openmx:openmx.git
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

4 years agoPrint error before printing values
jpritikin [Wed, 9 Jan 2013 15:39:10 +0000 (15:39 +0000)]
Print error before printing values

If your data is of length 500+ then you cannot see the error. Maybe we
should be using testthat instead of writing our own unit test library.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2362 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoExpectations don't have setFinalReturns
jpritikin [Tue, 8 Jan 2013 23:05:15 +0000 (23:05 +0000)]
Expectations don't have setFinalReturns

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2361 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdate mxCompare() to handle missing comparison parameter
tbates [Tue, 8 Jan 2013 12:26:32 +0000 (12:26 +0000)]
Update mxCompare() to handle missing comparison parameter
Now makes an empty compareSummaries list, which showFitStatistics() can correctly ignore.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2360 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoupdate showFitStatistics() to handle empty compareSummaries list
tbates [Tue, 8 Jan 2013 12:22:14 +0000 (12:22 +0000)]
update showFitStatistics() to handle empty compareSummaries list

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2359 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoIncorporate correction from Steve
jpritikin [Mon, 7 Jan 2013 14:02:49 +0000 (14:02 +0000)]
Incorporate correction from Steve

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2358 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix compiler warning
jpritikin [Mon, 7 Jan 2013 14:02:47 +0000 (14:02 +0000)]
Fix compiler warning

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2357 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd 'make torture' for gctorture
jpritikin [Fri, 4 Jan 2013 02:02:14 +0000 (02:02 +0000)]
Add 'make torture' for gctorture

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2356 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoImprove friendlyStringToLogical
jpritikin [Tue, 1 Jan 2013 11:12:27 +0000 (11:12 +0000)]
Improve friendlyStringToLogical

+ Add test

+ Only accept yes/no/1/0. Warn otherwise. If we are not strict now then
it becomes more difficult to add other options like "halfway" or "only
at end".

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2355 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoSome documentation on the internal architecture
jpritikin [Tue, 1 Jan 2013 02:35:29 +0000 (02:35 +0000)]
Some documentation on the internal architecture

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2354 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd regression test for RFitFunction and fix related bugs
jpritikin [Tue, 1 Jan 2013 02:35:27 +0000 (02:35 +0000)]
Add regression test for RFitFunction and fix related bugs

Also document how to report errors during
omxInitialMatrixAlgebraCompute. Note how the previous code pretended to
check for errors, but actually did not check. This is obfuscation,
technical debt, and unacceptable.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2353 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoShow warnings after running tests, by default
jpritikin [Tue, 1 Jan 2013 02:35:24 +0000 (02:35 +0000)]
Show warnings after running tests, by default

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2352 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAnalytic Gradients "1" should work as well as "Yes"
jpritikin [Tue, 1 Jan 2013 02:35:23 +0000 (02:35 +0000)]
Analytic Gradients "1" should work as well as "Yes"

I didn't try to discover where it was being set to "1"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2351 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTidy matchCaseInsensitive
jpritikin [Tue, 1 Jan 2013 02:35:21 +0000 (02:35 +0000)]
Tidy matchCaseInsensitive

Does it pain you to read t(5*t(m/5))? This is similar.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2350 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUpdated a comment in the example model, not that RAM returns standardized paths
tbates [Sun, 30 Dec 2012 20:03:47 +0000 (20:03 +0000)]
Updated a comment in the example model, not that RAM returns standardized paths
Also fixed some typos and clarified earlier example material

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2349 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdded comment to RAM model error, prompting user to view ?mxData when their model...
tbates [Sun, 30 Dec 2012 19:31:50 +0000 (19:31 +0000)]
Added comment to RAM model error, prompting user to view ?mxData when their model has no data
See ?mxData() to see how to add data to your model

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2348 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agojust a typo fix: "lifetype" --> "lifetime"
tbates [Sun, 30 Dec 2012 17:48:28 +0000 (17:48 +0000)]
just a typo fix: "lifetype" --> "lifetime"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2347 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReduce unnecessary data copying
jpritikin [Fri, 28 Dec 2012 20:14:34 +0000 (20:14 +0000)]
Reduce unnecessary data copying

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2346 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoPrevent the use of omxMatrix for factor data
jpritikin [Fri, 28 Dec 2012 20:10:28 +0000 (20:10 +0000)]
Prevent the use of omxMatrix for factor data

+ It is more efficient to store integer data as integers.

+ No internal code depends on this code path. Our test suite continues
to work. No documentation changes are needed.

+ MxThreshold.R:66 prevents the use of matrices in models that use
thresholds. There is no existing code affected by this change.

+ NA_REAL is not preserved when casting to integer. Instead of
NA_INTEGER, the result is (int)0.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2345 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReport error instead of SEGV
jpritikin [Fri, 28 Dec 2012 19:03:59 +0000 (19:03 +0000)]
Report error instead of SEGV

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2344 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUse appropriate unit test API
jpritikin [Fri, 28 Dec 2012 19:03:58 +0000 (19:03 +0000)]
Use appropriate unit test API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2343 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoUse the correct test for crazy numbers
jpritikin [Fri, 28 Dec 2012 18:41:48 +0000 (18:41 +0000)]
Use the correct test for crazy numbers

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2342 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out fit diagnostics into omxExamineFitOutput
jpritikin [Fri, 28 Dec 2012 18:29:57 +0000 (18:29 +0000)]
Factor out fit diagnostics into omxExamineFitOutput

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2341 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoExchange if/else and reindent for vastly improved clarity
jpritikin [Fri, 28 Dec 2012 18:29:55 +0000 (18:29 +0000)]
Exchange if/else and reindent for vastly improved clarity

