Some printf -> mxLog

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2774 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoEnable with IMX_OPT_ENGINE=CSOLNP
jpritikin [Sat, 27 Jul 2013 09:17:07 +0000 (09:17 +0000)]
Enable with IMX_OPT_ENGINE=CSOLNP

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2773 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAddress suspicious compiler warnings
jpritikin [Sat, 27 Jul 2013 09:16:54 +0000 (09:16 +0000)]
Address suspicious compiler warnings

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2772 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix compile errors
jpritikin [Sat, 27 Jul 2013 09:16:43 +0000 (09:16 +0000)]
Fix compile errors

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2771 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRprintf -> mxLog
jpritikin [Sat, 27 Jul 2013 09:16:30 +0000 (09:16 +0000)]
Rprintf -> mxLog

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2770 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename for C++
jpritikin [Sat, 27 Jul 2013 09:16:17 +0000 (09:16 +0000)]
Rename for C++

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2769 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMerge branch Csolnp
jpritikin [Sat, 27 Jul 2013 09:15:25 +0000 (09:15 +0000)]
Merge branch Csolnp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2768 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove obsolete performance counters
jpritikin [Fri, 26 Jul 2013 15:38:51 +0000 (15:38 +0000)]
Remove obsolete performance counters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2764 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRewrite Newton-Raphson with better math
jpritikin [Fri, 26 Jul 2013 15:38:44 +0000 (15:38 +0000)]
Rewrite Newton-Raphson with better math

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2763 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRework initialization of starting values
jpritikin [Fri, 26 Jul 2013 15:38:34 +0000 (15:38 +0000)]
Rework initialization of starting values

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2762 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFail if starting value is out of bounds
jpritikin [Fri, 26 Jul 2013 15:38:23 +0000 (15:38 +0000)]
Fail if starting value is out of bounds

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2761 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFail if an outcome is entirely unendorsed
jpritikin [Fri, 26 Jul 2013 15:38:13 +0000 (15:38 +0000)]
Fail if an outcome is entirely unendorsed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2760 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReport the empirical mean & cov
jpritikin [Fri, 26 Jul 2013 04:18:50 +0000 (04:18 +0000)]
Report the empirical mean & cov

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2757 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1