openmx:openmx.git
4 years agoOMX_STATIC_ARRAY_SIZE
jpritikin [Sat, 13 Apr 2013 18:21:20 +0000 (18:21 +0000)]
OMX_STATIC_ARRAY_SIZE

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2462 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove omxInitEmptyExpectation; switch to C allocator
jpritikin [Sat, 13 Apr 2013 18:21:19 +0000 (18:21 +0000)]
Remove omxInitEmptyExpectation; switch to C allocator

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2461 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoC-side support for submodels
jpritikin [Sat, 13 Apr 2013 18:21:17 +0000 (18:21 +0000)]
C-side support for submodels

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2460 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd OMXZERO macro
jpritikin [Sat, 13 Apr 2013 18:21:15 +0000 (18:21 +0000)]
Add OMXZERO macro

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2459 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove failing tests to failing directory
jpritikin [Fri, 12 Apr 2013 23:46:36 +0000 (23:46 +0000)]
Move failing tests to failing directory

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2458 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd deps on MASS and mvtnorm
jpritikin [Fri, 12 Apr 2013 14:25:08 +0000 (14:25 +0000)]
Add deps on MASS and mvtnorm

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2457 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove lots of UNPROTECTs
jpritikin [Fri, 5 Apr 2013 18:20:43 +0000 (18:20 +0000)]
Remove lots of UNPROTECTs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2456 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRefactor allocation of omxAlgebra.args
jpritikin [Fri, 5 Apr 2013 18:20:39 +0000 (18:20 +0000)]
Refactor allocation of omxAlgebra.args

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2455 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFinal returns ought to support matrices (?)
jpritikin [Fri, 5 Apr 2013 18:20:35 +0000 (18:20 +0000)]
Final returns ought to support matrices (?)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2454 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAvoid initial useless fit computation
jpritikin [Fri, 5 Apr 2013 18:20:32 +0000 (18:20 +0000)]
Avoid initial useless fit computation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2453 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRefrain from duplicating the model unless required by the fitfunction
jpritikin [Fri, 5 Apr 2013 18:20:28 +0000 (18:20 +0000)]
Refrain from duplicating the model unless required by the fitfunction

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2452 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoStore the associated R SEXP in omxMatrix instead of the localdata flag
jpritikin [Fri, 5 Apr 2013 18:20:23 +0000 (18:20 +0000)]
Store the associated R SEXP in omxMatrix instead of the localdata flag

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2451 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDeadcode removal
jpritikin [Fri, 5 Apr 2013 18:20:19 +0000 (18:20 +0000)]
Deadcode removal

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2450 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAutomatically balance PROTECT/UNPROTECT
jpritikin [Fri, 5 Apr 2013 18:20:16 +0000 (18:20 +0000)]
Automatically balance PROTECT/UNPROTECT

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2449 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorder initialization so free parameters are available for expectations
jpritikin [Fri, 5 Apr 2013 18:20:12 +0000 (18:20 +0000)]
Reorder initialization so free parameters are available for expectations

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2448 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoInitialize freeVarList and numFreeParam together
jpritikin [Fri, 5 Apr 2013 18:20:09 +0000 (18:20 +0000)]
Initialize freeVarList and numFreeParam together

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2447 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename omxNewMatrixFromMxIndex to omxMatrixLookupFromState1
jpritikin [Fri, 5 Apr 2013 18:20:05 +0000 (18:20 +0000)]
Rename omxNewMatrixFromMxIndex to omxMatrixLookupFromState1

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2446 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename omxNewDataFromMxDataPtr to omxDataLookupFromState
jpritikin [Fri, 5 Apr 2013 18:20:00 +0000 (18:20 +0000)]
Rename omxNewDataFromMxDataPtr to omxDataLookupFromState

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2445 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMxBaseExpectation submodels and container needs to be optional
jpritikin [Thu, 4 Apr 2013 04:44:36 +0000 (04:44 +0000)]
MxBaseExpectation submodels and container needs to be optional

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2444 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd missing mvtnorm dependency
jpritikin [Thu, 4 Apr 2013 04:44:32 +0000 (04:44 +0000)]
Add missing mvtnorm dependency

