openmx:openmx.git
3 years agoUpdate Users Guide pages A through F for the expectation-fit change.
mhunter [Thu, 20 Mar 2014 16:49:28 +0000 (16:49 +0000)]
Update Users Guide pages A through F for the expectation-fit change.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3166 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHint the correct way to customize the compiler/compiler options
jpritikin [Thu, 20 Mar 2014 15:28:37 +0000 (15:28 +0000)]
Hint the correct way to customize the compiler/compiler options

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3165 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMove HessianTest* to failing
jpritikin [Thu, 20 Mar 2014 13:20:48 +0000 (13:20 +0000)]
Move HessianTest* to failing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3164 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoKill some debugging related %lu warnings.
mhunter [Thu, 20 Mar 2014 13:19:53 +0000 (13:19 +0000)]
Kill some debugging related %lu warnings.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3163 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agotolerance in omxCheckCloseEnough changed for Csolnp
mzahery [Thu, 20 Mar 2014 13:04:19 +0000 (13:04 +0000)]
tolerance in omxCheckCloseEnough changed for Csolnp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3162 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoinversion function changed, gradient & Hessian returned, some code cleanings
mzahery [Thu, 20 Mar 2014 13:00:04 +0000 (13:00 +0000)]
inversion function changed, gradient & Hessian returned, some code cleanings

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3161 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReparameterize lower & upper drm bounds in logits (copied from mirt)
jpritikin [Wed, 19 Mar 2014 13:10:45 +0000 (13:10 +0000)]
Reparameterize lower & upper drm bounds in logits (copied from mirt)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3160 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agominor typo in message "symmmetric" -> symmetric
tbates [Wed, 19 Mar 2014 09:05:58 +0000 (09:05 +0000)]
minor typo in message "symmmetric" -> symmetric

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3159 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd info on using omxAssignFirstParameters with SetParameters
tbates [Wed, 19 Mar 2014 00:26:31 +0000 (00:26 +0000)]
Add info on using omxAssignFirstParameters with SetParameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3158 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdding how-to help, and help() link for new objectives
tbates [Wed, 19 Mar 2014 00:21:14 +0000 (00:21 +0000)]
Adding how-to help, and help() link for new objectives

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3157 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd mxOption for max stack depth
jpritikin [Tue, 18 Mar 2014 17:31:35 +0000 (17:31 +0000)]
Add mxOption for max stack depth

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3156 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd runtime verbose option to multigroup fitfunction
jpritikin [Tue, 18 Mar 2014 14:27:01 +0000 (14:27 +0000)]
Add runtime verbose option to multigroup fitfunction

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3155 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoComplain about ... args in mxComputeOnce
jpritikin [Tue, 18 Mar 2014 14:26:57 +0000 (14:26 +0000)]
Complain about ... args in mxComputeOnce

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3154 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSet version back to zero
jpritikin [Tue, 18 Mar 2014 14:26:53 +0000 (14:26 +0000)]
Set version back to zero

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3153 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCause gdb to report child's exit status
jpritikin [Tue, 18 Mar 2014 02:00:01 +0000 (02:00 +0000)]
Cause gdb to report child's exit status

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3152 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd dependencies to the C/C++ compile
jpritikin [Mon, 17 Mar 2014 21:23:04 +0000 (21:23 +0000)]
Add dependencies to the C/C++ compile

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3151 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agocran-install does not need to build the tar.gz blob
jpritikin [Mon, 17 Mar 2014 21:22:55 +0000 (21:22 +0000)]
cran-install does not need to build the tar.gz blob

Similar changes are needed for the NPSOL rules

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3150 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd protect to MxRList and simplify API
jpritikin [Sun, 16 Mar 2014 22:46:38 +0000 (22:46 +0000)]
Add protect to MxRList and simplify API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3149 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd some control parameters for Mike Neale (not hooked up yet)
jpritikin [Sat, 15 Mar 2014 15:40:17 +0000 (15:40 +0000)]
Add some control parameters for Mike Neale (not hooked up yet)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3148 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFactor out lots of calls to Rf_mkChar
jpritikin [Sat, 15 Mar 2014 12:24:04 +0000 (12:24 +0000)]
Factor out lots of calls to Rf_mkChar

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3147 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove "at iteration" from error
jpritikin [Sat, 15 Mar 2014 12:24:02 +0000 (12:24 +0000)]
Remove "at iteration" from error

+ Otherwise it is hard to write a test that matches against a known
error message

