openmx:proteins-proteins-openmx.git
4 years agoFix remaining bugs (i hope) homer
Joshua Nathaniel Pritikin [Fri, 26 Apr 2013 13:52:36 +0000 (09:52 -0400)]
Fix remaining bugs (i hope)

4 years agosnapshot
Joshua Nathaniel Pritikin [Wed, 24 Apr 2013 02:24:27 +0000 (22:24 -0400)]
snapshot

4 years agoLeave fitType alone
Joshua Nathaniel Pritikin [Wed, 24 Apr 2013 02:19:00 +0000 (22:19 -0400)]
Leave fitType alone

4 years agoAdd omxGetFitOfExpectation
Joshua Nathaniel Pritikin [Wed, 24 Apr 2013 02:15:40 +0000 (22:15 -0400)]
Add omxGetFitOfExpectation

4 years agoIgnore extra algebras, for now
Joshua Nathaniel Pritikin [Wed, 24 Apr 2013 02:14:48 +0000 (22:14 -0400)]
Ignore extra algebras, for now

4 years agoStore freeVar deps in a std::vector (maybe unnecessary)
Joshua Nathaniel Pritikin [Tue, 23 Apr 2013 21:36:01 +0000 (17:36 -0400)]
Store freeVar deps in a std::vector (maybe unnecessary)

4 years agoAdd omxNewInternalFitFunction API
Joshua Nathaniel Pritikin [Tue, 23 Apr 2013 16:12:28 +0000 (12:12 -0400)]
Add omxNewInternalFitFunction API

4 years agoStore expectationList in std::vector
Joshua Nathaniel Pritikin [Tue, 23 Apr 2013 15:37:38 +0000 (11:37 -0400)]
Store expectationList in std::vector

4 years agoSplit fit function initialization similar to expectations
Joshua Nathaniel Pritikin [Tue, 23 Apr 2013 13:22:36 +0000 (09:22 -0400)]
Split fit function initialization similar to expectations

4 years agoStore algebraList in std::vector
Joshua Nathaniel Pritikin [Mon, 22 Apr 2013 19:56:54 +0000 (15:56 -0400)]
Store algebraList in std::vector

4 years agoMxFitFunctionMultigroup
Joshua Nathaniel Pritikin [Mon, 22 Apr 2013 14:35:04 +0000 (10:35 -0400)]
MxFitFunctionMultigroup

4 years agoMove processing of mxData keys
Joshua Nathaniel Pritikin [Mon, 22 Apr 2013 18:26:28 +0000 (14:26 -0400)]
Move processing of mxData keys

4 years agosnapshot
Joshua Nathaniel Pritikin [Sun, 21 Apr 2013 02:04:36 +0000 (22:04 -0400)]
snapshot

4 years agoStore foreignKeys in std::vector
Joshua Nathaniel Pritikin [Sat, 20 Apr 2013 16:22:19 +0000 (12:22 -0400)]
Store foreignKeys in std::vector

4 years ago1 level flattening working
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 19:07:54 +0000 (15:07 -0400)]
1 level flattening working

4 years agosnapshot
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 18:11:10 +0000 (14:11 -0400)]
snapshot

4 years agoSnapshot
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 18:24:14 +0000 (14:24 -0400)]
Snapshot

4 years agoReady to actually do the transformation
Joshua Nathaniel Pritikin [Wed, 10 Apr 2013 15:53:41 +0000 (11:53 -0400)]
Ready to actually do the transformation

4 years agoSnapshot
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 16:42:42 +0000 (12:42 -0400)]
Snapshot

4 years agoH matrices getting created
Joshua Nathaniel Pritikin [Mon, 25 Mar 2013 18:26:55 +0000 (14:26 -0400)]
H matrices getting created

4 years agoDocument potential code cleanup plan
Joshua Nathaniel Pritikin [Sun, 24 Mar 2013 18:26:11 +0000 (14:26 -0400)]
Document potential code cleanup plan

4 years agoStore dataList in std::vector
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 16:58:15 +0000 (12:58 -0400)]
Store dataList in std::vector

