 PROGRAMMER CHANGE LOG  (User-visible changes between releases are in NEWS)
 ---------------------
	
2003-01-05  Chris Jackson  <chris.jackson@ic.ac.uk>

	* DESCRIPTION: Version 0.2 released. 
	
	* inst/doc/msm-manual.pdf: PDF manual completed. 

2003-01-03  Chris Jackson  <chris.jackson@ic.ac.uk>

	* man: Heart transplant data added as an example data set

	* man: Aesthetic cleanups of all help pages

	* R/msm.R: New function crudeinits.msm to estimate a set of
	initial values for transition rates by assuming data represent
	the only transition times. 
 
	* R/msm.R: New function statetable.msm to calculate frequencies of
	successive state pairs in data

	* R/outputs.R: Methodology changed for prevalencemisc.msm to make
	it more similar to prevalence.msm, avoiding confusion.  Observed
	counts now common to both, and separated out into a new function
	observed.msm. Then prevalencemisc.msm (and the internal C onestep)
	was removed and prevalence.msm was made general to both
	misclassification and non-misclassification models.

2002-12-18  Chris Jackson  <chris.jackson@ic.ac.uk>

	* src/lik.c: Bugfix. nms changed to nst in likelihood-calculating
	functions.  Fixes failure to calculate the likelihood where some
	states where some states are observed without error, but are not
	death states (Thanks to Martyn Plummer).

	* R/simul.R: Bugfix in getobs.msm, which led to the entrance to
	not being observed for models with absorbing states,
	
2002-12-09  Chris Jackson  <chris.jackson@ic.ac.uk>

	* R/outputs.R: new function odds.msm to calculate odds ratios for
	misclassification probabilities.

	* R/outputs.R: new function ematrix.msm. Calls new internal
	functions, including qematrix.msm. 

2002-12-03  Chris Jackson  <chris.jackson@ic.ac.uk>

	* R/outputs.R: new function qratio.msm for estimating ratios of
	intensities and (via new function qratio.se.msm) their standard
	errors. Documentation in man/qratio.msm.Rd.
	
2002-12-02  Chris Jackson  <chris.jackson@ic.ac.uk>

	* R/outputs.R: new internal function qmatrix.diagse.msm 
	
	* R/msm.R  Null components of msm objects removed, e.g. 
	misclassification parameters for non-misclassification models. 

2002-11-27  Chris Jackson  <chris.jackson@ic.ac.uk>

	* R:  File msm.R split into msm.R, outputs.R and utils.R. 
	
	* R/msm.R. New functions absorbing.msm and transient.msm which 
	give the indices of the absorbing or transient states of the model. 

	* R/msm.R. (plot.msm) Now accepts a "covariates" argument for
	covariates at which to evaluate the survival probabilities. 

	* R/msm.R. Functions which operate on msm objects now have the
	msm object argument named "x", instead of "msm", for consistency.

	* man/qmatrix.msm.Rd, man/pmatrix.msm.Rd, man/sojourn.msm.Rd. Updated
	documentation.

	* R/msm.R (msm). The contents of msm objects has been
	reorganised. The first component of Qmatrices is now called
	"logbaseline" and gives the estimates of the log intensites as
	returned from the optimisation.  Components "qcenter" and
	"ecenter" are removed, as they were named confusingly. The
	component 'Pmatrix' is also removed, as it is obsoleted by the
	function 'pmatrix.msm'.  New component 'foundse' is a logical
	indicating whether the Hessian is positive definite, i.e. whether
	standard errors are available.
	
	* R/msm.R (sojourn.msm) Function rewritten to allow a given set of
	covariate values, using the new qmatrix.msm.  Now takes a fitted
	msm model as its argument, and the component "mean" in the return
	is changed to "estimate".

	* R/msm.R (qmatrix.msm). New function to compute transition
	intensity matrix at given covariate values.

	* R/msm.R (pmatrix.msm). New function to compute transition
	probability matrix at given covariate values.

	* R/simul.R (simmulti.msm): Check for ordered patient IDs, and
	sort input data if not ordered.  Also check for duplicated
	observation times and remove them. Default for 'death' argument
	changed to FALSE for consistency with msm(). Give column names to
	the simulated data.

2002-11-13  Chris Jackson  <chris.jackson@ic.ac.uk>

	* R/msm.R: New function msm.check.qmatrix to test for consistency
	of Markov chain intensity matrices.

	* R/msm.R, man/totlos.Rd: New function totlos.msm to estimate total length of stay in a 
	state, with documentation.

	* src/lik.c, src/pijt.c: Unused and uninitialised variables fixed so the library builds
	cleanly with -Wall.		

2002-11-08  Chris Jackson  <chris.jackson@ic.ac.uk>

	* src/lik.c: Debugging print statements removed from onestep

	* msm_0.1.tar.gz: First release 