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2443 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename omxNewMatrixFromIndexSlot to omxNewMatrixFromSlot
jpritikin [Sat, 30 Mar 2013 19:23:06 +0000 (19:23 +0000)]
Rename omxNewMatrixFromIndexSlot to omxNewMatrixFromSlot

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2442 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove deadcode
jpritikin [Sat, 30 Mar 2013 19:23:04 +0000 (19:23 +0000)]
Remove deadcode

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2441 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTeach MxExpectation to store its relationship in the model tree
jpritikin [Sat, 30 Mar 2013 02:18:07 +0000 (02:18 +0000)]
Teach MxExpectation to store its relationship in the model tree

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2440 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove @info from MxBaseExpectation (it moved to MxBaseFitFunction)
jpritikin [Sat, 30 Mar 2013 02:18:02 +0000 (02:18 +0000)]
Remove @info from MxBaseExpectation (it moved to MxBaseFitFunction)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2439 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoNote license terms on code copied from R
jpritikin [Sat, 30 Mar 2013 02:17:57 +0000 (02:17 +0000)]
Note license terms on code copied from R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2438 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTidy fitMatrix setup
jpritikin [Fri, 29 Mar 2013 15:58:17 +0000 (15:58 +0000)]
Tidy fitMatrix setup

+ globalState fields are already initialized to 0

+ The use of isNull implies fitfunction != NULL always

+ Hide this small code in a function just makes execution harder to read

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2437 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReindent, whitespace only
jpritikin [Thu, 28 Mar 2013 12:40:05 +0000 (12:40 +0000)]
Reindent, whitespace only

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2436 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUse consistent function names
jpritikin [Wed, 27 Mar 2013 15:58:03 +0000 (15:58 +0000)]
Use consistent function names

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2435 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix broken error message & add test
jpritikin [Tue, 26 Mar 2013 19:35:09 +0000 (19:35 +0000)]
Fix broken error message & add test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2434 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd default A,S,F matrix names for mxExpectationRAM
jpritikin [Tue, 26 Mar 2013 19:35:07 +0000 (19:35 +0000)]
Add default A,S,F matrix names for mxExpectationRAM

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2433 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove orphaned, no-longer-accurate comment
jpritikin [Tue, 26 Mar 2013 19:35:05 +0000 (19:35 +0000)]
Remove orphaned, no-longer-accurate comment

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2432 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove unreachable code (& comment)
jpritikin [Tue, 26 Mar 2013 18:30:58 +0000 (18:30 +0000)]
Remove unreachable code (& comment)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2431 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReindent, whitespace only
jpritikin [Tue, 26 Mar 2013 18:30:56 +0000 (18:30 +0000)]
Reindent, whitespace only

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2430 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoProcess submodels concurrently with manifest & latent variables (early)
jpritikin [Sat, 23 Mar 2013 21:33:48 +0000 (21:33 +0000)]
Process submodels concurrently with manifest & latent variables (early)

In hierarchical container models, mxPath can refer to manifests and
latents within submodels. Therefore, submodels need to be added to
the mxModel prior to mxPath processing.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2429 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoNo longer need to evaluate match.call
jpritikin [Sat, 23 Mar 2013 21:33:46 +0000 (21:33 +0000)]
No longer need to evaluate match.call

Due to recent change "Simplify error reporting of unrecognized arguments
to mxModel"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2428 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSimplify error reporting of unrecognized arguments to mxModel
jpritikin [Sat, 23 Mar 2013 17:33:47 +0000 (17:33 +0000)]
Simplify error reporting of unrecognized arguments to mxModel

+ Instead of printing exactly what is indigestible, we just deparse the
value. This makes it a little more difficult for users to identify what
went wrong when they pass gibberish into mxModel. For example:

Old behavior:

  Error: Cannot add the following item(s) into the model: 'rpf.drm()'

New behavior:

  Error: Cannot add the following item(s) into the model: '<S4 object of class structure("rpf.1dim.drm", package = "rpf")>'

+ The internal code becames simpler and easier to maintain. That is
the main motivation for this change. I need to make another change
that is vastly simplified by this change.

