OpenMx trunk

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Updated: 1 day 21 hours ago

Remove "at iteration" from error + Otherwise it is hard to write a test that matches against a k...

Sat, 03/15/2014 - 08:24
In openmx/openmx.git:master 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

Make elementwise algebra ops conformable for the scalar-matrix case git-svn-id: http://openmx.ps...

Fri, 03/14/2014 - 20:32
In openmx/openmx.git:master 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

Continue with omxMatrix API simplification git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk...

Fri, 03/14/2014 - 20:32
In openmx/openmx.git:master Continue with omxMatrix API simplification git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3144 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Resolved scope issue with isnan and isinf functions. git-svn-id: http://openmx.psyc.virginia.edu...

Fri, 03/14/2014 - 11:00
In openmx/openmx.git:master Resolved scope issue with isnan and isinf functions. git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3143 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

WLS Progress: no seg fault now, but still not good estimates and really bad standard errors. git...

Thu, 03/13/2014 - 23:55
In openmx/openmx.git:master 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

Re-architect fitfunction derivatives API using Eigen Why do we need another matrix algebra libra...

Thu, 03/13/2014 - 16:32
In openmx/openmx.git:master 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

Add Eigen, next commit hooks it up git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3140 df...

Thu, 03/13/2014 - 16:31
In openmx/openmx.git:master Add Eigen, next commit hooks it up git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3140 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Added error checking to state space expectations and checked the error checking with a passing mo...

Thu, 03/13/2014 - 14:01
In openmx/openmx.git:master 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

Enable R_NO_REMAP for a cleaner namespace git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@...

Wed, 03/12/2014 - 10:46
In openmx/openmx.git:master Enable R_NO_REMAP for a cleaner namespace git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3138 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Anchor regex at beginning of path git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3137 df8...

Wed, 03/12/2014 - 10:46
In openmx/openmx.git:master Anchor regex at beginning of path git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3137 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Add check for algebra dimnames git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3136 df83fd...

Wed, 03/12/2014 - 10:46
In openmx/openmx.git:master Add check for algebra dimnames git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3136 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Don't use R to calculate our algebra result matrix dimensions git-svn-id: http://openmx.psyc.vir...

Sun, 03/09/2014 - 21:36
In openmx/openmx.git:master 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

Initial compute protocol for the whole tree of dependencies git-svn-id: http://openmx.psyc.virgi...

Sun, 03/09/2014 - 21:36
In openmx/openmx.git:master 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

Don't rely on R to evaluate our algebra Also, improve logging and remove confusing deadcode in t...

Sun, 03/09/2014 - 21:36
In openmx/openmx.git:master 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

Remove non-reproducable pointer addresses from logs For those of us who would like to use diff t...

Sun, 03/09/2014 - 15:54
In openmx/openmx.git:master 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

More omxMatrix API cleanup git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3131 df83fd30-4...

Sun, 03/09/2014 - 15:53
In openmx/openmx.git:master More omxMatrix API cleanup git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3131 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Remove deadcode (dead after free.set fixes) git-svn-id: http://openmx.psyc.virginia.edu/svn/trun...

Sun, 03/09/2014 - 15:53
In openmx/openmx.git:master Remove deadcode (dead after free.set fixes) git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3130 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Rearrange ComputeEM for SEM integration git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@31...

Fri, 03/07/2014 - 15:03
In openmx/openmx.git:master Rearrange ComputeEM for SEM integration git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3129 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Reorg code for latent distribution git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3128 df...

Fri, 03/07/2014 - 15:03
In openmx/openmx.git:master Reorg code for latent distribution git-svn-id: http://openmx.psyc.virginia.edu/svn/trunk@3128 df83fd30-4cca-4c36-ab9d-e8b5583ccbd1

Add a 3rd string argument to omxExpectation computeFun "how" git-svn-id: http://openmx.psyc.virg...

Fri, 03/07/2014 - 15:02
In openmx/openmx.git:master 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