4 years agoInitialize fit functions after expectations
Joshua Nathaniel Pritikin [Fri, 19 Apr 2013 18:23:49 +0000 (14:23 -0400)]
Initialize fit functions after expectations

4 years agoEncapsulate encoding of omxMatrix.matrixNumber
Joshua Nathaniel Pritikin [Thu, 18 Apr 2013 19:21:43 +0000 (15:21 -0400)]
Encapsulate encoding of omxMatrix.matrixNumber

4 years agoStore matrixList as a std::vector
Joshua Nathaniel Pritikin [Wed, 17 Apr 2013 18:00:34 +0000 (14:00 -0400)]
Store matrixList as a std::vector

4 years agoStore freeVar locations in a std::vector
Joshua Nathaniel Pritikin [Wed, 17 Apr 2013 16:05:42 +0000 (12:05 -0400)]
Store freeVar locations in a std::vector

4 years agoSwitch to C++
Joshua Nathaniel Pritikin [Wed, 17 Apr 2013 13:20:49 +0000 (09:20 -0400)]
Switch to C++

4 years agoImprove omxData API
Joshua Nathaniel Pritikin [Sat, 20 Apr 2013 16:03:09 +0000 (12:03 -0400)]
Improve omxData API

4 years agoSimplify layout of omxData
jpritikin [Fri, 19 Apr 2013 22:45:29 +0000 (22:45 +0000)]
Simplify layout of omxData

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2475 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove unused fields from omxData
jpritikin [Fri, 19 Apr 2013 19:38:31 +0000 (19:38 +0000)]
Remove unused fields from omxData

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2474 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSimplify omxData API
jpritikin [Fri, 19 Apr 2013 17:14:22 +0000 (17:14 +0000)]
Simplify omxData API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2473 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAllocate omxData with Calloc
jpritikin [Fri, 19 Apr 2013 17:14:22 +0000 (17:14 +0000)]
Allocate omxData with Calloc

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2472 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSimplify management of omxData.type
jpritikin [Fri, 19 Apr 2013 17:14:21 +0000 (17:14 +0000)]
Simplify management of omxData.type

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2471 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMissed one of the errors in bivariate saturated models. Should be completely fixed...
mhunter [Fri, 19 Apr 2013 16:43:18 +0000 (16:43 +0000)]
Missed one of the errors in bivariate saturated models.  Should be completely fixed now.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2470 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years ago(Hopefully) fixed the error with the numerous bivariate saturated models. I believe...
mhunter [Fri, 19 Apr 2013 16:11:54 +0000 (16:11 +0000)]
(Hopefully) fixed the error with the numerous bivariate saturated models.  I believe it was a data generation problem with MASS::mvrnorm in which different operating systems returned the data with columns in different orders.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2469 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPrep for C++ (part 2)
jpritikin [Wed, 17 Apr 2013 15:37:14 +0000 (15:37 +0000)]
Prep for C++ (part 2)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2468 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPrep for C++ compilation
jpritikin [Wed, 17 Apr 2013 01:43:47 +0000 (01:43 +0000)]
Prep for C++ compilation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2467 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd userdata argument for sort helper (like qsort_r)
jpritikin [Wed, 17 Apr 2013 01:43:42 +0000 (01:43 +0000)]
Add userdata argument for sort helper (like qsort_r)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2466 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoExpectations only need 1 name
jpritikin [Tue, 16 Apr 2013 19:13:16 +0000 (19:13 +0000)]
Expectations only need 1 name

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2465 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFixed maximum number of dimensions bug so that only dimensions other than those ...
mneale [Tue, 16 Apr 2013 15:04:51 +0000 (15:04 +0000)]
Fixed maximum number of dimensions bug so that only dimensions other than those -inf to +inf are counted

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2464 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd API for internal expectations; remove redundent copy of rObj
jpritikin [Sat, 13 Apr 2013 18:21:23 +0000 (18:21 +0000)]
Add API for internal expectations; remove redundent copy of rObj

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2463 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

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