+ The user probably wants to know the parameter vector that caused the
error instead of the iteration number. This is available via
checkpointing.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3146 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMake elementwise algebra ops conformable for the scalar-matrix case
jpritikin [Sat, 15 Mar 2014 00:32:16 +0000 (00:32 +0000)]
Make elementwise algebra ops conformable for the scalar-matrix case

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3145 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoContinue with omxMatrix API simplification
jpritikin [Sat, 15 Mar 2014 00:32:12 +0000 (00:32 +0000)]
Continue with omxMatrix API simplification

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3144 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoResolved scope issue with isnan and isinf functions.
mhunter [Fri, 14 Mar 2014 15:00:42 +0000 (15:00 +0000)]
Resolved scope issue with isnan and isinf functions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3143 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoWLS Progress: no seg fault now, but still not good estimates and really bad standard...
mhunter [Fri, 14 Mar 2014 03:55:16 +0000 (03:55 +0000)]
WLS Progress: no seg fault now, but still not good estimates and really bad standard errors.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3142 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRe-architect fitfunction derivatives API using Eigen
jpritikin [Thu, 13 Mar 2014 20:32:18 +0000 (20:32 +0000)]
Re-architect fitfunction derivatives API using Eigen

Why do we need another matrix algebra library? We already have two, that
is, omxMatrix (original) and Matrix (from CSOLNP). For IFA models with
many items, it is essential to perform a sparse matrix-vector product
(Hessian %*% gradient) in Newton-Raphson. I initially wrote bespoke code
for sparse matrix-vector product. This was working well. However, it
came to my attention that inverting the Hessian can also benefit from
sparse matrix algebra. Rather than re-invent the wheel, Eigen looks like
a promising implementation.

Additional changes:

+ Internal derivatives are no longer reported back to R. You need to use
mxComputeReportDeriv to request them. Report derivs by default seemed
like a bad idea if they are so big that we are using a sparse
representation.

+ MxComputeNumericDeriv got a verbose parameter to enable debugging at
runtime.

+ ifa-drm-wide.R is moved to the failing directory temporarily. This
commit does not optimize manipulation of the Hessian but uses a simple
dense representation. dsytrf/dsytri are used to invert the Hessian. This
doesn't scale, but the improved accuracy results in many fewer
Newton-Raphson iterations highlighting the poor accuracy of the replaced
code.

+ Eigen has a great debug mode that NaN initializes memory and does
bounds checking. With these tools to assist debugging, I decided to
never store the lower triangle of a Hessian.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3141 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd Eigen, next commit hooks it up
jpritikin [Thu, 13 Mar 2014 20:31:56 +0000 (20:31 +0000)]
Add Eigen, next commit hooks it up

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3140 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded error checking to state space expectations and checked the error checking with...
mhunter [Thu, 13 Mar 2014 18:01:42 +0000 (18:01 +0000)]
Added error checking to state space expectations and checked the error checking with a passing model using omxCheckError.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3139 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEnable R_NO_REMAP for a cleaner namespace
jpritikin [Wed, 12 Mar 2014 14:46:27 +0000 (14:46 +0000)]
Enable R_NO_REMAP for a cleaner namespace

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3138 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAnchor regex at beginning of path
jpritikin [Wed, 12 Mar 2014 14:46:18 +0000 (14:46 +0000)]
Anchor regex at beginning of path

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3137 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd check for algebra dimnames
jpritikin [Wed, 12 Mar 2014 14:46:16 +0000 (14:46 +0000)]
Add check for algebra dimnames

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3136 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't use R to calculate our algebra result matrix dimensions
jpritikin [Mon, 10 Mar 2014 01:36:48 +0000 (01:36 +0000)]
Don't use R to calculate our algebra result matrix dimensions

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3135 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoInitial compute protocol for the whole tree of dependencies
jpritikin [Mon, 10 Mar 2014 01:36:44 +0000 (01:36 +0000)]
Initial compute protocol for the whole tree of dependencies

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3134 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't rely on R to evaluate our algebra
jpritikin [Mon, 10 Mar 2014 01:36:39 +0000 (01:36 +0000)]
Don't rely on R to evaluate our algebra

Also, improve logging and remove confusing deadcode in the
initialization path.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3133 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove non-reproducable pointer addresses from logs
jpritikin [Sun, 9 Mar 2014 19:54:06 +0000 (19:54 +0000)]
Remove non-reproducable pointer addresses from logs

For those of us who would like to use diff to examine changes in log
output.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3132 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMore omxMatrix API cleanup
jpritikin [Sun, 9 Mar 2014 19:53:48 +0000 (19:53 +0000)]
More omxMatrix API cleanup