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2340 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd varargs replacement for omxRaiseError
jpritikin [Fri, 28 Dec 2012 18:29:54 +0000 (18:29 +0000)]
Add varargs replacement for omxRaiseError

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2339 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoAdd infrastructure for optional matrices
jpritikin [Wed, 26 Dec 2012 14:32:03 +0000 (14:32 +0000)]
Add infrastructure for optional matrices

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2338 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoClarify the purpose of the openmp lock and improve the wrapper
jpritikin [Wed, 26 Dec 2012 14:32:02 +0000 (14:32 +0000)]
Clarify the purpose of the openmp lock and improve the wrapper

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2337 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix R_registerRoutines and R_init
jpritikin [Wed, 26 Dec 2012 14:32:00 +0000 (14:32 +0000)]
Fix R_registerRoutines and R_init

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2336 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove unused openmp lock
jpritikin [Wed, 26 Dec 2012 14:31:57 +0000 (14:31 +0000)]
Remove unused openmp lock

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2335 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoMake omxCheckCloseEnough compare missingness pattern too
jpritikin [Wed, 26 Dec 2012 14:31:55 +0000 (14:31 +0000)]
Make omxCheckCloseEnough compare missingness pattern too

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2334 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDoc rules should depend on rox
jpritikin [Wed, 26 Dec 2012 14:31:54 +0000 (14:31 +0000)]
Doc rules should depend on rox

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2333 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoComplain if any starting values are missing
jpritikin [Wed, 26 Dec 2012 14:31:53 +0000 (14:31 +0000)]
Complain if any starting values are missing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2332 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove duplicate openmp config option
jpritikin [Wed, 26 Dec 2012 14:31:50 +0000 (14:31 +0000)]
Remove duplicate openmp config option

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2331 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove confusing redundent condition
jpritikin [Sun, 23 Dec 2012 17:14:03 +0000 (17:14 +0000)]
Remove confusing redundent condition

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2330 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoCreate temp-files directory (used in some tests)
jpritikin [Sun, 23 Dec 2012 17:14:01 +0000 (17:14 +0000)]
Create temp-files directory (used in some tests)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2329 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoBugfix for ignoring Hessian calculation when fitfunction is missing.
mspiegel [Fri, 21 Dec 2012 20:55:31 +0000 (20:55 +0000)]
Bugfix for ignoring Hessian calculation when fitfunction is missing.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2328 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix uninitialised memory access in omxSelectRows & omxSelectCols
jpritikin [Wed, 19 Dec 2012 20:12:11 +0000 (20:12 +0000)]
Fix uninitialised memory access in omxSelectRows & omxSelectCols

Bug only affected non-square matrices

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2327 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove out-of-date comment
jpritikin [Wed, 19 Dec 2012 20:12:10 +0000 (20:12 +0000)]
Remove out-of-date comment

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2326 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTidy SymbolTable
jpritikin [Wed, 19 Dec 2012 11:23:11 +0000 (11:23 +0000)]
Tidy SymbolTable

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2325 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFactor out omxMatrix export to R
jpritikin [Mon, 17 Dec 2012 15:49:15 +0000 (15:49 +0000)]
Factor out omxMatrix export to R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2324 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove pointless Makefile acrobatics for Rd files
jpritikin [Mon, 17 Dec 2012 15:49:13 +0000 (15:49 +0000)]
Remove pointless Makefile acrobatics for Rd files

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2323 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoRemove deadcode
jpritikin [Fri, 14 Dec 2012 18:00:23 +0000 (18:00 +0000)]
Remove deadcode

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2322 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDelineate frontend/backend boundary (continued)
jpritikin [Fri, 14 Dec 2012 17:08:25 +0000 (17:08 +0000)]
Delineate frontend/backend boundary (continued)

Oops, forgot to test previous change

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2321 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDelineate frontend/backend boundary
jpritikin [Fri, 14 Dec 2012 17:04:19 +0000 (17:04 +0000)]
Delineate frontend/backend boundary

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2320 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFor state space expectation, reset initial state (x) and error cov (P) whenever start...
mhunter [Fri, 14 Dec 2012 13:56:32 +0000 (13:56 +0000)]
For state space expectation, reset initial state (x) and error cov (P) whenever starting back at row 0.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2319 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDocument dependency tracking system
jpritikin [Thu, 13 Dec 2012 21:34:52 +0000 (21:34 +0000)]
Document dependency tracking system

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2318 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoTrivial cleanups
jpritikin [Thu, 13 Dec 2012 14:46:37 +0000 (14:46 +0000)]
Trivial cleanups

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2317 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoNewline terminate debug message
jpritikin [Thu, 13 Dec 2012 14:36:08 +0000 (14:36 +0000)]
Newline terminate debug message

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2316 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDocument how to change CFLAGS
jpritikin [Tue, 11 Dec 2012 17:49:41 +0000 (17:49 +0000)]
Document how to change CFLAGS

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2315 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoReindent
jpritikin [Tue, 11 Dec 2012 17:49:40 +0000 (17:49 +0000)]
Reindent

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2314 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoFix indentation
jpritikin [Tue, 11 Dec 2012 14:17:16 +0000 (14:17 +0000)]
Fix indentation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2313 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoConfigure emacs intentation
jpritikin [Tue, 11 Dec 2012 14:17:14 +0000 (14:17 +0000)]
Configure emacs intentation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2312 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

4 years agoDon't expect all Expectations to have dataColumns and thresholds
jpritikin [Tue, 11 Dec 2012 13:24:53 +0000 (13:24 +0000)]
Don't expect all Expectations to have dataColumns and thresholds

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2311 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1