+ There could be a performance benefit. I did not test this, but it
is vaguely plausible. c(first, func.call[['...']]) might take a long
time to evaluate if there are 1000s of arguments.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2427 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoNo need to install rox, move it to dev-only dir
jpritikin [Sat, 23 Mar 2013 17:33:46 +0000 (17:33 +0000)]
No need to install rox, move it to dev-only dir

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2426 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCentralize definitions of generic class unions
jpritikin [Sat, 23 Mar 2013 17:33:44 +0000 (17:33 +0000)]
Centralize definitions of generic class unions

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2425 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd preliminary helper functions for calculating weight matrices in weighted least...
mhunter [Sat, 23 Mar 2013 02:27:55 +0000 (02:27 +0000)]
Add preliminary helper functions for calculating weight matrices in weighted least squares.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2424 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out interpretation of mxPath's connect argument
jpritikin [Sat, 16 Mar 2013 17:32:35 +0000 (17:32 +0000)]
Factor out interpretation of mxPath's connect argument

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2423 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMark MxLISRELModel as wholely unimplemented
jpritikin [Sat, 16 Mar 2013 17:13:34 +0000 (17:13 +0000)]
Mark MxLISRELModel as wholely unimplemented

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2422 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove cut & pasted deadcode from MxLISRELModel.R
jpritikin [Sat, 16 Mar 2013 16:37:49 +0000 (16:37 +0000)]
Remove cut & pasted deadcode from MxLISRELModel.R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2421 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove debug code
jpritikin [Sat, 16 Mar 2013 16:27:41 +0000 (16:27 +0000)]
Remove debug code

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2420 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAutomatically set up source directory for gdb
jpritikin [Fri, 15 Mar 2013 18:13:41 +0000 (18:13 +0000)]
Automatically set up source directory for gdb

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2419 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove encapsulation and remove deadcode
jpritikin [Fri, 15 Mar 2013 18:13:38 +0000 (18:13 +0000)]
Improve encapsulation and remove deadcode

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2418 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename omxFastRAMInverse and move to omxMatrix
jpritikin [Fri, 15 Mar 2013 18:13:37 +0000 (18:13 +0000)]
Rename omxFastRAMInverse and move to omxMatrix

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2417 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove commented PPML code from LISRELExpectation
jpritikin [Fri, 15 Mar 2013 18:13:35 +0000 (18:13 +0000)]
Remove commented PPML code from LISRELExpectation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2416 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReindent, whitespace only change
jpritikin [Fri, 15 Mar 2013 18:13:33 +0000 (18:13 +0000)]
Reindent, whitespace only change

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2415 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPPML Update: Largely rewritten PPML module with test permutor and new suite of test...
dhackett [Wed, 13 Mar 2013 23:10:28 +0000 (23:10 +0000)]
PPML Update: Largely rewritten PPML module with test permutor and new suite of test cases.  Functional with the exception of certain cases (optimized numerical solutions to models with data specified in covariance matrix plus means format).  Non-functional cases should be caught by the module's filter and allowed to run as normal.

Known Issues:
-Two of the test cases do not pass.  One of the failures is possibly due to issues with the conversion from Objectives to Fits/Expectations.
-Tests occasionally find questionable solutions, with very low (negative) Minus2LL values, lower than the minimum found by OpenMx.  Allowing the optimizer to try to improve on these questionable solutions throws an error (Expected covariance matrix is non-positive definite).

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2414 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRe-checked in WLS fit function, formerly objecitve. I'm not saying it works, but...
mhunter [Fri, 8 Mar 2013 23:09:34 +0000 (23:09 +0000)]
Re-checked in WLS fit function, formerly objecitve.  I'm not saying it works, but I am saying it doesn't break anything.  It's a starting point.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2413 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agofix insertMeansPathRAM to catch arrows=2
tbates [Sun, 3 Mar 2013 22:46:21 +0000 (22:46 +0000)]
fix insertMeansPathRAM to catch arrows=2

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2412 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCope with Windows style stringification of inf
jpritikin [Sun, 3 Mar 2013 22:30:22 +0000 (22:30 +0000)]
Cope with Windows style stringification of inf