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3131 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove deadcode (dead after free.set fixes)
jpritikin [Sun, 9 Mar 2014 19:53:43 +0000 (19:53 +0000)]
Remove deadcode (dead after free.set fixes)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3130 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRearrange ComputeEM for SEM integration
jpritikin [Fri, 7 Mar 2014 19:03:07 +0000 (19:03 +0000)]
Rearrange ComputeEM for SEM integration

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3129 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorg code for latent distribution
jpritikin [Fri, 7 Mar 2014 19:03:00 +0000 (19:03 +0000)]
Reorg code for latent distribution

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3128 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd a 3rd string argument to omxExpectation computeFun "how"
jpritikin [Fri, 7 Mar 2014 19:02:56 +0000 (19:02 +0000)]
Add a 3rd string argument to omxExpectation computeFun "how"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3127 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPrepare to simplify omxMatrix API
jpritikin [Fri, 7 Mar 2014 19:02:52 +0000 (19:02 +0000)]
Prepare to simplify omxMatrix API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3126 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDoc mxFitFunctionMultigroup
jpritikin [Fri, 7 Mar 2014 19:02:51 +0000 (19:02 +0000)]
Doc mxFitFunctionMultigroup

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3125 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix various bugs in free.set variable groups
jpritikin [Fri, 7 Mar 2014 19:02:47 +0000 (19:02 +0000)]
Fix various bugs in free.set variable groups

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3124 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd tests for convergence speed
jpritikin [Thu, 6 Mar 2014 23:49:29 +0000 (23:49 +0000)]
Add tests for convergence speed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3123 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix uninitialized memory read in Ramsay1975
jpritikin [Thu, 6 Mar 2014 23:49:20 +0000 (23:49 +0000)]
Fix uninitialized memory read in Ramsay1975

I didn't research when I introduced this bug. The symptom was that the
path taken from starting values to the MLE differed randomly between
runs. Occasionally, runs exhibited slight differences in the MLE. This
was due to inconsistent parameter acceleration in ComputeEM.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3122 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSlightly optimize analytic latent distribution parameter Hessian (update test)
jpritikin [Thu, 6 Mar 2014 16:30:52 +0000 (16:30 +0000)]
Slightly optimize analytic latent distribution parameter Hessian (update test)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3121 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOptimize gradient/meat when no items parameters are free
jpritikin [Thu, 6 Mar 2014 13:55:01 +0000 (13:55 +0000)]
Optimize gradient/meat when no items parameters are free

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3120 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSlightly optimize analytic latent distribution parameter Hessian
jpritikin [Thu, 6 Mar 2014 13:55:00 +0000 (13:55 +0000)]
Slightly optimize analytic latent distribution parameter Hessian

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3119 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProgress on WLS: Fit function adjustments and data debugging.
mhunter [Thu, 6 Mar 2014 06:08:18 +0000 (06:08 +0000)]
Progress on WLS: Fit function adjustments and data debugging.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3118 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded helpful comment to Windows Makevars file.
mhunter [Thu, 6 Mar 2014 05:58:43 +0000 (05:58 +0000)]
Added helpful comment to Windows Makevars file.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3117 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProgress toward WLS: build frontend observed threshold variable indexing
mhunter [Thu, 6 Mar 2014 05:57:44 +0000 (05:57 +0000)]
Progress toward WLS: build frontend observed threshold variable indexing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3116 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoElementWISE multiplication etc
mhunter [Thu, 6 Mar 2014 02:17:33 +0000 (02:17 +0000)]
ElementWISE multiplication etc

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3115 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoModified State Space error checking to be more informative.
mhunter [Wed, 5 Mar 2014 21:46:52 +0000 (21:46 +0000)]
Modified State Space error checking to be more informative.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3114 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded failing model for vector=TRUE fitfunctions.
mhunter [Wed, 5 Mar 2014 15:41:04 +0000 (15:41 +0000)]
Added failing model for vector=TRUE fitfunctions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3113 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoChange backend initialization order
jpritikin [Wed, 5 Mar 2014 00:55:58 +0000 (00:55 +0000)]
Change backend initialization order

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3112 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdjust buildbot gdb script
jpritikin [Wed, 5 Mar 2014 00:55:50 +0000 (00:55 +0000)]
Adjust buildbot gdb script

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3111 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoD'oh, fix test for error in mxLog
jpritikin [Wed, 5 Mar 2014 00:55:42 +0000 (00:55 +0000)]
D'oh, fix test for error in mxLog

