openmx:openmx.git
3 years agoRun roxygen prior to building docs
jpritikin [Mon, 18 Aug 2014 11:25:29 +0000 (11:25 +0000)]
Run roxygen prior to building docs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3763 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPermit BA81 mean & variance specified with algebras
jpritikin [Mon, 18 Aug 2014 11:24:03 +0000 (11:24 +0000)]
Permit BA81 mean & variance specified with algebras

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3762 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRename omxSaturatedModel to mxNullModels per dev discussion
jpritikin [Mon, 18 Aug 2014 11:23:56 +0000 (11:23 +0000)]
Rename omxSaturatedModel to mxNullModels per dev discussion

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3761 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFixup doc build
jpritikin [Mon, 18 Aug 2014 11:23:42 +0000 (11:23 +0000)]
Fixup doc build

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3760 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoIncorporate doc feedback from Tim Brick
jpritikin [Mon, 18 Aug 2014 11:23:34 +0000 (11:23 +0000)]
Incorporate doc feedback from Tim Brick

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3759 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCheck whether we recover the parameters
jpritikin [Mon, 18 Aug 2014 11:23:26 +0000 (11:23 +0000)]
Check whether we recover the parameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3758 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove error messages
jpritikin [Mon, 18 Aug 2014 11:23:18 +0000 (11:23 +0000)]
Improve error messages

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3757 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove deadcode
jpritikin [Sat, 16 Aug 2014 05:09:11 +0000 (05:09 +0000)]
Remove deadcode

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3756 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRefuse to clear model slots by assignment to NULL and say why
jpritikin [Sat, 16 Aug 2014 05:09:03 +0000 (05:09 +0000)]
Refuse to clear model slots by assignment to NULL and say why

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3755 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove minItemsPerScore option
jpritikin [Sat, 16 Aug 2014 05:08:54 +0000 (05:08 +0000)]
Remove minItemsPerScore option

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3754 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDo a slightly better job with 'make clean'
jpritikin [Sat, 16 Aug 2014 05:08:43 +0000 (05:08 +0000)]
Do a slightly better job with 'make clean'

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3753 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix state space in FIML joint.
mhunter [Fri, 15 Aug 2014 15:10:55 +0000 (15:10 +0000)]
Fix state space in FIML joint.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3752 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSwitch default optimizer back to CSOLNP
jpritikin [Fri, 15 Aug 2014 13:40:17 +0000 (13:40 +0000)]
Switch default optimizer back to CSOLNP

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3751 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove some commented out code from Summary.
mhunter [Mon, 11 Aug 2014 16:54:34 +0000 (16:54 +0000)]
Remove some commented out code from Summary.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3750 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMade MxSummary have prettier printing of Chi-Square and RMSEA with CI. Also added...
mhunter [Mon, 11 Aug 2014 16:52:37 +0000 (16:52 +0000)]
Made MxSummary have prettier printing of Chi-Square and RMSEA with CI.  Also added more checks for SummaryCheck.R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3749 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCheck for null infoDefinite in summary
jpritikin [Mon, 11 Aug 2014 14:31:15 +0000 (14:31 +0000)]
Check for null infoDefinite in summary

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3748 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoExtinguish globalState
jpritikin [Mon, 11 Aug 2014 14:31:08 +0000 (14:31 +0000)]
Extinguish globalState

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3747 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove cut & paste code duplication
jpritikin [Mon, 11 Aug 2014 14:30:51 +0000 (14:30 +0000)]
Remove cut & paste code duplication

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3746 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPermit compilation without NLOPT
jpritikin [Mon, 11 Aug 2014 14:30:44 +0000 (14:30 +0000)]
Permit compilation without NLOPT

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3745 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoNLOPT and Simulated annealing added
mzahery [Mon, 11 Aug 2014 05:21:27 +0000 (05:21 +0000)]
NLOPT and Simulated annealing added

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3744 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReport condition number when standard erorrs are enabled
jpritikin [Sat, 9 Aug 2014 00:30:11 +0000 (00:30 +0000)]
Report condition number when standard erorrs are enabled

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3743 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove destruction order
jpritikin [Fri, 8 Aug 2014 14:35:05 +0000 (14:35 +0000)]
Improve destruction order

