openmx:openmx.git
5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 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

5 years agoMore minor changes for state space expectation. The expectation and likelihood calcu...
mhunter [Tue, 11 Dec 2012 06:13:38 +0000 (06:13 +0000)]
More minor changes for state space expectation.  The expectation and likelihood calculations are now correct for the first pass through the data.  However, I need to make a processing adjustment for the subsequent passes.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2310 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoAdded setter/mutator method to state space expectation
mhunter [Tue, 11 Dec 2012 04:44:08 +0000 (04:44 +0000)]
Added setter/mutator method to state space expectation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2309 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoRemoved some of the debugging that I had added. Retrospectively, I deemed it unneces...
mhunter [Tue, 11 Dec 2012 01:47:06 +0000 (01:47 +0000)]
Removed some of the debugging that I had added.  Retrospectively, I deemed it unnecessary.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2308 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoImplement omxPrintData
jpritikin [Mon, 10 Dec 2012 21:55:33 +0000 (21:55 +0000)]
Implement omxPrintData

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2307 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoSanity check shape of FitFunction@expectation slot
jpritikin [Mon, 10 Dec 2012 19:13:29 +0000 (19:13 +0000)]
Sanity check shape of FitFunction@expectation slot

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2306 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoRemove (duplicate) unused parameter
jpritikin [Mon, 10 Dec 2012 19:13:27 +0000 (19:13 +0000)]
Remove (duplicate) unused parameter

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2305 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoMove table into the single place where it is used
jpritikin [Mon, 10 Dec 2012 15:04:16 +0000 (15:04 +0000)]
Move table into the single place where it is used

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2304 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoFix 'fitType' scope and reindent
jpritikin [Mon, 10 Dec 2012 15:04:15 +0000 (15:04 +0000)]
Fix 'fitType' scope and reindent

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2303 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoAdd sensible error if imxAddDependency is called with no sources
jpritikin [Mon, 10 Dec 2012 15:04:13 +0000 (15:04 +0000)]
Add sensible error if imxAddDependency is called with no sources

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2302 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoDebugging state space expectation. Corrected new debug flag in Makevars.win. Added...
mhunter [Sat, 8 Dec 2012 13:25:31 +0000 (13:25 +0000)]
Debugging state space expectation.  Corrected new debug flag in Makevars.win.  Added some debugging info to FIML.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2300 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoChecked in some WLS changes. Debugging state space expectation. Added a debug flag...
mhunter [Fri, 7 Dec 2012 20:10:45 +0000 (20:10 +0000)]
Checked in some WLS changes.  Debugging state space expectation.  Added a debug flag to Makevars.win.  Added some debugging to FIML.  Implemented omxDPOTRF and omxDPOTRI wrappers around BLAS functions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2299 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoRemove unused struct field
jpritikin [Fri, 7 Dec 2012 15:36:31 +0000 (15:36 +0000)]
Remove unused struct field

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2298 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoDid lots of debugging for state space expectation. One odd problem remains: OpenMx...
mhunter [Fri, 7 Dec 2012 07:50:42 +0000 (07:50 +0000)]
Did lots of debugging for state space expectation.  One odd problem remains: OpenMx thinks there are no free parameters and does not call the FIML fit function.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2297 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoChecked in failing test of state space expectation for debugging
mhunter [Fri, 7 Dec 2012 01:01:39 +0000 (01:01 +0000)]
Checked in failing test of state space expectation for debugging

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2296 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoBug fix for printing confidence interval (row, col)
mspiegel [Thu, 6 Dec 2012 00:33:55 +0000 (00:33 +0000)]
Bug fix for printing confidence interval (row, col)
designation in checkpoint file.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2295 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoMade some minor changes to FIML fit function to allow for handling the state space...
mhunter [Sat, 1 Dec 2012 00:17:26 +0000 (00:17 +0000)]
Made some minor changes to FIML fit function to allow for handling the state space expectation.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2294 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoAutomated conversion of the demo directory
jpritikin [Fri, 30 Nov 2012 20:51:34 +0000 (20:51 +0000)]
Automated conversion of the demo directory

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@2293 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoManually convert demos that use vector=TRUE in an objective
jpritikin [Fri, 30 Nov 2012 20:51:31 +0000 (20:51 +0000)]
Manually convert demos that use vector=TRUE in an objective

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2292 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoperl -pi -e 's/mxAlgebraObjective/mxFitFunctionAlgebra/g'
jpritikin [Fri, 30 Nov 2012 19:04:21 +0000 (19:04 +0000)]
perl -pi -e 's/mxAlgebraObjective/mxFitFunctionAlgebra/g'

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2291 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoConvert to fit/expectation
jpritikin [Fri, 30 Nov 2012 18:16:41 +0000 (18:16 +0000)]
Convert to fit/expectation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2290 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoTurn off more executable bits
jpritikin [Fri, 30 Nov 2012 18:16:40 +0000 (18:16 +0000)]
Turn off more executable bits

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2289 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoAnd rolling back an accidental change to the DESCRIPTION file.
tbrick [Wed, 28 Nov 2012 10:36:25 +0000 (10:36 +0000)]
And rolling back an accidental change to the DESCRIPTION file.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2288 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoConverted a few demos to fit/expectation. Also fixed a minor bug where mxExpectationN...
tbrick [Wed, 28 Nov 2012 10:34:59 +0000 (10:34 +0000)]
Converted a few demos to fit/expectation. Also fixed a minor bug where mxExpectationNormal incorrectly required a means vector.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2287 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoMerging the FitExpectation branch into the trunk.
mspiegel [Sun, 25 Nov 2012 00:42:16 +0000 (00:42 +0000)]
Merging the FitExpectation branch into the trunk.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2286 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

5 years agoTurn off execute bits
jpritikin [Fri, 23 Nov 2012 21:44:12 +0000 (21:44 +0000)]
Turn off execute bits

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@2280 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1