openmx:openmx.git
4 years agoMove failing test to failing dir
jpritikin [Thu, 10 Oct 2013 14:57:31 +0000 (14:57 +0000)]
Move failing test to failing dir

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2939 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd documentation (more cran prep)
jpritikin [Thu, 10 Oct 2013 14:52:52 +0000 (14:52 +0000)]
Add documentation (more cran prep)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2938 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd failing test
jpritikin [Thu, 10 Oct 2013 13:57:14 +0000 (13:57 +0000)]
Add failing test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2937 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename PPML.Test.Test back to imxPPML.Test.Test
jpritikin [Fri, 4 Oct 2013 19:15:15 +0000 (19:15 +0000)]
Rename PPML.Test.Test back to imxPPML.Test.Test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2936 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix operator< per http://gcc.gnu.org/bugzilla/show_bug.cgi?id=58562
jpritikin [Fri, 4 Oct 2013 14:49:59 +0000 (14:49 +0000)]
Fix operator< per gcc.gnu.org/bugzilla/show_bug.cgi?id=58562

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2935 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix dependencies
jpritikin [Fri, 4 Oct 2013 14:49:59 +0000 (14:49 +0000)]
Fix dependencies

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2934 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix order of multiply to avoid floating point overflow
jpritikin [Fri, 4 Oct 2013 13:40:20 +0000 (13:40 +0000)]
Fix order of multiply to avoid floating point overflow

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2933 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDocument a bunch of imx functions
jpritikin [Thu, 3 Oct 2013 19:04:37 +0000 (19:04 +0000)]
Document a bunch of imx functions

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2932 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename a few more PPML functions
jpritikin [Thu, 3 Oct 2013 19:04:37 +0000 (19:04 +0000)]
Rename a few more PPML functions

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2931 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd myself as an author
jpritikin [Thu, 3 Oct 2013 19:04:37 +0000 (19:04 +0000)]
Add myself as an author

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2930 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename functions to avoid exporting
jpritikin [Thu, 3 Oct 2013 19:04:36 +0000 (19:04 +0000)]
Rename functions to avoid exporting

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2929 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out code style check
jpritikin [Thu, 3 Oct 2013 19:04:35 +0000 (19:04 +0000)]
Factor out code style check

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2928 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTry again to fix Windows NPSOL build
jpritikin [Thu, 3 Oct 2013 14:37:32 +0000 (14:37 +0000)]
Try again to fix Windows NPSOL build

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2927 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd more ignores
jpritikin [Thu, 3 Oct 2013 14:32:08 +0000 (14:32 +0000)]
Add more ignores

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2926 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix shell escaping for windows build
jpritikin [Thu, 3 Oct 2013 14:32:07 +0000 (14:32 +0000)]
Fix shell escaping for windows build

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2925 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out rox generated documentation list
jpritikin [Thu, 3 Oct 2013 14:32:07 +0000 (14:32 +0000)]
Factor out rox generated documentation list

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2924 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTry to fix windows NPSOL build
jpritikin [Thu, 3 Oct 2013 14:20:24 +0000 (14:20 +0000)]
Try to fix windows NPSOL build

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2923 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename most PPML functions to keep them unexported
jpritikin [Thu, 3 Oct 2013 14:13:31 +0000 (14:13 +0000)]
Rename most PPML functions to keep them unexported

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2922 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDocument new cran make targets
jpritikin [Thu, 3 Oct 2013 14:13:30 +0000 (14:13 +0000)]
Document new cran make targets

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2921 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix example in LISREL documentation.
mhunter [Thu, 3 Oct 2013 13:45:27 +0000 (13:45 +0000)]
Fix example in LISREL documentation.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2920 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSpell out parameter name for pmvnorm
jpritikin [Thu, 3 Oct 2013 13:41:34 +0000 (13:41 +0000)]
Spell out parameter name for pmvnorm

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2919 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix windows to build with/without NPSOL
jpritikin [Thu, 3 Oct 2013 13:41:34 +0000 (13:41 +0000)]
Fix windows to build with/without NPSOL

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2918 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix build without NPSOL
jpritikin [Wed, 2 Oct 2013 17:54:47 +0000 (17:54 +0000)]
Fix build without NPSOL

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2917 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFail with a sensible message if an old version of RPF is installed
jpritikin [Tue, 1 Oct 2013 13:09:28 +0000 (13:09 +0000)]
Fail with a sensible message if an old version of RPF is installed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2916 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReport # of H-G terms in debug info
jpritikin [Tue, 1 Oct 2013 13:09:27 +0000 (13:09 +0000)]
Report # of H-G terms in debug info

