ChangeLog

2016-11-02 THIS FILE IS NO LONGER MAINTAINED. Detailed changes are visible through the commits on https://github.com/chjackson/msm

2016-10-19 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  Bug fix to prevalence.msm with factor subject IDs

2016-10-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* Vignette sources moved from "src/doc" to "vignettes" on CRAN
	request.

	* DESCRIPTION: Version 1.6.4 released to CRAN and r-forge

2016-06-03 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>


	* R/utils.R: Bug fix for qtnorm with vectorised arguments.  Thanks
	to James Gibbons for the report.

	* DESCRIPTION: Version 1.6.3 released to r-forge.

2016-03-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Bug fix for dropping censored states. Thanks to
	Casimir Sofeu for the report.

	* DESCRIPTION: Version 1.6.2 released to r-forge.

2016-03-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.6.1 released to CRAN.

2016-03-07 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* tests: tests updated to work with the development version of
	testthat.

2016-02-18 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c,R/msm.R: Bug fix and documentation clarification for
	models with "obstrue" and "ematrix".

	* R/draic.R: Bug fix for initprobs, and only allow expected
	information if all panel data.

	* R/msm.R: Bug fix for printing CIs with pci and all fixedpars.

	* DESCRIPTION: Version 1.6.1 released to r-forge.

2015-11-17 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.6 released to r-forge and CRAN.

2015-11-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: Several bug fixes in calculation of the derivatives
	for multivariate HMMs.

	* R/msm.R(msm.form.obstrue): Better detection of when obstrue is
	supplied as an indicator or a true state + NA.

2015-10-07 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(msm.form.qoutput): Bug fix for printing model output
	when only one transition rate is affected by covariates.  Thanks
	to Jordi Blanch for the report.

2015-09-14 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: More underflow correction for probabilities of hidden
	states in viterbi.msm. Thanks to Hannah Linder for the report.

	* R/msm.R: "death" argument in msm() is deprecated and renamed to
	"deathexact".

	* R/msm.R: censor.states now defaults to all transient states if
	not supplied, instead of complaining, even if there is no
	absorbing state.  Thanks to Jonathan Williams for the report.

	* DESCRIPTION: Version 1.5.3 released to r-forge.

2015-04-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(statetable.msm): Code simplified, now row names work
	with factor states.

2015-02-17 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.5.2 released to r-forge.

2015-02-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R, src/lik.c: obstrue can now contain the actual true
	state, instead of an indicator.  This allows the information from
	HMM outcomes generated conditionally on this state to be included
	in the model.

	* R/msm.R(na.find.msmdata): Fix of bug in na.find.msmdata that
	could lead to NAs being passed through to C and causing a crash.
	Triggered when state or time were NA and there were covariates.

2015-02-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/hmm-dists.R(hmmDIST): Fix of bug when HMM parameters come from
	named vectors.

2015-01-29 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(msm.form.qoutput) Bug fix in printing fitted model
	objects.

2015-01-16 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* hmm.R: "links" component dropped from hmodel objects, as it is
	no longer used.

	* simul.R: "keep" component added to simmulti.msm result.

	* R/hmm.R and others: Multivariate observations in HMMs with
	different models for each variable.  Limited testing so far.

2015-01-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  Correct version of the built vignette restored to the package
	(1.5 instead of 1.3.2).

	*  Experimental feature: multivariate observations in HMMs.  Start
	by supporting multiple outcomes from the same distribution at the
	same time, with the data supplied as a matrix.

	* DESCRIPTION: Version 1.5.1 released to r-forge.

2015-01-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.5 released to CRAN.

2014-12-12 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R,R/phase.R. Phase type models now allow HMM on top.  Bug
	fixes to these models.

	* DESCRIPTION: Version 1.4.3 released to r-forge.

2014-12-11 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  Posterior probability of the hidden state at each time in the
	Viterbi algorithm now conditions on all the data.

	* R/msm.R,R/outputs.R(various): Bug fixes to misclassification
	models where some states were misclassified as other states with
	probability 1, for both ematrix and hmmCat specifications.  Thanks
	to Li Su for the report.

	* DESCRIPTION: Version 1.4.2 released to r-forge.

2014-12-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c, R/outputs.R: Viterbi algorithm now also returns the
	probability of each hidden state at each time given the data up to
	that point.