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2411 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRun gctorture within gdb so we can get a stack trace
jpritikin [Sun, 3 Mar 2013 11:40:46 +0000 (11:40 +0000)]
Run gctorture within gdb so we can get a stack trace

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2410 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agominor fix to insertMeansPathRAM() 1. catch arrows != 1 in means paths; 2. reword...
tbates [Sun, 3 Mar 2013 00:55:07 +0000 (00:55 +0000)]
minor fix to insertMeansPathRAM() 1. catch arrows != 1 in means paths; 2. reword error

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2409 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRename mxRObjective and mxRowObjective
jpritikin [Fri, 1 Mar 2013 21:57:42 +0000 (21:57 +0000)]
Rename mxRObjective and mxRowObjective

perl -pi -e 's/mxRObjective/mxFitFunctionR/g' *.R
perl -pi -e 's/mxRowObjective/mxFitFunctionRow/g' *.R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2408 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Initialize freeVarList and numFreeParam together"
jpritikin [Fri, 1 Mar 2013 21:26:14 +0000 (21:26 +0000)]
Revert "Initialize freeVarList and numFreeParam together"

This reverts commit 170239b20d3c4877c1542c6c36da0d3db5f07774.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2407 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Reorder initialization so free parameters are available for expectations"
jpritikin [Fri, 1 Mar 2013 21:26:13 +0000 (21:26 +0000)]
Revert "Reorder initialization so free parameters are available for expectations"

This reverts commit 3c1c75b2c8986d9580b483e23e5b59b8c5a82a9f.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2406 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Automatically balance PROTECT/UNPROTECT"
jpritikin [Fri, 1 Mar 2013 21:26:13 +0000 (21:26 +0000)]
Revert "Automatically balance PROTECT/UNPROTECT"

This reverts commit 9bb94f37ea8f771c78da6aa1baa6b4e8562ebfa6.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2405 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Deadcode removal"
jpritikin [Fri, 1 Mar 2013 21:26:12 +0000 (21:26 +0000)]
Revert "Deadcode removal"

This reverts commit 3a2cd4e16405ab2d2a6ad5b10a13c1ea869e6ad6.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2404 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Store the associated R SEXP in omxMatrix instead of the localdata flag"
jpritikin [Fri, 1 Mar 2013 21:26:11 +0000 (21:26 +0000)]
Revert "Store the associated R SEXP in omxMatrix instead of the localdata flag"

This reverts commit a3dbe06d0495dc1a5591e48c87c8bc933bceed07.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2403 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRevert "Refrain from duplicating the model unless required by the fitfunction"
jpritikin [Fri, 1 Mar 2013 21:26:11 +0000 (21:26 +0000)]
Revert "Refrain from duplicating the model unless required by the fitfunction"

This reverts commit 320057054bc0dc40a9632143f63e0a0f99903a34.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2402 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRefrain from duplicating the model unless required by the fitfunction
jpritikin [Fri, 1 Mar 2013 21:22:14 +0000 (21:22 +0000)]
Refrain from duplicating the model unless required by the fitfunction

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2401 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoStore the associated R SEXP in omxMatrix instead of the localdata flag
jpritikin [Fri, 1 Mar 2013 21:22:13 +0000 (21:22 +0000)]
Store the associated R SEXP in omxMatrix instead of the localdata flag

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2400 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDeadcode removal
jpritikin [Fri, 1 Mar 2013 21:22:12 +0000 (21:22 +0000)]
Deadcode removal

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2399 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAutomatically balance PROTECT/UNPROTECT
jpritikin [Fri, 1 Mar 2013 21:22:12 +0000 (21:22 +0000)]
Automatically balance PROTECT/UNPROTECT

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2398 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReorder initialization so free parameters are available for expectations
jpritikin [Fri, 1 Mar 2013 21:22:11 +0000 (21:22 +0000)]
Reorder initialization so free parameters are available for expectations

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2397 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoInitialize freeVarList and numFreeParam together
jpritikin [Fri, 1 Mar 2013 21:22:11 +0000 (21:22 +0000)]
Initialize freeVarList and numFreeParam together