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2915 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDon't warn if the mxFactor attribute is missing on factors
jpritikin [Sun, 29 Sep 2013 10:46:19 +0000 (10:46 +0000)]
Don't warn if the mxFactor attribute is missing on factors

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2914 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix a few warnings
jpritikin [Sun, 29 Sep 2013 01:29:13 +0000 (01:29 +0000)]
Fix a few warnings

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2913 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoEnable extra gcc warning categories
jpritikin [Sun, 29 Sep 2013 01:29:09 +0000 (01:29 +0000)]
Enable extra gcc warning categories

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2912 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDon't warn about unknown (e.g., openmp) pragmas
jpritikin [Sun, 29 Sep 2013 01:29:06 +0000 (01:29 +0000)]
Don't warn about unknown (e.g., openmp) pragmas

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2911 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove mxFactor warning msg at urging of Tim Bates
jpritikin [Sat, 28 Sep 2013 17:43:02 +0000 (17:43 +0000)]
Improve mxFactor warning msg at urging of Tim Bates

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2910 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAllow summary to work with unnamed estimates
jpritikin [Fri, 27 Sep 2013 17:17:46 +0000 (17:17 +0000)]
Allow summary to work with unnamed estimates

The estimates really shouldn't be unnamed. We need to figure out where
the name is assigned and figure out why it isn't getting assigned.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2909 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReport initial fit value when iterating
jpritikin [Fri, 27 Sep 2013 17:17:46 +0000 (17:17 +0000)]
Report initial fit value when iterating

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2908 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove check whether all outcomes are represented in the data
jpritikin [Fri, 27 Sep 2013 17:17:45 +0000 (17:17 +0000)]
Remove check whether all outcomes are represented in the data

For multigroup models, the non-reference group might have
inadequate data to fit all the parameters but that should
not prevent an attempt at estimation.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2907 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSet factor levels up correctly
jpritikin [Fri, 27 Sep 2013 17:17:45 +0000 (17:17 +0000)]
Set factor levels up correctly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2906 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove omxPrintMatrix formatting
jpritikin [Thu, 26 Sep 2013 14:08:04 +0000 (14:08 +0000)]
Improve omxPrintMatrix formatting

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2905 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd newlines between rows in omxPrintMatrix
jpritikin [Thu, 26 Sep 2013 14:03:39 +0000 (14:03 +0000)]
Add newlines between rows in omxPrintMatrix

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2904 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdate state space documentation to reflect missing data changes.
mhunter [Wed, 25 Sep 2013 05:11:37 +0000 (05:11 +0000)]
Update state space documentation to reflect missing data changes.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2903 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoWorking missing data handling for state space expectation with a passing test. Hooray.
mhunter [Tue, 24 Sep 2013 17:45:21 +0000 (17:45 +0000)]
Working missing data handling for state space expectation with a passing test.  Hooray.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2902 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAllow for debugging in windows. Toward missing data handling in state space.
mhunter [Mon, 23 Sep 2013 15:49:13 +0000 (15:49 +0000)]
Allow for debugging in windows. Toward missing data handling in state space.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2901 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdded failing test of missing data in state space expectations.
mhunter [Mon, 23 Sep 2013 05:28:11 +0000 (05:28 +0000)]
Added failing test of missing data in state space expectations.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2900 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPossible working missing data handling for state space expectations. It does not...
mhunter [Sun, 22 Sep 2013 17:56:31 +0000 (17:56 +0000)]
Possible working missing data handling for state space expectations.  It does not cause new errors, and has passed a sanity check, but has not been thoroughly debugged or tested.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2899 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoProgress toward missing data handling in state space expectations.
mhunter [Sat, 21 Sep 2013 18:34:21 +0000 (18:34 +0000)]
Progress toward missing data handling in state space expectations.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2898 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFinished man page for state space expectations.
mhunter [Fri, 20 Sep 2013 07:10:07 +0000 (07:10 +0000)]
Finished man page for state space expectations.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2897 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFixed bug in state space expectations relating to data grabbing.
mhunter [Thu, 19 Sep 2013 05:54:53 +0000 (05:54 +0000)]
Fixed bug in state space expectations relating to data grabbing.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2896 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoChanged state space expectation argument names, and started to add example to man...
mhunter [Thu, 19 Sep 2013 04:45:41 +0000 (04:45 +0000)]
Changed state space expectation argument names, and started to add example to man page.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2895 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoChange starting value for variance away from zero.
mhunter [Mon, 16 Sep 2013 16:19:04 +0000 (16:19 +0000)]
Change starting value for variance away from zero.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2892 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoIdentified demo factor model by fixing variance to resolve ID problem when optimizing...
mhunter [Mon, 16 Sep 2013 16:05:30 +0000 (16:05 +0000)]
Identified demo factor model by fixing variance to resolve ID problem when optimizing with CSOLNP.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2891 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCSOLNP updated
mzahery [Thu, 12 Sep 2013 15:21:39 +0000 (15:21 +0000)]
CSOLNP updated