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3742 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMerge OMX_VERBOSE to OMX_DEBUG
jpritikin [Fri, 8 Aug 2014 14:34:57 +0000 (14:34 +0000)]
Merge OMX_VERBOSE to OMX_DEBUG

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3741 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSimplify copyParamToModel API
jpritikin [Fri, 8 Aug 2014 14:34:46 +0000 (14:34 +0000)]
Simplify copyParamToModel API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3740 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove deprecated naAction arg
jpritikin [Fri, 8 Aug 2014 14:34:35 +0000 (14:34 +0000)]
Remove deprecated naAction arg

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3739 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMove childList from omxState to FitContext
jpritikin [Fri, 8 Aug 2014 14:34:27 +0000 (14:34 +0000)]
Move childList from omxState to FitContext

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3738 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTrack whether a model has been run for submodels
jpritikin [Fri, 8 Aug 2014 06:18:20 +0000 (06:18 +0000)]
Track whether a model has been run for submodels

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3737 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemoved dredded paste0 calls. They prevent otherwise backward compatible code to...
mhunter [Fri, 8 Aug 2014 04:31:01 +0000 (04:31 +0000)]
Removed dredded paste0 calls.  They prevent otherwise backward compatible code to break.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3736 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoModify FIML Single Iteration Joint to accomodate State Space expectations for continu...
mhunter [Fri, 8 Aug 2014 04:24:17 +0000 (04:24 +0000)]
Modify FIML Single Iteration Joint to accomodate State Space expectations for continuous vars.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3735 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDistinguish between stale models and models which has not been run
jpritikin [Thu, 7 Aug 2014 15:43:10 +0000 (15:43 +0000)]
Distinguish between stale models and models which has not been run

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3734 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove reporting of CIs for non-free parameters
jpritikin [Thu, 7 Aug 2014 15:43:03 +0000 (15:43 +0000)]
Improve reporting of CIs for non-free parameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3733 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd more tests for fit statistics
jpritikin [Thu, 7 Aug 2014 15:42:52 +0000 (15:42 +0000)]
Add more tests for fit statistics

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3732 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSync ba81quad
jpritikin [Thu, 7 Aug 2014 15:42:40 +0000 (15:42 +0000)]
Sync ba81quad

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3731 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove as.IFAgroup (now in the RPF package)
jpritikin [Thu, 7 Aug 2014 15:42:33 +0000 (15:42 +0000)]
Remove as.IFAgroup (now in the RPF package)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3730 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoIgnore request for CIs if the label exists and is not a free parameter
jpritikin [Thu, 7 Aug 2014 06:04:30 +0000 (06:04 +0000)]
Ignore request for CIs if the label exists and is not a free parameter

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3729 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAvoid eigen decomposition if the covariance matrix is obviously PD
jpritikin [Thu, 7 Aug 2014 06:04:22 +0000 (06:04 +0000)]
Avoid eigen decomposition if the covariance matrix is obviously PD

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3728 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't report the saturated model if there is missing data
jpritikin [Thu, 7 Aug 2014 06:04:15 +0000 (06:04 +0000)]
Don't report the saturated model if there is missing data

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3727 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReally fix compiler warning
jpritikin [Thu, 7 Aug 2014 06:04:08 +0000 (06:04 +0000)]
Really fix compiler warning

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3726 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTrap errors in the computation of RMSEA CIs
jpritikin [Wed, 6 Aug 2014 03:35:03 +0000 (03:35 +0000)]
Trap errors in the computation of RMSEA CIs

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3725 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd IFA model support to omxSaturatedModel
jpritikin [Wed, 6 Aug 2014 03:34:53 +0000 (03:34 +0000)]
Add IFA model support to omxSaturatedModel

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3724 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd comment about RMSEA formula
jpritikin [Wed, 6 Aug 2014 03:34:39 +0000 (03:34 +0000)]
Add comment about RMSEA formula

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3723 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix minor compiler warning
jpritikin [Wed, 6 Aug 2014 03:34:32 +0000 (03:34 +0000)]
Fix minor compiler warning

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3722 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorganize omxSaturatedModel for better modularity
jpritikin [Wed, 6 Aug 2014 03:34:25 +0000 (03:34 +0000)]
Reorganize omxSaturatedModel for better modularity