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2396 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSelect a few tests for gctorture
jpritikin [Fri, 1 Mar 2013 21:22:10 +0000 (21:22 +0000)]
Select a few tests for gctorture

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2395 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoConvert mxFIMLObjective, mxMLObjective, and mxRAMObjective
jpritikin [Fri, 1 Mar 2013 18:31:12 +0000 (18:31 +0000)]
Convert mxFIMLObjective, mxMLObjective, and mxRAMObjective

    perl -pi -e 's/mxFIMLObjective/mxFitFunctionML(),mxExpectationNormal/g' *.R
    perl -pi -e 's/mxMLObjective/mxFitFunctionML(),mxExpectationNormal/g' *.R
    perl -pi -e 's/mxRAMObjective/mxFitFunctionML(),mxExpectationRAM/g' *.R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2394 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoManually convert test that use vector=TRUE to mxFitFunctionML
jpritikin [Fri, 1 Mar 2013 18:31:09 +0000 (18:31 +0000)]
Manually convert test that use vector=TRUE to mxFitFunctionML

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2393 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoEdited suggestion for solution when mxData are cov/cor and not symmetric.
mhunter [Fri, 1 Mar 2013 18:17:01 +0000 (18:17 +0000)]
Edited suggestion for solution when mxData are cov/cor and not symmetric.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2392 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTry hardcoding data
jpritikin [Fri, 1 Mar 2013 18:06:01 +0000 (18:06 +0000)]
Try hardcoding data

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2391 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdded suggestion for solution when mxData are cov/cor and not symmetric.
mhunter [Fri, 1 Mar 2013 18:00:53 +0000 (18:00 +0000)]
Added suggestion for solution when mxData are cov/cor and not symmetric.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2390 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdated copyright to 2013 for R/ demo/ models/passing and src/ folders, and also...
mhunter [Fri, 1 Mar 2013 17:32:54 +0000 (17:32 +0000)]
Updated copyright to 2013 for R/ demo/ models/passing and src/ folders, and also the LICENSE file.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2389 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove the slowest models to models/nightly
jpritikin [Mon, 25 Feb 2013 19:31:18 +0000 (19:31 +0000)]
Move the slowest models to models/nightly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2388 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAvoid writing to the filesystem in tests
jpritikin [Mon, 25 Feb 2013 19:26:20 +0000 (19:26 +0000)]
Avoid writing to the filesystem in tests

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2387 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd back test into nightly
jpritikin [Mon, 25 Feb 2013 03:44:13 +0000 (03:44 +0000)]
Add back test into nightly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2386 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoOutput test runtimes to CSV instead of to console
jpritikin [Mon, 25 Feb 2013 03:43:10 +0000 (03:43 +0000)]
Output test runtimes to CSV instead of to console

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2385 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReturn exit status properly
jpritikin [Sun, 24 Feb 2013 20:13:09 +0000 (20:13 +0000)]
Return exit status properly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2384 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMerge testNightly with testModels
jpritikin [Sun, 24 Feb 2013 20:06:41 +0000 (20:06 +0000)]
Merge testNightly with testModels

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2383 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoupdated to match new error (which now reports the test that failed in more detail
tbates [Sun, 24 Feb 2013 11:27:09 +0000 (11:27 +0000)]
updated to match new error (which now reports the test that failed in more detail
"1 or more elements of eigen(covMatrix)$values  <= 0"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2382 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdding call to all.equal() to check when asymmetry is due to rounding.
tbates [Sun, 24 Feb 2013 10:40:03 +0000 (10:40 +0000)]
Adding call to all.equal() to check when asymmetry is due to rounding.
Correcting suggestion for fixing this by reflecting upper tri into lower tri

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2381 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix capitalization inconsistency
jpritikin [Sun, 24 Feb 2013 03:19:20 +0000 (03:19 +0000)]
Fix capitalization inconsistency