	* data/msmdata.rda: statemax added to CAV data.

	* man: Document that generic AIC function AIC() works for msm
	models.

	* DESCRIPTION: Version 1.4.1 released to r-forge.

2014-12-08 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/phase.R,R/msm.R,Rd/2phase.Rd: New features for phase-type
	models.

2014-12-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/draic.R: Bug fixes in drlcv.msm (likelihood of big model on
	left-one-out subject was using the original instead of the
	refitted model, and used covariate centering
	inconsistently). Thanks to Howard Thom.

2014-12-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.initprobs2mat,msm.form.houtput): Bug fixes for
	covariates on initial state occupancy probabilities with
	structural zeros in.  Thanks to Jeffrey Eaton and Tara Mangal.

	* R/msm.R(msm.form.output): Clean up code, also ensure models
	fitted with 1.4 can be printed with 1.4.1.

2014-11-27 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/draic.R: Bug fix in "prob > 0" in drlcv.msm. Thanks to Howard
	Thom.

	* R/msm.R: colSums efficiency improvement in msm.add.qcovs,
	msm.form.dq.  Thanks to Jeffrey Eaton.

2014-11-19 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Allow qmatrix to be passed to pmatrix.msm, and a
	list of qmatrices to pmatrix.piecewise.msm, instead of a fitted
	model.

2014-11-18 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: qmatrix.msm and related functions tidied up.

	* R/outputs.R,R/msm.R: Don't print CIs for fixed parameters in
	output formatting functions.

	* R/msm.R: Warn that polynomial contrasts aren't supported.

2014-11-11 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/pijt.c(MatrixExpEXPM): give error if optimiser has chosen
	overflowing parameter values.  Stops infinite loops seen on
	Windows.

2014-11-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Documentation and error message for factor states.

2014-10-31 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(efpt.msm): Support tostate as character.

	* man/plot.survfit.msm: Reference Turnbull method.

	* src/lik.c(GetCensored): Fixed valgrind uninitialized value warning.

2014-09-22 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/optim.R(deriv.test): require namespace instead of loading
	numDeriv

2014-07-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/analyticp.c: memory leaks removed.

2014-07-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.4 released to CRAN.

2014-07-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Default CI method for pnext.msm changed to
	"normal", since delta method may not respect probability <1
	constraint.

2014-06-23 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  C interface changed from .C to .Call.

	*  Added ppass.msm for passage probabilites.

	* DESCRIPTION: Version 1.3.3 released to r-forge.

2014-06 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: Bug fix in infosimple: info was not being initialized
	at zero, leading to occasional random output.

	* DESCRIPTION: Version 1.3.2 released to r-forge.

2014-06 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* tests: Test suite tidied up and converted to use "testthat" package.

	* R/boot.R(efpt.ci.msm): Bug fix for bootstrap and efpt.msm.

	* src/lik.c(likhidden): Give informative warning for initial
	outcomes in HMMs which are impossible for given initial state
	probabilites and outcome models.  Makes use of a global variable
	in a private environment called msm.globals.

	* draic.msm, drlcv.msm added.

2014-06 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  If msm is called with hessian=FALSE, then the Fisher (expected)
	information is used to obtain standard errors and CIs, which may
	be preferable if the observed Hessian is very intensive to
	approximate or its estimate is nonsingular / nonpositive-definite.

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  Analytic derivatives available for most hidden Markov models and
	models with censored states (excluding unknown initial state
	probabilities, constraints on misclassification / categorical
	outcome probabilities and their covariates, and truncated or
	measurement error distributions).  This should speed up
	optimisation with the BFGS or CG methods.  The corresponding
	Fisher information matrix is also available for misclassification
	(categorical/identity outcome) models.

	*  The BFGS optimisation method is now the default, rather than
	Nelder-Mead.

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* msm.optim.fixed, msm.rep.constraints: Bug fix for constraints on
	misclassification probabilities and fixed parameters.

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* msm.R(msm.mnlogit.transform): Bug fix: reapply sum to 1
	constraint after applying constraints to baseline probabilities in
	HMMs.  May affect results.

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* hmm.R(msm.econstr2hconstr): internal constraints in
	misclassification models mapped to 1,2,... using match(constr,
	unique(constr))

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* msm.R(msm.unfixallparams): Don't unconstrain constraints, so
	derivatives of fully fixed models refer to constrained pars.