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3721 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFactor out processing of the run argument to omxSaturatedModel
jpritikin [Wed, 6 Aug 2014 03:34:16 +0000 (03:34 +0000)]
Factor out processing of the run argument to omxSaturatedModel

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3720 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove our own version of std::max
jpritikin [Tue, 5 Aug 2014 05:47:03 +0000 (05:47 +0000)]
Remove our own version of std::max

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3719 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoConsolidate FIML to omxFIMLSingleIterationJoint (except for state space)
jpritikin [Tue, 5 Aug 2014 05:46:56 +0000 (05:46 +0000)]
Consolidate FIML to omxFIMLSingleIterationJoint (except for state space)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3718 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix failing FIML test
jpritikin [Mon, 4 Aug 2014 10:28:53 +0000 (10:28 +0000)]
Fix failing FIML test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3717 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove a bunch of duplicated code in FIML
jpritikin [Mon, 4 Aug 2014 08:38:45 +0000 (08:38 +0000)]
Remove a bunch of duplicated code in FIML

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3716 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDeadcode
jpritikin [Mon, 4 Aug 2014 08:38:36 +0000 (08:38 +0000)]
Deadcode

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3715 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDistinguish local variable name from omxState.currentRow
jpritikin [Mon, 4 Aug 2014 08:38:29 +0000 (08:38 +0000)]
Distinguish local variable name from omxState.currentRow

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3714 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRewrite frontend to get rid of generateDefinitionLocations
jpritikin [Sun, 3 Aug 2014 06:19:46 +0000 (06:19 +0000)]
Rewrite frontend to get rid of generateDefinitionLocations

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3713 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSwitch from absolute to relative tolerance
jpritikin [Sun, 3 Aug 2014 06:19:37 +0000 (06:19 +0000)]
Switch from absolute to relative tolerance

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3712 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoA-SEM refinement
jpritikin [Fri, 1 Aug 2014 13:40:17 +0000 (13:40 +0000)]
A-SEM refinement

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3711 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd Oakes1999 EM information matrix method
jpritikin [Fri, 1 Aug 2014 13:40:07 +0000 (13:40 +0000)]
Add Oakes1999 EM information matrix method

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3710 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAllow MxDataDynamic to aggregate >1 BA81 expectation
jpritikin [Fri, 1 Aug 2014 02:45:46 +0000 (02:45 +0000)]
Allow MxDataDynamic to aggregate >1 BA81 expectation

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3709 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSet up setVarGroup handler for MxAlgebraFitFunction
jpritikin [Fri, 1 Aug 2014 01:12:42 +0000 (01:12 +0000)]
Set up setVarGroup handler for MxAlgebraFitFunction

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3708 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd independent flag to mxComputeSequence
jpritikin [Fri, 1 Aug 2014 01:12:35 +0000 (01:12 +0000)]
Add independent flag to mxComputeSequence

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3707 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHandle model.mat[R,C] labels in BA81 latent distribution
jpritikin [Fri, 1 Aug 2014 01:12:27 +0000 (01:12 +0000)]
Handle model.mat[R,C] labels in BA81 latent distribution

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3706 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImplement new unprotect strategy
jpritikin [Thu, 31 Jul 2014 15:47:00 +0000 (15:47 +0000)]
Implement new unprotect strategy

The old idiom was

Rf_protect(foo);
// do stuff
Rf_unprotect(1);  //foo

The second line expresses the hope that we are unprotecting the same
thing that we protected. However, this can fail when "do stuff" involves
anything non-trivial. If there is a protect (or worse, an extra
unprotect) inside "do stuff" then the unprotect will not unprotect foo
but something else.