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3110 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSet up the usual gdb breakpoints automatically
jpritikin [Wed, 5 Mar 2014 00:55:38 +0000 (00:55 +0000)]
Set up the usual gdb breakpoints automatically

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3109 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCorrect matrix dimensions in test
jpritikin [Wed, 5 Mar 2014 00:55:35 +0000 (00:55 +0000)]
Correct matrix dimensions in test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3108 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix spectral norm for R 2.14
jpritikin [Wed, 5 Mar 2014 00:55:31 +0000 (00:55 +0000)]
Fix spectral norm for R 2.14

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3107 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAllow simultaneous computation of gradient and gradient covariance
jpritikin [Mon, 3 Mar 2014 18:12:00 +0000 (18:12 +0000)]
Allow simultaneous computation of gradient and gradient covariance

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3106 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdjust precision of close enough checks
jpritikin [Mon, 3 Mar 2014 18:11:57 +0000 (18:11 +0000)]
Adjust precision of close enough checks

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3105 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOptionally force a PD covariance matrix (not enabled)
jpritikin [Sun, 2 Mar 2014 22:22:42 +0000 (22:22 +0000)]
Optionally force a PD covariance matrix (not enabled)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3104 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSwitch verbose from a logical to an integer
jpritikin [Sun, 2 Mar 2014 22:22:37 +0000 (22:22 +0000)]
Switch verbose from a logical to an integer

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3103 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRevert "Entertain a sample covariance formula"
jpritikin [Sun, 2 Mar 2014 22:22:34 +0000 (22:22 +0000)]
Revert "Entertain a sample covariance formula"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3102 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEntertain a sample covariance formula
jpritikin [Sun, 2 Mar 2014 22:22:25 +0000 (22:22 +0000)]
Entertain a sample covariance formula

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3101 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorg for latent distribution parameter equal constraints
jpritikin [Sun, 2 Mar 2014 22:22:19 +0000 (22:22 +0000)]
Reorg for latent distribution parameter equal constraints

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3100 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFactor out code to force a matrix to be positive semi-definite
jpritikin [Sun, 2 Mar 2014 19:18:48 +0000 (19:18 +0000)]
Factor out code to force a matrix to be positive semi-definite

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3099 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't throw an exception from within a critical section
jpritikin [Sun, 2 Mar 2014 19:18:46 +0000 (19:18 +0000)]
Don't throw an exception from within a critical section

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3098 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix test for mxComputeOnce API change
jpritikin [Sun, 2 Mar 2014 19:18:42 +0000 (19:18 +0000)]
Fix test for mxComputeOnce API change

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3097 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoLimit retries for logging
jpritikin [Sun, 2 Mar 2014 19:18:38 +0000 (19:18 +0000)]
Limit retries for logging

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3096 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix buildbot test failure
jpritikin [Sat, 1 Mar 2014 00:48:22 +0000 (00:48 +0000)]
Fix buildbot test failure

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3095 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove mxComputeOnce, mxComputeEM APIs
jpritikin [Fri, 28 Feb 2014 22:15:58 +0000 (22:15 +0000)]
Improve mxComputeOnce, mxComputeEM APIs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3094 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUpdate references to mxFitFunctionAlgebra and correct dot multiplication explanation...
tbates [Fri, 28 Feb 2014 20:57:32 +0000 (20:57 +0000)]
Update references to mxFitFunctionAlgebra and correct dot multiplication explanation in mxAlgebra.Rd

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3093 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUse ... to force named arguments (part 2)
jpritikin [Thu, 27 Feb 2014 22:09:35 +0000 (22:09 +0000)]
Use ... to force named arguments (part 2)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3092 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUse ... to force named arguments
jpritikin [Thu, 27 Feb 2014 21:55:34 +0000 (21:55 +0000)]
Use ... to force named arguments

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3091 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRename EM fit functions to match DLR (1977) terminology
jpritikin [Thu, 27 Feb 2014 21:55:32 +0000 (21:55 +0000)]
Rename EM fit functions to match DLR (1977) terminology

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3090 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMove positive definite check from ComputeSE to ComputeEM
jpritikin [Thu, 27 Feb 2014 21:42:55 +0000 (21:42 +0000)]
Move positive definite check from ComputeSE to ComputeEM

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3089 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoLots of work on SEM
jpritikin [Thu, 27 Feb 2014 21:42:48 +0000 (21:42 +0000)]
Lots of work on SEM

