openmx:openmx.git
3 years agoDisentangle Ramsay1975 caution settings (maybe improves dynamic behavior)
jpritikin [Sat, 22 Mar 2014 22:48:17 +0000 (22:48 +0000)]
Disentangle Ramsay1975 caution settings (maybe improves dynamic behavior)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3198 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMake compile objects depend on the compile flags
jpritikin [Sat, 22 Mar 2014 22:48:11 +0000 (22:48 +0000)]
Make compile objects depend on the compile flags

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3197 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoBetter names for mvn parameters
jpritikin [Sat, 22 Mar 2014 17:56:09 +0000 (17:56 +0000)]
Better names for mvn parameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3196 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix mxCI for a vector of parameter names; add test
jpritikin [Sat, 22 Mar 2014 17:56:07 +0000 (17:56 +0000)]
Fix mxCI for a vector of parameter names; add test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3195 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove diagnostics
jpritikin [Sat, 22 Mar 2014 17:56:03 +0000 (17:56 +0000)]
Improve diagnostics

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3194 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRestore some support for row major storage
jpritikin [Sat, 22 Mar 2014 14:29:24 +0000 (14:29 +0000)]
Restore some support for row major storage

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3193 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAvoid needless compiles
jpritikin [Sat, 22 Mar 2014 14:29:22 +0000 (14:29 +0000)]
Avoid needless compiles

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3192 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove a bit more automatic version stamp stuff
jpritikin [Sat, 22 Mar 2014 09:55:17 +0000 (09:55 +0000)]
Remove a bit more automatic version stamp stuff

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3191 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHook up numerical integration precision parameters
jpritikin [Sat, 22 Mar 2014 09:50:46 +0000 (09:50 +0000)]
Hook up numerical integration precision parameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3190 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove automatic version stamping
yang [Fri, 21 Mar 2014 21:25:58 +0000 (21:25 +0000)]
Remove automatic version stamping

We have accidentally messed up the version too many times. Let's try
managing the version manually for now.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3189 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoImprove detection of CPU architecture
yang [Fri, 21 Mar 2014 21:25:58 +0000 (21:25 +0000)]
Improve detection of CPU architecture

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3188 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRevert "test from yang"
yang [Fri, 21 Mar 2014 21:03:42 +0000 (21:03 +0000)]
Revert "test from yang"

This reverts commit bd1d3d201abe126da9d09cc435e3186361088f41.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3187 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agotest from yang
yang [Fri, 21 Mar 2014 21:01:51 +0000 (21:01 +0000)]
test from yang

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3186 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFor WLS when flattening cov, do it to upper triangle BY ROW so it matches the variabl...
mhunter [Fri, 21 Mar 2014 20:36:49 +0000 (20:36 +0000)]
For WLS when flattening cov, do it to upper triangle BY ROW so it matches the variable ordering of the lower triangle by column.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3185 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMinor bug fix in saturated model generator
mhunter [Fri, 21 Mar 2014 18:26:46 +0000 (18:26 +0000)]
Minor bug fix in saturated model generator

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3182 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReset fake version back to zero
jpritikin [Fri, 21 Mar 2014 18:20:56 +0000 (18:20 +0000)]
Reset fake version back to zero

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3181 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTemporarily quarentine test failing with CSOLNP
jpritikin [Fri, 21 Mar 2014 18:20:54 +0000 (18:20 +0000)]
Temporarily quarentine test failing with CSOLNP

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3180 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRevert "inversion function changed, gradient & Hessian returned, some code cleanings"
jpritikin [Fri, 21 Mar 2014 18:20:49 +0000 (18:20 +0000)]
Revert "inversion function changed, gradient & Hessian returned, some code cleanings"

This reverts commit 91e3dd6484120ed9b53f02c6b148bc246379f9dc.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3179 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHelp gcc issue more accurate warnings
jpritikin [Fri, 21 Mar 2014 18:06:39 +0000 (18:06 +0000)]
Help gcc issue more accurate warnings

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3178 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFixed WLS expected thresholds processing (i.e. for data of type acov)
mhunter [Fri, 21 Mar 2014 17:35:56 +0000 (17:35 +0000)]
Fixed WLS expected thresholds processing (i.e. for data of type acov)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3177 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTest both NPSOL and CSOLNP if both are available
jpritikin [Fri, 21 Mar 2014 14:00:40 +0000 (14:00 +0000)]
Test both NPSOL and CSOLNP if both are available