The new strategy is to check whether the protect stack is
at the same place where we protected, ensuring that our
protects are always balanced by unprotects. It is still
required to think about what is necessary to protect,
but now there is less chance of something going wrong
in the unprotect part.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3705 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUse proper define to index freeVarGroups
jpritikin [Thu, 31 Jul 2014 15:46:40 +0000 (15:46 +0000)]
Use proper define to index freeVarGroups

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3704 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFor summary(verbose=F), suppress SE and bounds if all NA
jpritikin [Wed, 30 Jul 2014 17:12:52 +0000 (17:12 +0000)]
For summary(verbose=F), suppress SE and bounds if all NA

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3703 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMxDataDynamic pretty printing
jpritikin [Wed, 30 Jul 2014 17:12:44 +0000 (17:12 +0000)]
MxDataDynamic pretty printing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3702 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd more unprotects
jpritikin [Wed, 30 Jul 2014 11:21:31 +0000 (11:21 +0000)]
Add more unprotects

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3701 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorder initialization sequence
jpritikin [Wed, 30 Jul 2014 11:21:23 +0000 (11:21 +0000)]
Reorder initialization sequence

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3700 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoBA81: Cope with only mean or only cov (but not both)
jpritikin [Wed, 30 Jul 2014 11:21:14 +0000 (11:21 +0000)]
BA81: Cope with only mean or only cov (but not both)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3699 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRelax tolerance
jpritikin [Wed, 30 Jul 2014 11:21:05 +0000 (11:21 +0000)]
Relax tolerance

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3698 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agominor error msg change: show user the verboten list of names
tbates [Tue, 29 Jul 2014 20:31:01 +0000 (20:31 +0000)]
minor error msg change: show user the verboten list of names

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3697 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd some unprotects
jpritikin [Tue, 29 Jul 2014 12:42:11 +0000 (12:42 +0000)]
Add some unprotects

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3696 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd fast path to matchDefinitionVariable
jpritikin [Tue, 29 Jul 2014 11:38:13 +0000 (11:38 +0000)]
Add fast path to matchDefinitionVariable

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3695 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDo same work in fewer matches
jpritikin [Tue, 29 Jul 2014 11:38:06 +0000 (11:38 +0000)]
Do same work in fewer matches

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3694 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove very expensive deadcode from MxFlatModel
jpritikin [Tue, 29 Jul 2014 11:37:56 +0000 (11:37 +0000)]
Remove very expensive deadcode from MxFlatModel

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3693 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoIf not found, don't search for defintion vars twice
jpritikin [Tue, 29 Jul 2014 11:37:48 +0000 (11:37 +0000)]
If not found, don't search for defintion vars twice

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3692 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMake checkVariablesHelper more efficient
jpritikin [Tue, 29 Jul 2014 11:37:38 +0000 (11:37 +0000)]
Make checkVariablesHelper more efficient

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3691 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't blindly cast all NA columns to double
jpritikin [Tue, 29 Jul 2014 11:37:29 +0000 (11:37 +0000)]
Don't blindly cast all NA columns to double

When the column is a factor, it needs to stay integer

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3690 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDelete unsupported autodiff
jpritikin [Tue, 29 Jul 2014 11:37:19 +0000 (11:37 +0000)]
Delete unsupported autodiff

On Mon, Jul 28, 2014 at 01:40:53AM -0400, Bob Carpenter wrote:
> The big problem with using Eigen directly is that it doesn't
> support mixed types (double and autodiff var) in its matrix operators.
> And you really don't want to autodiff the algorithms themselves
> if you don't have to --- a lot of the linear algebra operations have
> analytic gradients (as do the matrix operators).

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3689 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd failing NPSOL test
jpritikin [Mon, 28 Jul 2014 09:09:40 +0000 (09:09 +0000)]
Add failing NPSOL test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3688 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOnly warn once about the model being modified since run
jpritikin [Mon, 28 Jul 2014 08:47:01 +0000 (08:47 +0000)]
Only warn once about the model being modified since run

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3687 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProhibit clashes between model and matrix names in type='RAM' models
jpritikin [Mon, 28 Jul 2014 08:46:51 +0000 (08:46 +0000)]
Prohibit clashes between model and matrix names in type='RAM' models

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3686 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoClear modified-since-run flag on submodels
jpritikin [Mon, 28 Jul 2014 08:46:41 +0000 (08:46 +0000)]
Clear modified-since-run flag on submodels

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3685 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSelect SEM algorithm by name instead of number
jpritikin [Sun, 27 Jul 2014 05:43:50 +0000 (05:43 +0000)]
Select SEM algorithm by name instead of number

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3684 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPermit more than 1 fitfunction in mxComputeOnce
jpritikin [Sun, 27 Jul 2014 05:43:43 +0000 (05:43 +0000)]
Permit more than 1 fitfunction in mxComputeOnce