2014-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  Various help pages now document the objects and data structures
	used internally and returned by msm() in the fitted model object.

2014-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* msm.R and others: major rewrite of much of the internal code
	that deals with reading the data and passing it to models.  This
	uses model frames and model formulae more efficiently.  As a
	result the "data" component of the msm has a different structure:
	a list with one component "mf", the model frame, containing all
	original variables required for the model fit.  This and related
	data structures can can be extracted with the new
	"model.frame.msm" and "model.matrix.msm" methods.

	* outputs.R: new print method now the default, and new functions
	msm.form.qoutput and msm.form.eoutput to produce the printed
	numbers in the same arrangement.

	* msm.R: Centering of "timeperiod" covariates in "pci" models is
	now done consistently with other covariates, i.e. with last
	observation omitted.

	* outputs.R(factorcov2numeric.msm): bug fix for misclassification
	covariates.

	* msm.R(crudeinits.msm): Times consistency check added.

	* msm.R(msm.check.model): Model consistency check error messages
	now report row numbers before missing data are omitted.

	* hmm.R(msm.form.hcmodel): Bug fix for when initial values for HMM
	covariate effects of wrong length, this should ignore and carry
	on.

	* pearson.R: Bug fix for when integral for accurate p-value
	doesn't converge.

	* lik.c: Don't recalculate P matrices for timelag / obstype /
	covariate combinations that occur more than once.  This may speed
	up some hidden Markov or censoring models.

2014-04-11 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* msm.R(msm.form.params): Fix of bug which broke models with
	covariates on initial state occupancy.

2014-04-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R,R/outputs.R: Parallel processing using "doParallel"
	added for bootstrapping and bootstrap CIs.

2014-04-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/optim.R: Optimisation methods abstracted into their own
	functions.

2014-04-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.3.1 released to r-forge.

2014-04-03 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.add.qcovs,msm.add.dqcovs): Fix of drop=FALSE bug for
	data with only one transition.

2014-04-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Fix of obscure bug that broke some subject-specific
	likelihoods, caused by omitting obstype.obs from data object.

2014-04-01 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Time-dependent covariates supported in totlos.msm.

	* R/outputs.R(envisits.msm, totlos.msm): New facility for expected
	number of visits.

2014-02-26 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/mstate.R,man/msm2Surv.Rd: New function for exporting data in
	counting process format for use with survival and mstate.

2014-02-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Handle convergence failure codes from optim().

2014-02-20 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(mattotrans): printnew.msm fixed for 2-state
	models. Thanks to Martyn Plummer.

2014-01-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.3 released to CRAN.

2014-01-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* inst/doc/msm-manual.Rnw: Fixed error in analytic p13(t) in
	section 1.4.

2013-12-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Experimental new print method available as
	printnew.msm.

	* srcR/pijt.c(MatrixExpPade): Fix for int coercion from special
	values, to pass CRAN UBSanitizer check.

	* src/analyticp.c: Some algebra rearranged to fix potential
	division by zeros.

	* src/analyticp.c, R/msm.R(msm.form.qmodel): Corrected permutation
	for Q matrix, fixing bug from 1.2.3 which broke models with
	non-standard state ordering.

	* R/outputs.R: New "start" argument to efpt.msm, allowing
	averaging over a set of starting states.

	* DESCRIPTION: Datasets now lazy loaded so data() not required.

2013-10-07 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.2.7 released to r-forge.

2013-10-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(observed.msm): Don't use Viterbi imputed states at
	change points when computing observed prevalences in "pci" models
	with piecewise-constant intensities.

2013-10-01 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.mninvlogit.transform): Fix for bug with
	misclassification models with only one misclassification
	probability.

	* src/lik.c: Match Q matrices with covariates from start of
	transition, not end, in likelihoods and derivatives by subject.

2013-09-13 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: "missing" for some null default arguments in msm()
	changed to is.null.

	* DESCRIPTION: Version 1.2.6 released to r-forge.

2013-08-30 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.R): Give an informative error if trying to use
	gen.inits with a HMM, and document that this is not supported.

2013-08-20 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.check.times): Row numbers reported in error message
	about different states at the same time corrected to account for
	missing data.  Thanks to Lucy Leigh for the report.