+ Support for latent parameters
+ Various simulation studies
+ Lots of code reorg

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3088 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove diagnostics
jpritikin [Thu, 27 Feb 2014 21:42:30 +0000 (21:42 +0000)]
Improve diagnostics

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3087 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove some conformability checks by showing the dimension mismatch
jpritikin [Wed, 26 Feb 2014 15:50:20 +0000 (15:50 +0000)]
Improve some conformability checks by showing the dimension mismatch

Actually this error check might be deadcode if we catch
conformability problems at the R level. I'm not sure.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3086 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAlways report @output$fit but don't report @output$minimum unless it is
jpritikin [Thu, 20 Feb 2014 21:35:05 +0000 (21:35 +0000)]
Always report @output$fit but don't report @output$minimum unless it is

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3085 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProperly ignore items with no free parameters
jpritikin [Wed, 19 Feb 2014 18:32:39 +0000 (18:32 +0000)]
Properly ignore items with no free parameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3084 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProhibit rows with no information for some factor
jpritikin [Wed, 19 Feb 2014 18:32:39 +0000 (18:32 +0000)]
Prohibit rows with no information for some factor

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3083 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoState Space changes: 1 Add ability to use inputs, 2 add error checking, 3 update...
mhunter [Tue, 18 Feb 2014 06:27:40 +0000 (06:27 +0000)]
State Space changes: 1 Add ability to use inputs, 2 add error checking, 3 update documentation.  WLS Changes: trying some debugging.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3082 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFixed typos in state space man page.
mhunter [Mon, 17 Feb 2014 21:26:20 +0000 (21:26 +0000)]
Fixed typos in state space man page.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3081 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRename ComputeEstimatedHessian to ComputeNumericDeriv
jpritikin [Sun, 16 Feb 2014 14:09:00 +0000 (14:09 +0000)]
Rename ComputeEstimatedHessian to ComputeNumericDeriv

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3080 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPrevent export of some internal classes
jpritikin [Fri, 14 Feb 2014 16:09:04 +0000 (16:09 +0000)]
Prevent export of some internal classes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3079 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDocument optimizers
jpritikin [Fri, 14 Feb 2014 16:08:58 +0000 (16:08 +0000)]
Document optimizers

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3078 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemoved mxConstraint from state space example, using parameter label equal to result...
mhunter [Thu, 13 Feb 2014 21:09:22 +0000 (21:09 +0000)]
Removed mxConstraint from state space example, using parameter label equal to result of mxAlgebra instead.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3077 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRevert "Rename classes not intended for export"
jpritikin [Thu, 13 Feb 2014 15:03:53 +0000 (15:03 +0000)]
Revert "Rename classes not intended for export"

This reverts commit 9bfd22030128fc4dab7eadf68075523329779741.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3076 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRename classes not intended for export
jpritikin [Thu, 13 Feb 2014 14:04:45 +0000 (14:04 +0000)]
Rename classes not intended for export

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3075 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd documentation
jpritikin [Thu, 13 Feb 2014 00:53:28 +0000 (00:53 +0000)]
Add documentation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3074 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix broken test
jpritikin [Wed, 12 Feb 2014 01:12:23 +0000 (01:12 +0000)]
Fix broken test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3073 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMake debug output contingent of a debugInternal flag
jpritikin [Mon, 10 Feb 2014 13:12:29 +0000 (13:12 +0000)]
Make debug output contingent of a debugInternal flag

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3072 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMove BA81 expectation output/debug stuff to @output and @debug slots
jpritikin [Mon, 10 Feb 2014 13:12:24 +0000 (13:12 +0000)]
Move BA81 expectation output/debug stuff to @output and @debug slots

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3071 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix possible uninitialized memory read
jpritikin [Mon, 10 Feb 2014 13:12:18 +0000 (13:12 +0000)]
Fix possible uninitialized memory read

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3070 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUsing the name "stderr" with #pragma omp critical can cause conflicts when building...
rkirkpatrick [Thu, 6 Feb 2014 22:10:15 +0000 (22:10 +0000)]
Using the name "stderr" with #pragma omp critical can cause conflicts when building multithread binaries under Windows.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3068 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix jumbled array index in sandwich
jpritikin [Sun, 2 Feb 2014 18:58:30 +0000 (18:58 +0000)]
Fix jumbled array index in sandwich

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3067 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix sandwich for two-tier models
jpritikin [Sat, 1 Feb 2014 03:51:01 +0000 (03:51 +0000)]
Fix sandwich for two-tier models

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3066 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1