tbrick [Sat, 7 Feb 2015 18:55:35 +0000 (18:55 +0000)]
Fixed a bug where could not be accessed from a model object, and adjusted one test to match.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4238
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tbrick [Sat, 7 Feb 2015 18:52:08 +0000 (18:52 +0000)]
Fixed some typos and mistakes in omxConstrainThresholds.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4237
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mhunter [Sat, 7 Feb 2015 13:33:22 +0000 (13:33 +0000)]
Stop Roxygen from making Rd file for non-exported function
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4236
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jpritikin [Sat, 7 Feb 2015 00:39:31 +0000 (00:39 +0000)]
Flip inverted test
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4235
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jpritikin [Sat, 7 Feb 2015 00:33:33 +0000 (00:33 +0000)]
Exclude DESCRIPTION.in from tarball
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4234
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jpritikin [Sat, 7 Feb 2015 00:33:32 +0000 (00:33 +0000)]
Put a cap on the growth of cran-check diagnostics
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4233
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jpritikin [Sat, 7 Feb 2015 00:33:30 +0000 (00:33 +0000)]
Add rule to extract DESCRIPTION
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4232
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jpritikin [Sat, 7 Feb 2015 00:33:29 +0000 (00:33 +0000)]
Don't make everything depend on clean
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4231
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jpritikin [Sat, 7 Feb 2015 00:33:27 +0000 (00:33 +0000)]
Show content listing of tarball prior to cran-check
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4230
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jpritikin [Sat, 7 Feb 2015 00:33:26 +0000 (00:33 +0000)]
Rename mxLog_wrapper to avoid exporting
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4229
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jpritikin [Sat, 7 Feb 2015 00:33:24 +0000 (00:33 +0000)]
Doc matrix exp/log
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4228
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jpritikin [Thu, 5 Feb 2015 22:19:53 +0000 (22:19 +0000)]
Repair failing test
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4227
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tbrick [Thu, 5 Feb 2015 14:57:14 +0000 (14:57 +0000)]
Re-added omxConstrainThresholds.R to DESCRIPTION.in.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4226
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tbrick [Thu, 5 Feb 2015 14:22:50 +0000 (14:22 +0000)]
Possibly working version of omxConstrainThresholds. Sets thresholds, but does not work at starting values. Needs further development.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4225
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jpritikin [Thu, 5 Feb 2015 14:09:34 +0000 (14:09 +0000)]
Ensure per-row likelihoods reflect the correct parameter estimates
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4224
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jpritikin [Thu, 5 Feb 2015 14:09:33 +0000 (14:09 +0000)]
Revert "Added omxConstrainThresholds.R to the DESCRIPTION list."
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4223
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tbrick [Wed, 4 Feb 2015 23:26:34 +0000 (23:26 +0000)]
Re-enabled automatic return of FIML row likelihoods.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4222
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tbrick [Wed, 4 Feb 2015 23:23:51 +0000 (23:23 +0000)]
Added omxConstrainThresholds.R to the DESCRIPTION list. Otherwise, building fails.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4221
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mhunter [Wed, 4 Feb 2015 19:45:06 +0000 (19:45 +0000)]
Update copyright for R files
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4220
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mhunter [Wed, 4 Feb 2015 19:39:50 +0000 (19:39 +0000)]
Add Matrix package to Suggests
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4219
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mhunter [Wed, 4 Feb 2015 19:34:39 +0000 (19:34 +0000)]
Document argument for WLS data
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4218
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mhunter [Wed, 4 Feb 2015 19:11:55 +0000 (19:11 +0000)]
Another typo found by cran check
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4217
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mhunter [Wed, 4 Feb 2015 18:53:45 +0000 (18:53 +0000)]
another full argument match
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4216
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mhunter [Wed, 4 Feb 2015 18:51:02 +0000 (18:51 +0000)]
Use full argument name match instead of partial
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4215
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mhunter [Wed, 4 Feb 2015 18:48:27 +0000 (18:48 +0000)]
Correct typo in LISREL model
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4214
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mhunter [Wed, 4 Feb 2015 18:36:17 +0000 (18:36 +0000)]
mxData code/documentation sync
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4213
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mhunter [Wed, 4 Feb 2015 18:34:08 +0000 (18:34 +0000)]
Progress on LISREL Paths
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4212
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mhunter [Wed, 4 Feb 2015 18:24:01 +0000 (18:24 +0000)]
Fix broken alias link
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4211
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mhunter [Wed, 4 Feb 2015 17:47:32 +0000 (17:47 +0000)]
Clean cran check errors from demo
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4210
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mhunter [Tue, 3 Feb 2015 17:41:24 +0000 (17:41 +0000)]
Adjust state space documentation to match the code that uses contemporaneous input effects
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4209
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mhunter [Tue, 3 Feb 2015 00:17:14 +0000 (00:17 +0000)]
Definition variable evaluation bug fix when data sorting is turned off
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4208
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jpritikin [Mon, 2 Feb 2015 14:30:53 +0000 (14:30 +0000)]
Store the gradient when we perform finite differences for the Hessian
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4207
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jpritikin [Mon, 2 Feb 2015 13:42:31 +0000 (13:42 +0000)]
Make model identified (somebody forgot to include the means)
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4206
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jpritikin [Sun, 1 Feb 2015 20:17:11 +0000 (20:17 +0000)]
CSOLNP fails if the sense of the constraint is reversed
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4205
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rkirkpatrick [Fri, 30 Jan 2015 15:38:05 +0000 (15:38 +0000)]
Make test model that's not supposed to use derivatives actually not use them, and patch bug the faulty test model was hiding.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4204
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mhunter [Fri, 30 Jan 2015 04:23:53 +0000 (04:23 +0000)]
Manifest paths allowed for LISREL
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4203
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mhunter [Fri, 30 Jan 2015 04:04:31 +0000 (04:04 +0000)]
Latent paths allowed for LISREL
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4202
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jpritikin [Thu, 29 Jan 2015 13:27:24 +0000 (13:27 +0000)]