2013-07-30 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: formula for totlos.msm implemented, which is vastly
	more efficient than the numerical integration used previously.
	Debugging outputs left in 1.2.3 also removed.

	* R/msm.R, src/*.c: Likelihood calculations use expm from the expm
	package by default where matrix exponentiation is required.  As a
	result msm now depends on the expm package.

	* R/utils.R: MatrixExp now uses expm from the expm package by
	default.

	* R/various: some fixes for bugs introduced by the range facility.

	* DESCRIPTION: Version 1.2.5 released to r-forge.

2013-07-22 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/(various): Range constraints can now be given for HMM outcome
	parameters, through a new argument "hranges" to msm(). This may
	improve HMM identifiability.  Thanks to Soon-Ee Cheah for the
	suggestion.

	* R/constants.R: Scale parameters of Weibull and t HMM outcome
	distributions now restricted properly to be positive in estimation.

	* DESCRIPTION: Version 1.2.4 released to r-forge.

2013-07-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: MatrixExp rewritten to use C code for series method
	and analytic solutions for Markov models, avoiding code
	duplication.

2013-07-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: If available, loglikelihood derivatives, expected and
	(if requested) observed information are returned in paramdata
	component for all models. If all parameters fixed, these are over
	all parameters.  If some are fixed, than these are just over the
	parameters that are optimised.

	* R/outputs.R: surface.msm fixed for models fitted with Fisher
	scoring.

2013-06-06 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: totlos.msm was calculating the wrong thing for
	fromt > 0.

	* DESCRIPTION: Version 1.2.3 released to r-forge.

2013-06-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Corrected data rows mismatch in bootstrapping with
	imputed sampling times after deaths in Pearson statistic.

	* src/lik.c: Memory crash bug in Viterbi fixed.

2013-06-03 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* (Most R and C files): Major restructuring of the internals.
	Main change is to adjust all parameters for covariates in R rather
	than C, making for much tidier code. New R functions for applying
	transformations and inverse transformations.

	* src/pijt.c: Derivatives of the likelihood for non-hidden models
	now work properly with negative constraints.

	* R/msm.R: Initial state occupancy probabilities are estimated on
	the multivariate logit scale, rather than univariate logit, and
	confidence intervals are calculated using the normal simulation
	method.  Probability for the baseline category "initpbase" is now
	a labelled parameter.

	* R/msm.R: When centering covariates around their means for the
	default likelihood calculation, the means used are now after
	dropping missing values and subjects with one observation, not
	before.  Thanks to Howard Thom for the report.

	* Relatedly, the covariate values for subjects' last observations
	are not included in this mean, since they don't contribute to the
	likelihood, so interpretation of initial values for the qmatrix,
	and outputs for covariates="mean", will now be very slightly
	different.

2013-05-28 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* inst/doc/msm-manual.Rnw: Likelihood for exact times still had
	wrong sign for qii (see version 1.1.2).

2013-05-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* inst/doc/msm-manual.Rnw: Added advice about "function cannot be
	evaluated at initial parameters".

2013-05-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: New interface for supplying different covariates on
	different transition intensities.

	* R/msm.R: Redundant constraint check and factor warning fixed and
	cleaned.

2013-05-23 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.form.covdata): checks on constraints and covinits
	separated into new functions.

	* R/msm.R(msm.form.covmodel): wrong names in error message for
	constraint length checking.

2013-05-21 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.form.data): Handle factor states (with levels
	1:nstates) by converting to numeric.

	* R/msm.R, src/lik.c: Can now print subject-specific
	log-likelihoods at the MLE via logLik.msm().

	* DESCRIPTION: Version 1.2.2 released to r-forge.

2013-05-19 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: qtnorm, qmenorm, qmeunif and qpexp changed to use
	qgeneric. Their results should be the same.

	* R/utils.R: long-redundant identity function finally removed.

2013-05-18 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: qgeneric function copied from flexsurv
	package and modified to handle argument clashes.

	* R/utils.R: Return NaN for all dpqr(tnorm,menorm,meunif) if lower
	bound greater than upper bound.

2013-05-17 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Don't warn if not all states observed in data for
	misclassification models (typo bugfix in msm.form.data).

2013-05-16 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R,R/hmm.R,src/lik.c: Allow matrix by patient to be
	supplied for the initial state occupancy probabilities.

	* DESCRIPTION: Version 1.2.1 released to r-forge.