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2890 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove error message
jpritikin [Thu, 12 Sep 2013 14:21:24 +0000 (14:21 +0000)]
Improve error message

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2889 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFixed a bug where ML fit functions with raw data (FIML) and vector=TRUE set were...
tbrick [Thu, 12 Sep 2013 11:39:42 +0000 (11:39 +0000)]
Fixed a bug where ML fit functions with raw data (FIML) and vector=TRUE set were returning a single value instead of a vector.  Also updated the CHANGES file a little.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2888 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRun all test with Csolnp
jpritikin [Fri, 6 Sep 2013 20:23:33 +0000 (20:23 +0000)]
Run all test with Csolnp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2883 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAddress valgrind issues in Csolnp
jpritikin [Fri, 6 Sep 2013 20:23:32 +0000 (20:23 +0000)]
Address valgrind issues in Csolnp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2882 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCSOLNP fixed
mzahery [Fri, 6 Sep 2013 19:35:32 +0000 (19:35 +0000)]
CSOLNP fixed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2881 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoConditionalize the rest of CSOLNP debug prints
jpritikin [Fri, 6 Sep 2013 19:21:35 +0000 (19:21 +0000)]
Conditionalize the rest of CSOLNP debug prints

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2880 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd 'make test-csolnp'
jpritikin [Fri, 6 Sep 2013 18:48:29 +0000 (18:48 +0000)]
Add 'make test-csolnp'

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2878 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCSOLNP Initialize y
mzahery [Fri, 6 Sep 2013 18:36:25 +0000 (18:36 +0000)]
CSOLNP Initialize y

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2877 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix valgrind complaint about debug code
jpritikin [Fri, 6 Sep 2013 18:28:44 +0000 (18:28 +0000)]
Fix valgrind complaint about debug code

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2876 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoGenerate dsym for MacOS debug symbols
jpritikin [Fri, 6 Sep 2013 18:22:16 +0000 (18:22 +0000)]
Generate dsym for MacOS debug symbols

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2875 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReindent
jpritikin [Fri, 6 Sep 2013 18:19:46 +0000 (18:19 +0000)]
Reindent

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2874 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCorrections to CSOLNP
jpritikin [Fri, 6 Sep 2013 18:19:45 +0000 (18:19 +0000)]
Corrections to CSOLNP

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2873 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRuntime conditionalize debug output
jpritikin [Fri, 6 Sep 2013 14:49:15 +0000 (14:49 +0000)]
Runtime conditionalize debug output

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2872 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoKeep NPSOL as the default for now
jpritikin [Thu, 5 Sep 2013 19:19:15 +0000 (19:19 +0000)]
Keep NPSOL as the default for now

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2871 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove version from DESCRIPTION
jpritikin [Thu, 5 Sep 2013 19:19:12 +0000 (19:19 +0000)]
Remove version from DESCRIPTION

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2870 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCSOLNP
mzahery [Thu, 5 Sep 2013 16:29:10 +0000 (16:29 +0000)]
CSOLNP

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2869 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemoved a debugging line I'd accidentally left in when adding thresholds to MxRAMModels.
tbrick [Mon, 2 Sep 2013 16:21:38 +0000 (16:21 +0000)]
Removed a debugging line I'd accidentally left in when adding thresholds to MxRAMModels.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2868 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoInitial check-in of mxThreshold() path function and one associated test.
tbrick [Sun, 1 Sep 2013 13:55:23 +0000 (13:55 +0000)]
Initial check-in of mxThreshold() path function and one associated test.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2867 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemember N-R max caution across E-M cycles
jpritikin [Thu, 22 Aug 2013 07:13:45 +0000 (07:13 +0000)]
Remember N-R max caution across E-M cycles

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2865 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

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