Add lower bounds on the variances
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4201
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rkirkpatrick [Wed, 28 Jan 2015 18:44:15 +0000 (18:44 +0000)]
Change from Rf_protect() statements to use of the ScopedProtect class.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4200
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rkirkpatrick [Wed, 28 Jan 2015 18:19:16 +0000 (18:19 +0000)]
Clean up and streamline code for GREML derivatives.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4199
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rkirkpatrick [Wed, 28 Jan 2015 18:10:07 +0000 (18:10 +0000)]
GREML test script should make sure the model runs both with and without analytic derivatives.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4198
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jpritikin [Wed, 28 Jan 2015 15:47:27 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 12/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4197
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jpritikin [Wed, 28 Jan 2015 15:47:25 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 11/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4196
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jpritikin [Wed, 28 Jan 2015 15:47:22 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 10/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4195
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jpritikin [Wed, 28 Jan 2015 15:47:19 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 9/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4194
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jpritikin [Wed, 28 Jan 2015 15:47:16 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 8/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4193
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jpritikin [Wed, 28 Jan 2015 15:47:12 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 7/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4192
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jpritikin [Wed, 28 Jan 2015 15:47:11 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 6/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4191
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jpritikin [Wed, 28 Jan 2015 15:47:09 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 5/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4190
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jpritikin [Wed, 28 Jan 2015 15:47:07 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 4/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4189
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jpritikin [Wed, 28 Jan 2015 15:47:05 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 3/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4188
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jpritikin [Wed, 28 Jan 2015 15:47:03 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 2/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4187
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jpritikin [Wed, 28 Jan 2015 15:47:01 +0000 (15:47 +0000)]
Carefully refactor confidence intervals 1/12
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4186
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jpritikin [Wed, 28 Jan 2015 15:46:59 +0000 (15:46 +0000)]
Add diag
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4185
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rkirkpatrick [Tue, 27 Jan 2015 20:35:24 +0000 (20:35 +0000)]
Inelegantly coded but working implementation of analytic GREML derivatives.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4184
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jpritikin [Tue, 27 Jan 2015 19:10:15 +0000 (19:10 +0000)]
Improve test organization
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4183
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jpritikin [Tue, 27 Jan 2015 14:16:54 +0000 (14:16 +0000)]
Repair free memory read in debug code (no serious consequences)
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4182
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jpritikin [Tue, 27 Jan 2015 14:16:53 +0000 (14:16 +0000)]
Allow 'make clean' to succeed without a pre-existing build dir
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4181
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jpritikin [Mon, 26 Jan 2015 16:58:17 +0000 (16:58 +0000)]
Simplify verbose plumbing
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4180
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jpritikin [Mon, 26 Jan 2015 16:58:14 +0000 (16:58 +0000)]
Improve error message
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4179
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jpritikin [Mon, 26 Jan 2015 16:58:12 +0000 (16:58 +0000)]
Doc defvar.row argument
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jpritikin [Mon, 26 Jan 2015 16:10:24 +0000 (16:10 +0000)]
Continue refactor of ComputeGD
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4177
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jpritikin [Mon, 26 Jan 2015 16:10:21 +0000 (16:10 +0000)]
Remove commented debug code
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4176
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jpritikin [Mon, 26 Jan 2015 16:10:19 +0000 (16:10 +0000)]
Factor out diagnostics
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4175
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jpritikin [Mon, 26 Jan 2015 16:10:17 +0000 (16:10 +0000)]
CSOLNP: Move control parameters into CSOLNPFit structure
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4174
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jpritikin [Mon, 26 Jan 2015 16:10:14 +0000 (16:10 +0000)]
Reimagine CSOLNPFit as GradientOptimizerAPI
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jpritikin [Mon, 26 Jan 2015 16:10:11 +0000 (16:10 +0000)]
Begin refactor of optimizer interface
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4172
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jpritikin [Mon, 26 Jan 2015 16:10:09 +0000 (16:10 +0000)]
Don't try to nudge zero starts again
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jpritikin [Sat, 24 Jan 2015 11:31:34 +0000 (11:31 +0000)]
Better implementation for IterationError
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4170
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mhunter [Sat, 24 Jan 2015 05:37:35 +0000 (05:37 +0000)]
Fix man page for check id
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4169
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mhunter [Sat, 24 Jan 2015 00:46:46 +0000 (00:46 +0000)]
Add ability to do means paths for LISREL type models.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4168
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jpritikin [Fri, 23 Jan 2015 21:54:20 +0000 (21:54 +0000)]
Tweak suggested debug options
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4167
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jpritikin [Fri, 23 Jan 2015 21:54:17 +0000 (21:54 +0000)]
Tiny code cleanup of NPSOL CIs
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4166
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jpritikin [Fri, 23 Jan 2015 21:54:13 +0000 (21:54 +0000)]
Report iteration error when threads are enabled
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4165
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mhunter [Fri, 23 Jan 2015 21:19:50 +0000 (21:19 +0000)]
Do not freak out. It is just updating the copyright.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4164
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tbrick [Fri, 23 Jan 2015 14:20:19 +0000 (14:20 +0000)]
Corrected a bug where out-of-order threshold errors were not reported.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4163
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rkirkpatrick [Thu, 22 Jan 2015 16:26:10 +0000 (16:26 +0000)]
Improve Hessian inversion in mxStandardizeRAMpaths().