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3176 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix uninitialized memory read in multivariate normal information matrix
jpritikin [Fri, 21 Mar 2014 13:19:25 +0000 (13:19 +0000)]
Fix uninitialized memory read in multivariate normal information matrix

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3175 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEnsure save-gcno is part of all target
jpritikin [Fri, 21 Mar 2014 13:19:24 +0000 (13:19 +0000)]
Ensure save-gcno is part of all target

I'm not sure why this isn't necessary.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3174 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoTwo more Users Guide pages updated for e-f change
mhunter [Thu, 20 Mar 2014 21:41:06 +0000 (21:41 +0000)]
Two more Users Guide pages updated for e-f change

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3173 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFinish killing %lu related debugging compiler warnings.
mhunter [Thu, 20 Mar 2014 20:20:20 +0000 (20:20 +0000)]
Finish killing %lu related debugging compiler warnings.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3172 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMore expectation-fit Users Guide changes
mhunter [Thu, 20 Mar 2014 18:06:47 +0000 (18:06 +0000)]
More expectation-fit Users Guide changes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3171 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOmit tarball busy work from 'make install' similar to 'make cran-install'
jpritikin [Thu, 20 Mar 2014 17:56:09 +0000 (17:56 +0000)]
Omit tarball busy work from 'make install' similar to 'make cran-install'

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3170 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPull libnpsol.a from our website (linux only, so far)
jpritikin [Thu, 20 Mar 2014 17:56:08 +0000 (17:56 +0000)]
Pull libnpsol.a from our website (linux only, so far)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3169 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUsers Guide fit-expectation changes
mhunter [Thu, 20 Mar 2014 17:50:02 +0000 (17:50 +0000)]
Users Guide fit-expectation changes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3168 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUsers Guide Row FIML Fit changes
mhunter [Thu, 20 Mar 2014 17:32:00 +0000 (17:32 +0000)]
Users Guide Row FIML Fit changes

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3167 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoUpdate Users Guide pages A through F for the expectation-fit change.
mhunter [Thu, 20 Mar 2014 16:49:28 +0000 (16:49 +0000)]
Update Users Guide pages A through F for the expectation-fit change.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3166 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoHint the correct way to customize the compiler/compiler options
jpritikin [Thu, 20 Mar 2014 15:28:37 +0000 (15:28 +0000)]
Hint the correct way to customize the compiler/compiler options

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3165 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMove HessianTest* to failing
jpritikin [Thu, 20 Mar 2014 13:20:48 +0000 (13:20 +0000)]
Move HessianTest* to failing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3164 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoKill some debugging related %lu warnings.
mhunter [Thu, 20 Mar 2014 13:19:53 +0000 (13:19 +0000)]
Kill some debugging related %lu warnings.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3163 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agotolerance in omxCheckCloseEnough changed for Csolnp
mzahery [Thu, 20 Mar 2014 13:04:19 +0000 (13:04 +0000)]
tolerance in omxCheckCloseEnough changed for Csolnp

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3162 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoinversion function changed, gradient & Hessian returned, some code cleanings
mzahery [Thu, 20 Mar 2014 13:00:04 +0000 (13:00 +0000)]
inversion function changed, gradient & Hessian returned, some code cleanings

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3161 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReparameterize lower & upper drm bounds in logits (copied from mirt)
jpritikin [Wed, 19 Mar 2014 13:10:45 +0000 (13:10 +0000)]
Reparameterize lower & upper drm bounds in logits (copied from mirt)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3160 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agominor typo in message "symmmetric" -> symmetric
tbates [Wed, 19 Mar 2014 09:05:58 +0000 (09:05 +0000)]
minor typo in message "symmmetric" -> symmetric

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3159 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd info on using omxAssignFirstParameters with SetParameters
tbates [Wed, 19 Mar 2014 00:26:31 +0000 (00:26 +0000)]
Add info on using omxAssignFirstParameters with SetParameters

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3158 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdding how-to help, and help() link for new objectives
tbates [Wed, 19 Mar 2014 00:21:14 +0000 (00:21 +0000)]
Adding how-to help, and help() link for new objectives

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3157 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd mxOption for max stack depth
jpritikin [Tue, 18 Mar 2014 17:31:35 +0000 (17:31 +0000)]
Add mxOption for max stack depth

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3156 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd runtime verbose option to multigroup fitfunction
jpritikin [Tue, 18 Mar 2014 14:27:01 +0000 (14:27 +0000)]
Add runtime verbose option to multigroup fitfunction

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3155 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoComplain about ... args in mxComputeOnce
jpritikin [Tue, 18 Mar 2014 14:26:57 +0000 (14:26 +0000)]
Complain about ... args in mxComputeOnce

