Joshua Nathaniel Pritikin [Wed, 7 Jan 2015 14:11:13 +0000 (09:11 -0500)]
Switch to stan
Joshua Nathaniel Pritikin [Tue, 6 Jan 2015 19:22:12 +0000 (14:22 -0500)]
Show how to compute fit only
Joshua Nathaniel Pritikin [Tue, 6 Jan 2015 18:57:59 +0000 (13:57 -0500)]
Fix API
Joshua Nathaniel Pritikin [Tue, 6 Jan 2015 18:53:43 +0000 (13:53 -0500)]
Remove deadcode
Joshua Nathaniel Pritikin [Tue, 6 Jan 2015 18:48:59 +0000 (13:48 -0500)]
Working
Joshua Nathaniel Pritikin [Sat, 3 Jan 2015 22:02:22 +0000 (17:02 -0500)]
snap
Joshua Nathaniel Pritikin [Sat, 3 Jan 2015 19:00:47 +0000 (14:00 -0500)]
Simplify
Joshua Nathaniel Pritikin [Fri, 2 Jan 2015 20:37:32 +0000 (15:37 -0500)]
Tidy includes
Joshua Nathaniel Pritikin [Fri, 2 Jan 2015 12:51:37 +0000 (07:51 -0500)]
rm boost
Joshua Nathaniel Pritikin [Fri, 2 Jan 2015 12:40:49 +0000 (07:40 -0500)]
Simplify more
Joshua Nathaniel Pritikin [Tue, 30 Dec 2014 15:32:51 +0000 (10:32 -0500)]
Remove prob_grad
Joshua Nathaniel Pritikin [Tue, 30 Dec 2014 15:28:07 +0000 (10:28 -0500)]
Simplfiy
Joshua Nathaniel Pritikin [Tue, 30 Dec 2014 15:08:07 +0000 (10:08 -0500)]
Tidy
Joshua Nathaniel Pritikin [Sun, 28 Dec 2014 21:42:42 +0000 (16:42 -0500)]
Tidy more
Joshua Nathaniel Pritikin [Sat, 27 Dec 2014 02:50:37 +0000 (21:50 -0500)]
Simplify
Joshua Nathaniel Pritikin [Sat, 27 Dec 2014 02:45:19 +0000 (21:45 -0500)]
Simplfiy
Joshua Nathaniel Pritikin [Sat, 27 Dec 2014 02:44:30 +0000 (21:44 -0500)]
Simplfiy
Joshua Nathaniel Pritikin [Sat, 27 Dec 2014 02:34:43 +0000 (21:34 -0500)]
simplify
Joshua Nathaniel Pritikin [Sat, 2 Aug 2014 09:03:39 +0000 (14:33 +0530)]
Basic stuff working
Joshua Nathaniel Pritikin [Tue, 6 Jan 2015 20:16:29 +0000 (15:16 -0500)]
Add EigenMatrixAdaptor
jpritikin [Wed, 7 Jan 2015 18:48:30 +0000 (18:48 +0000)]
Deadcode
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4130
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jpritikin [Wed, 7 Jan 2015 18:46:26 +0000 (18:46 +0000)]
Use 'int' for Eigen rows and columns
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4129
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jpritikin [Wed, 7 Jan 2015 18:45:23 +0000 (18:45 +0000)]
Add omxEnsureColumnMajor API
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4128
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jpritikin [Wed, 7 Jan 2015 16:05:41 +0000 (16:05 +0000)]
Remove '#define EPSILON'; clashes with stan headers
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4127
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jpritikin [Wed, 7 Jan 2015 16:04:24 +0000 (16:04 +0000)]
Prevent Varadhan2008 from failing near convergence
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4126
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jpritikin [Wed, 7 Jan 2015 16:03:36 +0000 (16:03 +0000)]
Throw error on attempt to invert incomplete Hessian
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4125
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jpritikin [Fri, 19 Dec 2014 16:05:02 +0000 (16:05 +0000)]
CSOLNP: Correct exclusion of inequality constraints from gradient/Hessian
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4124
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jpritikin [Thu, 18 Dec 2014 19:29:35 +0000 (19:29 +0000)]
Remove unused variable
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4123
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jpritikin [Thu, 18 Dec 2014 18:47:17 +0000 (18:47 +0000)]
When checkpointing fit, record who requested it
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4122
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jpritikin [Thu, 18 Dec 2014 18:41:04 +0000 (18:41 +0000)]
Allow test to run on both optimizers
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4121
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jpritikin [Thu, 18 Dec 2014 18:41:03 +0000 (18:41 +0000)]
Add CIs to continuous time model
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4120
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jpritikin [Thu, 18 Dec 2014 18:41:01 +0000 (18:41 +0000)]
Add some omxCheckCloseEnough
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4119
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jpritikin [Thu, 18 Dec 2014 18:40:59 +0000 (18:40 +0000)]
Deadcode removal
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4118
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jpritikin [Thu, 18 Dec 2014 18:40:57 +0000 (18:40 +0000)]
Restore parallel processing for CIs
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4117
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jpritikin [Thu, 18 Dec 2014 18:40:54 +0000 (18:40 +0000)]
Add a checkpoint entry for each CI attempt
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4116
