Administration

At today's developers meeting, the OpenMx 1.0 feature set was discussed. First, a wishlist of features was compiled. From the wishlist a subset of features was selected for the 1.0 release. Our target for implementing these features is May 13th. When we have reached the goal of implementing these features, a 0.9 release will be created. At which point, there will be a feature freeze from the 0.9 to 1.0 release. Performance improvements may occur between the 0.9 to 1.0 releases. The month of June is the goal for the 1.0 release.

The wishlist:

• Mike Wilde progress on swift apply in R
  - create *apply() analogs for swift, in similar style to snow package
  - eventually create a swift package in R, or contribute to the snow package

• Steve: short cut in mxFIMLObjectiveFunction() using means = 0 as a shortcut for vector of zeros with free=TRUE.
• as a first step for easy thresholds write a function that takes an ordinal data input and returns a thresholds matrix
• fetch from the back-burner the project to pretty-print a OpenMx object as a script
• create a CRAN package from the twins workshop
  

The summary() function has been reimplemented. It now ignores columns in a dataset that are not used in a FIML objective function. It also now handles independent submodels more intelligently. The old implementation ran in about 10 seconds for models/failing/OneFactorCovRAMSpeedup.R (with numberIndicators = 80). The new implementation runs in about 0.5 seconds.

A short developers meeting was held today at the Twin Workshop. Our regular weekly meetings will resume next Friday at the usual time (1:00 PM EST). Here are the notes from today's meeting.

• Incorporate some/all of the helper functions from the twins workshop into the OpenMx package. R help is needed for these functions.
• The summary function is very slow on large models. Hermine + Steve will send Mike S. their scripts for debugging.
• Add a timestamp to the summary statement, showing when the model was executed.

We've changed the test suite such that messages to standard error are not redirected to /dev/null. Why did we do this? When R detects a stack imbalance in the garbage collection (a memory leak) it does not throw an error, and it does not throw a warning. Instead the R interpreter writes output directly to standard error.

Here are the minutes from today's developers meeting.

1. write a different mxThresholds() conformability checking when there are multiple matrices/algebras
2. add a special case for a logical vector of NAs
3. set function precision for the ordinal case to 1e-09
4. can we add constants to constraints?
5. look at filling in the values for diagonal matrices
6. implement d2v() function
7. implement v2d() function
8. add to the summary() and output the OpenMx version number
9. write a function that prints the covariance and means matrices
   

As of r1033 in the repository, the OpenMx package has its own name space when it is loaded in R. This is the "right" way to publish packages in R, and we intended to add a name space some time ago. But the namespace mechanics are scary and poorly documented.

Now the following names are exported to the user:

• Any function of the form: mx***()
• Any function of the form: omx***()
• Matrix functions implemented in the library: tr, "%&%", vech, vechs
• S4 operators: "[","[[", "$"
• S4 methods: summary, nrow, ncol, length, dimnames, show, print

Happy new years! Here is the TODO list generated from today's developer meeting.

• Add 'hide' argument to mxRun(). Default value is TRUE. Determines whether to return the hidden matrices and algebra generated during the workflow.
• Add start and stop wall-clock times to the output of mxRun(). Separate run time into front-end time and back-end time.
• Implement \mnor() in OpenMx before the Twin Workshop.
• Fix the bugs in FIMLRowAlgebra.R example.
• Add page on the OpenMx site for error messages
• Fix the bug in categoricalDefinitionTest.R example.
  

In r1011, some improvements have been made to definition variables. Definition variables can now be used inside algebra expressions. Additionally, definition variables inside of MxMatrices will populate to the 1st row before conformability checking. What this means in plain English: you do not need to specify the starting values for definition variables.