-*- text -*-

USER-VISIBLE CHANGES (for detailed changes see ChangeLog in the source package)
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Version 0.4 (January 7, 2005)
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* Censored observations are now supported, via new "censor" and
  "censor.states" arguments.  A censored observation is unknown, but
  known to be one of a particular set of states.

A major update to msm is under development, for release in the first
half of 2005. This will support hidden Markov models with general
response distributions.


Version 0.3.3 (September 18, 2004)
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* Maintenance release with minor fixes and enhancements ready for
R-2.0.0. 


Version 0.3.2 (March 25, 2004)
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* More than one death state is now permitted, through the "death"
argument. Death states are those whose exact entry time is known,
but the state at the previous instant before death is unknown.

* The "tunit" argument has been abolished.  Death times are now
assumed to be exact rather than known within one day.  This makes
more sense since for longitudinal studies, all observations are
usually recorded to within one basic time unit, not just death
times.

* Cleanups of the manual and minor fixes, as detailed in ChangeLog.


Version 0.3.1 (October 14, 2003)
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* Bug fix. The likelihood was being wrongly calculated in cases when
both the data represent exact transition times and the transition
intensity matrix had repeated eigenvalues. 

* The "death" argument is no longer ignored when exacttimes=TRUE, as
it is reasonable to have the entry time into one state accurate to
within one day, and all other times exactly accurate.

* More memory problems should be fixed. 


Version 0.3 (September 29, 2003)
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* Two errors in the calculation of the likelihood for a multi-state
model have been corrected. These bugs affect only models with
reversible transition matrices, that is, models which allow
progression and regression between states.

* The first bug occurred when death times were known to within one time
unit (death = TRUE) - the likelihood calculation did not account for
reversible states.

* The second bug occurred when the data represent exact transition times
(exacttimes = TRUE). The likelihood calculation did not properly
account for reversible states.

* Baseline transition intensities, or misclassification probabilities,
can now be constrained to be equal to each other, in the same manner
as covariate effects. Specified by new arguments "qconstraint" or
"econstraint".

* The memory allocation problems of version 0.2 have been fixed. 


Version 0.22 (June 30, 2003)
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* Fixed some minor bugs, as detailed in ChangeLog. 

* New function, pmatrix.piecewise.msm, for calculating transition
probability matrices for processes with piecewise-constant
intensities.


Version 0.21 (June 3, 2003)
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* Fixed a handful of minor bugs, as detailed in ChangeLog. 

* Minor edits and additions to the manual.

* The subject ID can now be factor or character.


Version 0.2 (January 2003)
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* A full manual in PDF format is included in the doc directory. This
gives the mathematical background behind multi-state modelling, and a
tutorial in the typical use of the functions in the msm package.

* Many more methods for extracting summary statistics from the fitted
model are included.  These are generally called with the fitted model
as the argument, plus an optional argument indicating the assumed
covariate values. The functions include qmatrix.msm, ematrix.msm,
pmatrix.msm, qratio.msm, sojourn.msm, totlos.msm, hazard.msm,
odds.msm, prevalence.msm. 

* New function statetable.msm to calculate frequencies of transitions
between pairs of states observed in the data.

* New function crudeinits.msm to estimate transition intensities
assuming the data represent the exact transition times of the Markov
process. These can be used as initial values in the msm function for
fitting the model. 

* prevalencemisc.msm has been removed, as its methodology was
overcomplicated and confusing.  The methods used in prevalence.msm
have been extended naturally to deal with misclassification models.

* Fix of a bug in the likelihood calculation for misclassification
models (the number of non-death states was assumed to be the same as
the number of states that could be misclassified, leading to failure
to calculate the likelihood for models where some states are observed
without error, but are not death states. ) Thanks to Martyn Plummer
for reporting this.

* Fix of a bug in the simulation routines (getobs.msm, called by
simmulti.msm), where for models with absorbing states, the absorbing 
state is not retained in the simulated data.   

* New heart transplant example data set, as used in the manual, so
that all the examples given in the manual can be run by the user.

* Tidying of the help pages. 


Version 0.1 (November 2002)
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* First release. 