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jpritikin [Thu, 18 Dec 2014 18:40:52 +0000 (18:40 +0000)]
Add "Checkpoint Fullpath" to override output destination
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4115
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jpritikin [Thu, 18 Dec 2014 18:40:50 +0000 (18:40 +0000)]
Make mxOption(model, val) return the global setting or the model's override
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4114
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jpritikin [Thu, 18 Dec 2014 12:07:18 +0000 (12:07 +0000)]
Move to failing
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4113
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mhunter [Thu, 18 Dec 2014 04:29:58 +0000 (04:29 +0000)]
Add WLS standard error and chi-square functions
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4112
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jpritikin [Thu, 18 Dec 2014 03:51:10 +0000 (03:51 +0000)]
Consolidate starting value nudging logic in ComputeGD
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4111
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jpritikin [Thu, 18 Dec 2014 03:51:07 +0000 (03:51 +0000)]
Try harder to keep CIs ordered properly vs estimate
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4110
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mhunter [Wed, 17 Dec 2014 20:44:42 +0000 (20:44 +0000)]
Add copyright to Multilevel example
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4109
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mhunter [Wed, 17 Dec 2014 20:44:18 +0000 (20:44 +0000)]
Add check for model identification checking function
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4108
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mhunter [Wed, 17 Dec 2014 18:57:50 +0000 (18:57 +0000)]
Another typo fix in previous commit
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4107
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mhunter [Wed, 17 Dec 2014 18:55:57 +0000 (18:55 +0000)]
Typo fix in previous commit
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4106
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mhunter [Wed, 17 Dec 2014 18:51:54 +0000 (18:51 +0000)]
Add partial identification information to ID check. Tells which parameters are not identified.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4105
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jpritikin [Wed, 17 Dec 2014 17:14:55 +0000 (17:14 +0000)]
CSOLNP: Avoid reuse of obm for more than 1 purpose
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4104
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jpritikin [Wed, 17 Dec 2014 16:00:33 +0000 (16:00 +0000)]
CSOLNP: Simplify CI calculation
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4103
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jpritikin [Wed, 17 Dec 2014 16:00:31 +0000 (16:00 +0000)]
CSOLNP: Tidy optimizer reporting
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4102
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jpritikin [Wed, 17 Dec 2014 16:00:28 +0000 (16:00 +0000)]
Relax tolerance
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4101
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jpritikin [Wed, 17 Dec 2014 02:27:13 +0000 (02:27 +0000)]
CSOLNP: Count the number of major iterations
Not sure if this is exactly right
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4100
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jpritikin [Tue, 16 Dec 2014 22:04:03 +0000 (22:04 +0000)]
Add Makefile rule to run the failing tests
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4099
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jpritikin [Tue, 16 Dec 2014 22:04:00 +0000 (22:04 +0000)]
CSOLNP: Return stuff via CSOLNPFit; isolate Matrix inside of subnp
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4098
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jpritikin [Tue, 16 Dec 2014 19:38:32 +0000 (19:38 +0000)]
CSOLNP: Remove some redundent information
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4097
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jpritikin [Tue, 16 Dec 2014 19:38:30 +0000 (19:38 +0000)]
Remove template argument from CSOLNP::solnp
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4096
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jpritikin [Tue, 16 Dec 2014 19:38:28 +0000 (19:38 +0000)]
Store equality & inequality results in CSOLNPFit
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4095
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yang [Tue, 16 Dec 2014 15:29:00 +0000 (15:29 +0000)]
Reduce variable lifetime
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4094