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3154 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSet version back to zero
jpritikin [Tue, 18 Mar 2014 14:26:53 +0000 (14:26 +0000)]
Set version back to zero

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3153 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCause gdb to report child's exit status
jpritikin [Tue, 18 Mar 2014 02:00:01 +0000 (02:00 +0000)]
Cause gdb to report child's exit status

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3152 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd dependencies to the C/C++ compile
jpritikin [Mon, 17 Mar 2014 21:23:04 +0000 (21:23 +0000)]
Add dependencies to the C/C++ compile

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3151 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agocran-install does not need to build the tar.gz blob
jpritikin [Mon, 17 Mar 2014 21:22:55 +0000 (21:22 +0000)]
cran-install does not need to build the tar.gz blob

Similar changes are needed for the NPSOL rules

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3150 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd protect to MxRList and simplify API
jpritikin [Sun, 16 Mar 2014 22:46:38 +0000 (22:46 +0000)]
Add protect to MxRList and simplify API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3149 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd some control parameters for Mike Neale (not hooked up yet)
jpritikin [Sat, 15 Mar 2014 15:40:17 +0000 (15:40 +0000)]
Add some control parameters for Mike Neale (not hooked up yet)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3148 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFactor out lots of calls to Rf_mkChar
jpritikin [Sat, 15 Mar 2014 12:24:04 +0000 (12:24 +0000)]
Factor out lots of calls to Rf_mkChar

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3147 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove "at iteration" from error
jpritikin [Sat, 15 Mar 2014 12:24:02 +0000 (12:24 +0000)]
Remove "at iteration" from error

+ Otherwise it is hard to write a test that matches against a known
error message

+ The user probably wants to know the parameter vector that caused the
error instead of the iteration number. This is available via
checkpointing.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3146 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMake elementwise algebra ops conformable for the scalar-matrix case
jpritikin [Sat, 15 Mar 2014 00:32:16 +0000 (00:32 +0000)]
Make elementwise algebra ops conformable for the scalar-matrix case

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3145 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoContinue with omxMatrix API simplification
jpritikin [Sat, 15 Mar 2014 00:32:12 +0000 (00:32 +0000)]
Continue with omxMatrix API simplification

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3144 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoResolved scope issue with isnan and isinf functions.
mhunter [Fri, 14 Mar 2014 15:00:42 +0000 (15:00 +0000)]
Resolved scope issue with isnan and isinf functions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3143 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoWLS Progress: no seg fault now, but still not good estimates and really bad standard...
mhunter [Fri, 14 Mar 2014 03:55:16 +0000 (03:55 +0000)]
WLS Progress: no seg fault now, but still not good estimates and really bad standard errors.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3142 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRe-architect fitfunction derivatives API using Eigen
jpritikin [Thu, 13 Mar 2014 20:32:18 +0000 (20:32 +0000)]
Re-architect fitfunction derivatives API using Eigen

Why do we need another matrix algebra library? We already have two, that
is, omxMatrix (original) and Matrix (from CSOLNP). For IFA models with
many items, it is essential to perform a sparse matrix-vector product
(Hessian %*% gradient) in Newton-Raphson. I initially wrote bespoke code
for sparse matrix-vector product. This was working well. However, it
came to my attention that inverting the Hessian can also benefit from
sparse matrix algebra. Rather than re-invent the wheel, Eigen looks like
a promising implementation.

Additional changes:

+ Internal derivatives are no longer reported back to R. You need to use
mxComputeReportDeriv to request them. Report derivs by default seemed
like a bad idea if they are so big that we are using a sparse
representation.

+ MxComputeNumericDeriv got a verbose parameter to enable debugging at
runtime.

+ ifa-drm-wide.R is moved to the failing directory temporarily. This
commit does not optimize manipulation of the Hessian but uses a simple
dense representation. dsytrf/dsytri are used to invert the Hessian. This
doesn't scale, but the improved accuracy results in many fewer
Newton-Raphson iterations highlighting the poor accuracy of the replaced
code.