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3683 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd sanity checks for gradient
jpritikin [Sun, 27 Jul 2014 05:43:34 +0000 (05:43 +0000)]
Add sanity checks for gradient

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3682 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd as.IFAgroup to encapsulate a model in an RPF friendly object
jpritikin [Sun, 27 Jul 2014 04:24:27 +0000 (04:24 +0000)]
Add as.IFAgroup to encapsulate a model in an RPF friendly object

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3681 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEnsure every factor loads on at least 1 item
jpritikin [Sun, 27 Jul 2014 04:24:10 +0000 (04:24 +0000)]
Ensure every factor loads on at least 1 item

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3680 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHide non-estimable parameters when factors=0
jpritikin [Sun, 27 Jul 2014 04:23:58 +0000 (04:23 +0000)]
Hide non-estimable parameters when factors=0

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3679 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoComputeEM: Count the number of iterations correctly
jpritikin [Sat, 26 Jul 2014 01:40:03 +0000 (01:40 +0000)]
ComputeEM: Count the number of iterations correctly

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3678 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoThe backend no longer resizes matrices that will be exported to R
jpritikin [Sat, 26 Jul 2014 01:39:53 +0000 (01:39 +0000)]
The backend no longer resizes matrices that will be exported to R

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3677 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't check *.rda for code style
jpritikin [Sat, 26 Jul 2014 01:39:46 +0000 (01:39 +0000)]
Don't check *.rda for code style

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3676 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSwitch to more accurate matrix log/exp
jpritikin [Sat, 26 Jul 2014 01:39:35 +0000 (01:39 +0000)]
Switch to more accurate matrix log/exp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3675 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdjust pretty-printing of MxData to match slot names
jpritikin [Fri, 25 Jul 2014 14:32:53 +0000 (14:32 +0000)]
Adjust pretty-printing of MxData to match slot names

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3674 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTeach Newton-Raphson about bad derivatives
jpritikin [Fri, 25 Jul 2014 14:32:43 +0000 (14:32 +0000)]
Teach Newton-Raphson about bad derivatives

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3673 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPrint model name in summary
mhunter [Fri, 25 Jul 2014 06:52:36 +0000 (06:52 +0000)]
Print model name in summary

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3672 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoChange error message in saturated model helper when algebra fit function detected.
mhunter [Thu, 24 Jul 2014 17:22:26 +0000 (17:22 +0000)]
Change error message in saturated model helper when algebra fit function detected.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3671 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix bug in RMSEA CI reporting in summary when verbose=TRUE
mhunter [Thu, 24 Jul 2014 16:07:22 +0000 (16:07 +0000)]
Fix bug in RMSEA CI reporting in summary when verbose=TRUE

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3670 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded hand written mxFitFunctionMultigroup.Rd (was jumbled up)
tbates [Wed, 23 Jul 2014 16:06:14 +0000 (16:06 +0000)]
Added hand written mxFitFunctionMultigroup.Rd (was jumbled up)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3669 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprovements to mxSummary: RMSEA conf intervals, Information table adjustments, guida...
mhunter [Wed, 23 Jul 2014 15:49:44 +0000 (15:49 +0000)]
Improvements to mxSummary: RMSEA conf intervals, Information table adjustments, guidance to help page, statement about missing fit indices.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3668 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoupdate mxVersion.R to print better and update mxVersion.Rd guide to modified function.
tbates [Wed, 23 Jul 2014 14:46:47 +0000 (14:46 +0000)]
update mxVersion.R to print better and update mxVersion.Rd guide to modified function.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3667 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agopassing tests are removed from models/failing
mzahery [Wed, 23 Jul 2014 03:30:20 +0000 (03:30 +0000)]
passing tests are removed from models/failing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3666 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPreviously failing tests are moved into passing
mzahery [Tue, 22 Jul 2014 20:56:57 +0000 (20:56 +0000)]
Previously failing tests are moved into passing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3665 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUpdate summary test to use new saturated model helper correctly b/c it now returns...
mhunter [Mon, 21 Jul 2014 14:30:10 +0000 (14:30 +0000)]
Update summary test to use new saturated model helper correctly b/c it now returns a list of the sat and ind models.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3664 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1