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4162
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jpritikin [Tue, 20 Jan 2015 20:34:57 +0000 (20:34 +0000)]
Permit run-time toggling of protect depth diagnostics
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4161
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rkirkpatrick [Tue, 20 Jan 2015 17:23:21 +0000 (17:23 +0000)]
Request GREML fixed effects via argument to expectation, not via compute plan, and move calculation of regression coefficients to the attribute-population step.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4160
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mhunter [Fri, 16 Jan 2015 19:59:39 +0000 (19:59 +0000)]
Remove oudated use of mx*Objective
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4159
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rkirkpatrick [Fri, 16 Jan 2015 17:01:15 +0000 (17:01 +0000)]
GREML fixed effects and test model; code cleanup.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4158
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jpritikin [Fri, 16 Jan 2015 15:25:30 +0000 (15:25 +0000)]
Fix test for optimizer; additionally test for mxCondenseMatrixSlots default
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4157
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jpritikin [Fri, 16 Jan 2015 15:25:29 +0000 (15:25 +0000)]
Tidy Makevars
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4156
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jpritikin [Fri, 16 Jan 2015 15:25:29 +0000 (15:25 +0000)]
Repair package dependencies
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4155
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jpritikin [Fri, 16 Jan 2015 15:25:29 +0000 (15:25 +0000)]
Revert recent CSOLNP changes
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jpritikin [Fri, 16 Jan 2015 15:25:28 +0000 (15:25 +0000)]
Ensure memory is not overwritten
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4153
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mhunter [Thu, 15 Jan 2015 23:38:54 +0000 (23:38 +0000)]
Documentation for check identification function
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4152
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mzahery [Thu, 15 Jan 2015 20:20:23 +0000 (20:20 +0000)]
CSOLNP: problems in recent Eigen commits fixed
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4151
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jpritikin [Wed, 14 Jan 2015 20:20:16 +0000 (20:20 +0000)]
Suggest gcc option -Og for debugging compatible optimization
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4150
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tbates [Wed, 14 Jan 2015 17:35:20 +0000 (17:35 +0000)]
check regression for bug where models cant be re-run
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4149
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rkirkpatrick [Wed, 14 Jan 2015 15:32:49 +0000 (15:32 +0000)]
Switch from Eigen::Map to the safer EigenMatrixAdaptor; trim deadcode.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4148
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jpritikin [Wed, 14 Jan 2015 14:30:05 +0000 (14:30 +0000)]
Small fix for CSOLNP: Gradually writing subnp function in Eigen
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4147
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tbates [Wed, 14 Jan 2015 13:37:30 +0000 (13:37 +0000)]
test if OpenMx is defaulting to NPSOL
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4146
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jpritikin [Tue, 13 Jan 2015 20:39:45 +0000 (20:39 +0000)]
Repair selection of default optimizer
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4145
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jpritikin [Tue, 13 Jan 2015 19:01:40 +0000 (19:01 +0000)]
Make EigenMatrixAdaptor compile (oops)
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4144
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jpritikin [Tue, 13 Jan 2015 18:45:56 +0000 (18:45 +0000)]
Add EigenMatrixAdaptor
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4143
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mzahery [Tue, 13 Jan 2015 18:04:39 +0000 (18:04 +0000)]
CSOLNP: correcting revision 4137
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4142
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rkirkpatrick [Tue, 13 Jan 2015 17:22:54 +0000 (17:22 +0000)]
Minimal, rough implementation of GREML.
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4141
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jpritikin [Sat, 10 Jan 2015 01:34:16 +0000 (01:34 +0000)]
Update CHANGES
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4140
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mzahery [Fri, 9 Jan 2015 21:01:31 +0000 (21:01 +0000)]
CSOLNP: Writing subnp function in Eigen (6)
git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@4139
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projects / openmx:openmx.git / log