+ Eigen has a great debug mode that NaN initializes memory and does
bounds checking. With these tools to assist debugging, I decided to
never store the lower triangle of a Hessian.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3141 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd Eigen, next commit hooks it up
jpritikin [Thu, 13 Mar 2014 20:31:56 +0000 (20:31 +0000)]
Add Eigen, next commit hooks it up

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3140 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded error checking to state space expectations and checked the error checking with...
mhunter [Thu, 13 Mar 2014 18:01:42 +0000 (18:01 +0000)]
Added error checking to state space expectations and checked the error checking with a passing model using omxCheckError.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3139 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEnable R_NO_REMAP for a cleaner namespace
jpritikin [Wed, 12 Mar 2014 14:46:27 +0000 (14:46 +0000)]
Enable R_NO_REMAP for a cleaner namespace

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3138 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAnchor regex at beginning of path
jpritikin [Wed, 12 Mar 2014 14:46:18 +0000 (14:46 +0000)]
Anchor regex at beginning of path

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3137 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd check for algebra dimnames
jpritikin [Wed, 12 Mar 2014 14:46:16 +0000 (14:46 +0000)]
Add check for algebra dimnames

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3136 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't use R to calculate our algebra result matrix dimensions
jpritikin [Mon, 10 Mar 2014 01:36:48 +0000 (01:36 +0000)]
Don't use R to calculate our algebra result matrix dimensions

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3135 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoInitial compute protocol for the whole tree of dependencies
jpritikin [Mon, 10 Mar 2014 01:36:44 +0000 (01:36 +0000)]
Initial compute protocol for the whole tree of dependencies

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3134 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't rely on R to evaluate our algebra
jpritikin [Mon, 10 Mar 2014 01:36:39 +0000 (01:36 +0000)]
Don't rely on R to evaluate our algebra

Also, improve logging and remove confusing deadcode in the
initialization path.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3133 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove non-reproducable pointer addresses from logs
jpritikin [Sun, 9 Mar 2014 19:54:06 +0000 (19:54 +0000)]
Remove non-reproducable pointer addresses from logs

For those of us who would like to use diff to examine changes in log
output.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3132 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoMore omxMatrix API cleanup
jpritikin [Sun, 9 Mar 2014 19:53:48 +0000 (19:53 +0000)]
More omxMatrix API cleanup

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3131 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRemove deadcode (dead after free.set fixes)
jpritikin [Sun, 9 Mar 2014 19:53:43 +0000 (19:53 +0000)]
Remove deadcode (dead after free.set fixes)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3130 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRearrange ComputeEM for SEM integration
jpritikin [Fri, 7 Mar 2014 19:03:07 +0000 (19:03 +0000)]
Rearrange ComputeEM for SEM integration

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3129 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorg code for latent distribution
jpritikin [Fri, 7 Mar 2014 19:03:00 +0000 (19:03 +0000)]
Reorg code for latent distribution

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3128 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd a 3rd string argument to omxExpectation computeFun "how"
jpritikin [Fri, 7 Mar 2014 19:02:56 +0000 (19:02 +0000)]
Add a 3rd string argument to omxExpectation computeFun "how"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3127 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoPrepare to simplify omxMatrix API
jpritikin [Fri, 7 Mar 2014 19:02:52 +0000 (19:02 +0000)]
Prepare to simplify omxMatrix API

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3126 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDoc mxFitFunctionMultigroup
jpritikin [Fri, 7 Mar 2014 19:02:51 +0000 (19:02 +0000)]
Doc mxFitFunctionMultigroup

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3125 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix various bugs in free.set variable groups
jpritikin [Fri, 7 Mar 2014 19:02:47 +0000 (19:02 +0000)]
Fix various bugs in free.set variable groups

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3124 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdd tests for convergence speed
jpritikin [Thu, 6 Mar 2014 23:49:29 +0000 (23:49 +0000)]
Add tests for convergence speed

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3123 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix uninitialized memory read in Ramsay1975
jpritikin [Thu, 6 Mar 2014 23:49:20 +0000 (23:49 +0000)]
Fix uninitialized memory read in Ramsay1975

I didn't research when I introduced this bug. The symptom was that the
path taken from starting values to the MLE differed randomly between
runs. Occasionally, runs exhibited slight differences in the MLE. This
was due to inconsistent parameter acceleration in ComputeEM.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3122 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSlightly optimize analytic latent distribution parameter Hessian (update test)
jpritikin [Thu, 6 Mar 2014 16:30:52 +0000 (16:30 +0000)]
Slightly optimize analytic latent distribution parameter Hessian (update test)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3121 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOptimize gradient/meat when no items parameters are free
jpritikin [Thu, 6 Mar 2014 13:55:01 +0000 (13:55 +0000)]
Optimize gradient/meat when no items parameters are free

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3120 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSlightly optimize analytic latent distribution parameter Hessian
jpritikin [Thu, 6 Mar 2014 13:55:00 +0000 (13:55 +0000)]
Slightly optimize analytic latent distribution parameter Hessian