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2380 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImproved mxData error messages: helpful suggestion when symmetry is broken by minor...
tbates [Sun, 24 Feb 2013 02:29:38 +0000 (02:29 +0000)]
Improved mxData error messages:  helpful suggestion when symmetry is broken by minor differences, and eigen() when not pos definite.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2379 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdated jointFactorModelsTest.R with hardcoded data
restabrook [Sun, 24 Feb 2013 00:16:49 +0000 (00:16 +0000)]
Updated jointFactorModelsTest.R with hardcoded data

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2378 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMake insensitive to random number generator precision
jpritikin [Fri, 22 Feb 2013 19:07:34 +0000 (19:07 +0000)]
Make insensitive to random number generator precision

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2377 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove failing tests to failing directory
jpritikin [Thu, 21 Feb 2013 19:33:28 +0000 (19:33 +0000)]
Move failing tests to failing directory

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2376 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoChanged state space exp and FIML to only compute inverse cov once per row of data
mhunter [Fri, 15 Feb 2013 19:03:58 +0000 (19:03 +0000)]
Changed state space exp and FIML to only compute inverse cov once per row of data

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2375 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoEdited State Space Expectation so that the expected means vector is only computed...
mhunter [Fri, 15 Feb 2013 06:13:52 +0000 (06:13 +0000)]
Edited State Space Expectation so that the expected means vector is only computed ONCE per row, not twice.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2374 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMoved State Space example from models/failing to models/passing
mhunter [Fri, 15 Feb 2013 01:15:21 +0000 (01:15 +0000)]
Moved State Space example from models/failing to models/passing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2373 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCheck in WLS for Continuous variables
mhunter [Tue, 12 Feb 2013 16:23:27 +0000 (16:23 +0000)]
Check in WLS for Continuous variables

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2372 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCompute fit and gradients at the same time
jpritikin [Sat, 2 Feb 2013 19:47:11 +0000 (19:47 +0000)]
Compute fit and gradients at the same time

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2371 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove obsolete CPU argument
jpritikin [Sat, 2 Feb 2013 19:47:07 +0000 (19:47 +0000)]
Remove obsolete CPU argument

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2370 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdded cov2cor and chol to supported functions. Noted how OpenMx implements diag(...
tbates [Sat, 26 Jan 2013 21:47:11 +0000 (21:47 +0000)]
Added cov2cor and chol to supported functions. Noted how OpenMx implements diag() functionality in safer functions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2369 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdate omxGetParameters.Rd
tbates [Sat, 19 Jan 2013 21:16:01 +0000 (21:16 +0000)]
Update omxGetParameters.Rd
1. "Return a vector of the free parameters" -> "vector of the chosen"
Update MxConstraint.R
1. Added a ... argument
2. Check that this is empty (as in other OpenMx fns)
3. Report use of operators outside legal set (<,>,==) as cause of ...  error

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2368 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMove script out of the Makefile to avoid quoting clashes
jpritikin [Fri, 18 Jan 2013 16:53:55 +0000 (16:53 +0000)]
Move script out of the Makefile to avoid quoting clashes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2367 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCope with old versions of subversion
jpritikin [Fri, 18 Jan 2013 16:46:04 +0000 (16:46 +0000)]
Cope with old versions of subversion

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2366 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd rule to create R_LIBS_USER directory
jpritikin [Fri, 18 Jan 2013 16:46:03 +0000 (16:46 +0000)]
Add rule to create R_LIBS_USER directory

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2365 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDon't run roxygen2 by default
jpritikin [Fri, 11 Jan 2013 16:08:01 +0000 (16:08 +0000)]
Don't run roxygen2 by default

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2364 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdated checkNamespaceHelper(model, topmodel, namespace)
tbates [Thu, 10 Jan 2013 16:22:16 +0000 (16:22 +0000)]
Updated checkNamespaceHelper(model, topmodel, namespace)

* Following on from  http://openmx.psyc.virginia.edu/thread/735, updated error message to be more like a highway barrier.
* Fixed side-effect in "NameParameterOverlap.R" so that it now checks for the new-style error

Now reads:
mxRun(model)
Error: In model 'model' the following are both named entities and free parameters: 'foo'
If you are trying to set a path using an mxAlgebra, then refer to the Algebra with square-bracket notation.
i.,e, instead of labels=" 'foo' " use: labels=" 'foo' [1,1]"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2363 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1