This directory, mspath/src/simulate, contains files that are not
intended for production use.

To test the program requires some independent method of verifying the
results and getting simulated data on which to run tests.  In this
directory I reimplement the basic likelihood calculations purely in
R.  The result is slow and has limited functionality compared to the
main package, but it does permit very detailed inspection of paths and
intermediate results.

The directory also includes some sample data and logs of some tests.
In some cases these were used to generate expected values for test
runs of R code (mspath/tests) and C code (mspath/src/test); however,
it may not be in sync with the current versions of those tests.

fakeCalc.R provides a drop-in replacement for the real calculators.
   Use it by specifying the calc=fakeCalc argument to mspath.
   Limitations:
      * no covariate effects on misclassification rates;
      * no duplicate observations within a step (same as real
        calculators);
      * absorbing state must be highest numbered state;
      * states must be numbered consecutively from 1 (same as real
        calculators);
      * path counts are only upper bounds
      * some counts are missing entirely.
      * probably others.
  It uses classes defined in ...

mspsim.R provides analogues to many of the lower-level C++ classes
   upon which calculation and simulation are based.

makeData.R makes simulated data and runs the real calculator against
   it.  Also provides a function to strip out huge amounts of
   redundant data.

mspsimData.R  Tests a variety of data and models.  You can evaluate
   this and then print the result variables.  The input data mimics
   that used in some of the real tests for mspath.

test02.R Tests whether covariates are lagged.  
   Basis of tests/test6.R

For the logs, note that they were from ESS sessions that often pulled
in new or revised code (e.g., the files above) without leaving a trace
of this activity in the log.

Manager_test.log  like managerCutoff C++ unit test.
   Illustrates expected calling pattern of functions in mspsim.R.

rlog01 other tests, some using Data1c.

SimResults.gnumeric Gnumeric spreadsheet of expected results.