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3119 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProgress on WLS: Fit function adjustments and data debugging.
mhunter [Thu, 6 Mar 2014 06:08:18 +0000 (06:08 +0000)]
Progress on WLS: Fit function adjustments and data debugging.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3118 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded helpful comment to Windows Makevars file.
mhunter [Thu, 6 Mar 2014 05:58:43 +0000 (05:58 +0000)]
Added helpful comment to Windows Makevars file.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3117 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoProgress toward WLS: build frontend observed threshold variable indexing
mhunter [Thu, 6 Mar 2014 05:57:44 +0000 (05:57 +0000)]
Progress toward WLS: build frontend observed threshold variable indexing

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3116 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoElementWISE multiplication etc
mhunter [Thu, 6 Mar 2014 02:17:33 +0000 (02:17 +0000)]
ElementWISE multiplication etc

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3115 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoModified State Space error checking to be more informative.
mhunter [Wed, 5 Mar 2014 21:46:52 +0000 (21:46 +0000)]
Modified State Space error checking to be more informative.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3114 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdded failing model for vector=TRUE fitfunctions.
mhunter [Wed, 5 Mar 2014 15:41:04 +0000 (15:41 +0000)]
Added failing model for vector=TRUE fitfunctions.

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3113 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoChange backend initialization order
jpritikin [Wed, 5 Mar 2014 00:55:58 +0000 (00:55 +0000)]
Change backend initialization order

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3112 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdjust buildbot gdb script
jpritikin [Wed, 5 Mar 2014 00:55:50 +0000 (00:55 +0000)]
Adjust buildbot gdb script

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3111 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoD'oh, fix test for error in mxLog
jpritikin [Wed, 5 Mar 2014 00:55:42 +0000 (00:55 +0000)]
D'oh, fix test for error in mxLog

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3110 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSet up the usual gdb breakpoints automatically
jpritikin [Wed, 5 Mar 2014 00:55:38 +0000 (00:55 +0000)]
Set up the usual gdb breakpoints automatically

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3109 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoCorrect matrix dimensions in test
jpritikin [Wed, 5 Mar 2014 00:55:35 +0000 (00:55 +0000)]
Correct matrix dimensions in test

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3108 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix spectral norm for R 2.14
jpritikin [Wed, 5 Mar 2014 00:55:31 +0000 (00:55 +0000)]
Fix spectral norm for R 2.14

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3107 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAllow simultaneous computation of gradient and gradient covariance
jpritikin [Mon, 3 Mar 2014 18:12:00 +0000 (18:12 +0000)]
Allow simultaneous computation of gradient and gradient covariance

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3106 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoAdjust precision of close enough checks
jpritikin [Mon, 3 Mar 2014 18:11:57 +0000 (18:11 +0000)]
Adjust precision of close enough checks

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3105 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoOptionally force a PD covariance matrix (not enabled)
jpritikin [Sun, 2 Mar 2014 22:22:42 +0000 (22:22 +0000)]
Optionally force a PD covariance matrix (not enabled)

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3104 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoSwitch verbose from a logical to an integer
jpritikin [Sun, 2 Mar 2014 22:22:37 +0000 (22:22 +0000)]
Switch verbose from a logical to an integer

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3103 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoRevert "Entertain a sample covariance formula"
jpritikin [Sun, 2 Mar 2014 22:22:34 +0000 (22:22 +0000)]
Revert "Entertain a sample covariance formula"

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3102 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoEntertain a sample covariance formula
jpritikin [Sun, 2 Mar 2014 22:22:25 +0000 (22:22 +0000)]
Entertain a sample covariance formula

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3101 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoReorg for latent distribution parameter equal constraints
jpritikin [Sun, 2 Mar 2014 22:22:19 +0000 (22:22 +0000)]
Reorg for latent distribution parameter equal constraints

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3100 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFactor out code to force a matrix to be positive semi-definite
jpritikin [Sun, 2 Mar 2014 19:18:48 +0000 (19:18 +0000)]
Factor out code to force a matrix to be positive semi-definite

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3099 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoDon't throw an exception from within a critical section
jpritikin [Sun, 2 Mar 2014 19:18:46 +0000 (19:18 +0000)]
Don't throw an exception from within a critical section

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3098 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

3 years agoFix test for mxComputeOnce API change
jpritikin [Sun, 2 Mar 2014 19:18:42 +0000 (19:18 +0000)]
Fix test for mxComputeOnce API change

git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3097 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1