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jpritikin [Tue, 16 Dec 2014 15:00:30 +0000 (15:00 +0000)]
Tidy some minor valgrind issues
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4093
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jpritikin [Tue, 16 Dec 2014 15:00:29 +0000 (15:00 +0000)]
Remove q() from test
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4092
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jpritikin [Tue, 16 Dec 2014 11:39:27 +0000 (11:39 +0000)]
Move nightly test to passing
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4091
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jpritikin [Tue, 16 Dec 2014 10:20:28 +0000 (10:20 +0000)]
CSOLNP: Convert control param to Eigen vector
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4090
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jpritikin [Tue, 16 Dec 2014 01:03:49 +0000 (01:03 +0000)]
CSOLNP: Move bounds to CSOLNPFit; remove lots of deadcode
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4089
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jpritikin [Mon, 15 Dec 2014 20:28:05 +0000 (20:28 +0000)]
CSOLNP: Move inequality bounds to CSOLNPFit
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4088
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jpritikin [Mon, 15 Dec 2014 20:28:03 +0000 (20:28 +0000)]
CSOLNP: Remove Matrix arg from CSOLNPFit::solFun
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4087
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jpritikin [Mon, 15 Dec 2014 17:36:15 +0000 (17:36 +0000)]
CSOLNP: Remove GLOB_ prefix since variables are no longer global
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4086
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jpritikin [Mon, 15 Dec 2014 17:36:13 +0000 (17:36 +0000)]
CSOLNP: Eliminate more globals
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4085
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jpritikin [Mon, 15 Dec 2014 17:36:11 +0000 (17:36 +0000)]
CSOLNP: Continue refactoring API
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4084
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jpritikin [Mon, 15 Dec 2014 17:36:10 +0000 (17:36 +0000)]
CSOLNP: Pass parameter vector using Eigen
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4083
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jpritikin [Mon, 15 Dec 2014 17:36:07 +0000 (17:36 +0000)]
CSOLNP: Rewrite omxProcessConstraintsCsolnp in Eigen
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4082
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jpritikin [Mon, 15 Dec 2014 17:36:04 +0000 (17:36 +0000)]
Document constraint types better (in source code)
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4081
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jpritikin [Mon, 15 Dec 2014 17:36:03 +0000 (17:36 +0000)]
CSOLNP: Don't bother creating the unused solEqB matrix
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4080
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jpritikin [Mon, 15 Dec 2014 17:36:00 +0000 (17:36 +0000)]
CSOLNP: Eliminate reliance on all-zero solEqB
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4079
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jpritikin [Mon, 15 Dec 2014 17:35:58 +0000 (17:35 +0000)]
Constraints bounds are determined by the type
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4078
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jpritikin [Mon, 15 Dec 2014 17:35:57 +0000 (17:35 +0000)]
Make it easier to run tests
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4077
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jpritikin [Mon, 15 Dec 2014 17:35:55 +0000 (17:35 +0000)]
Simplify setup of constraints
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4076
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jpritikin [Mon, 15 Dec 2014 12:55:28 +0000 (12:55 +0000)]
CSOLNP: Put in temporary fix for conformability of derivs with constraints
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4075
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jpritikin [Mon, 15 Dec 2014 03:13:16 +0000 (03:13 +0000)]
CSOLNP: Fix some problems revealed by Eigen conformability checking
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4074
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jpritikin [Mon, 15 Dec 2014 02:45:33 +0000 (02:45 +0000)]
Rework calculation of compiler args; add IMX_SAFE switch
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4073
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jpritikin [Sat, 13 Dec 2014 21:52:57 +0000 (21:52 +0000)]
Add test for omxGetParameters
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4072
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jpritikin [Sat, 13 Dec 2014 19:21:00 +0000 (19:21 +0000)]
Switch default optimizer back to CSOLNP
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4071
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jpritikin [Sat, 13 Dec 2014 19:18:43 +0000 (19:18 +0000)]
omxGetParameters: Omit duplicated parameters even when there are no submodels
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4070
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rkirkpatrick [Fri, 12 Dec 2014 16:40:47 +0000 (16:40 +0000)]
Tidy up MxMatrix-related error and warning messages; re-write MatrixErrorDetection.R to be much more thorough.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4069
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jpritikin [Thu, 11 Dec 2014 14:28:24 +0000 (14:28 +0000)]
BA81: Need to fail hard
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4068
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jpritikin [Wed, 10 Dec 2014 20:21:04 +0000 (20:21 +0000)]
BA81: Prohibit all NA rows
All NA rows screw up latent distribution estimates.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4067
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rkirkpatrick [Wed, 10 Dec 2014 19:11:05 +0000 (19:11 +0000)]
Small but important MxMatrix-related adjustments.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4066
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mhunter [Sun, 7 Dec 2014 14:29:50 +0000 (14:29 +0000)]
Add Jacobian-based model identification check.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4065
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mhunter [Sat, 6 Dec 2014 17:36:55 +0000 (17:36 +0000)]
Added method for getting cov, means, and thresh from LISREL expectation.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4064
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mhunter [Sat, 6 Dec 2014 15:52:55 +0000 (15:52 +0000)]
Added method for getting cov, means, and thresh from RAM expectation.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4063
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mhunter [Sat, 6 Dec 2014 15:52:13 +0000 (15:52 +0000)]
Added generic for getting expected covariance, means, and thresholds.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4062
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mhunter [Fri, 5 Dec 2014 20:55:29 +0000 (20:55 +0000)]
Small test for LISREL type, to be expanded as LISREL functionality expands.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4061
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mhunter [Fri, 5 Dec 2014 20:54:26 +0000 (20:54 +0000)]
LISREL model initialization.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4060
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rkirkpatrick [Fri, 5 Dec 2014 18:46:29 +0000 (18:46 +0000)]
Better MxMatrix verification to catch at runtime a lot of user blunders involving condenseSlots and @ <- .
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4059
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rkirkpatrick [Fri, 5 Dec 2014 16:58:27 +0000 (16:58 +0000)]
Conditionally "condense" the 'labels', 'free', 'lbound', and 'ubound' slots of MxMatrix objects.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4058
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jpritikin [Fri, 5 Dec 2014 16:44:49 +0000 (16:44 +0000)]
CSOLNP: Convert ind to Eigen; make easier to understand
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4057
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jpritikin [Fri, 5 Dec 2014 16:37:38 +0000 (16:37 +0000)]
Enable ubsan for gcc 4.9+
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4056
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jpritikin [Fri, 5 Dec 2014 16:37:38 +0000 (16:37 +0000)]
Make gcc happier
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4055
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jpritikin [Fri, 5 Dec 2014 15:46:43 +0000 (15:46 +0000)]
CSOLNP: Remove more deadcode
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4054
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jpritikin [Fri, 5 Dec 2014 15:34:49 +0000 (15:34 +0000)]
Avoid reuse of condif[123]
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4053
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tbates [Fri, 5 Dec 2014 14:53:14 +0000 (14:53 +0000)]
test if OpenMx disorders thresholds
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4052
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jpritikin [Fri, 5 Dec 2014 14:27:26 +0000 (14:27 +0000)]
CSOLNP: Remove bounds check; all Eigen ops are already bounds checked
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4051
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projects / openmx:openmx.git / log