2013-05-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: move gen.inits from msm.form.qmodel to main function.

2013-05-14 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.2 released

2013-05-08 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R,R/outputs.R: Misclassification models where some
	off-diagonal misclassification probabilities are 1 are now handled
	properly.  Thanks to Howard Thom for uncovering this.

2013-04-19 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: prevalence.msm can now produce expected values by
	integrating model predictions over the covariate histories
	observed in the data.

	* R/msm.R(msm.form.data): Drop subjects with only one observation
	remaining after dropping missing data (e.g. psor data).  This gives
	a more appropriate measure of the numbers at risk in prevalence.msm.

2013-04-18 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(summary.msm): Allow arguments to be passed through
	summary.msm to prevalence.msm.

	* R/outputs.R(pmatrix.piecewise.msm): Allow this to be used for
	time-homogeneous models with change point vector "times" of length
	0.

2013-04-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: New function efpt.msm for expected first passage
	times for time-homogeneous models.  Thanks to Howard Thom for the
	research.

	* R/outputs.R: totlos.msm now passes options to integrate() to
	bootstrapping functions.

2013-04-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.form.data: firstobs was wrong with missing data.

2013-04-08 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/simul.R, R/pearson.R: Function boot.param.msm renamed to
	simfitted.msm and made user-accessible.

2013-04-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Accurate p-values from Titman (Lifetime Data
	Analysis, 2009).

	* R/pearson.R: Degrees of freedom were being calculated
	incorrectly (via "n.zerofrom" variable) when user-defined groups
	included from-states.

	* R/simul.R: Include an option to simmulti.msm (and getobs.msm) to
	not drop absorbing-absorbing transitions.

2013-03-22 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Fix of bug in Pearson test introduced in version
	0.9.5, which affected the expected transitions to the final state
	(and resulting test statistics) for panel data without exact death
	times.

	* src/lik.c, src/pijt.c: Implement the Fisher information for
	non-hidden models without censored states.

	* R/msm.R: Implement a Fisher scoring algorithm which uses this
	expected information.

2013-02-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(observed.msm): Add a censoring time facility to
	optionally remove subjects from the risk set a certain time after
	they have reached an absorbing state.  Thanks to Andrew Titman.

2013-02-02 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: Bug fix for Viterbi with obstrue. Thanks to Linda
	Sharples.

	* R/outputs.R(print.msm): Don't print message about baseline
	covariate values in misclassification model outputs if there are
	no covariates.

2013-01-14 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(observed.msm): Bug fix for interp="midpoint" method
	in observed prevalence calculation.  Thanks to Erica Liu.

2012-12-10 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* tests/simple.R: Modified pmatrix.msm normal bootstrap test
	output to work with new seeding behaviour of rmvnorm.

	* DESCRIPTION: Version 1.1.4 released

2012-09-28 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/doc: Remember to copy the up-to-date manual source into src
	for new releases, as required by Linux distribution package
	builders.

	* DESCRIPTION: Version 1.1.3 released

2012-09-27 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* inst/doc/msm-manual.Rnw: Work around texi2dvi problem where
	non-breaking spaces appear as tildes.

2012-09-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(qematrix.msm): Bug fix for user-supplied covariate
	values when center=FALSE.  Thanks to Vikki O'Neill for the report.

2012-09-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/boot.msm.Rd: Documented failure of boot.msm to handle
	user-defined objects that clash with built-in objects.

2012-09-21 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Use BFGS method for one-parameter optimisation unless
	method supplied explicitly, avoiding warning about unreliability
	of Nelder-Mead.

2012-07-31 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Browser was still on for pearson.msm.  Thanks to
	Chyi-Hung Hsu.

	* DESCRIPTION: Version 1.1.2 released

2012-05-28 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* (various files): New Student t distribution for hidden Markov
	model outcomes.  Thanks to Darren Gillis.

2012-05-11 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.check.times): Bug fix in data consistency checks
	with unsorted subject IDs. Thanks to Kelly Williams-Sieg for the
	report.

	* DESCRIPTION: Version 1.1.1 released

2012-05-01 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: Corner cases in qtnorm fixed. Thanks to Art Owen for
	the report.

	* R/boot.R: Multicore functionality removed from this release
	since doSMP was removed from CRAN.  Will restore when a stable
	preferred cross-platform solution emerges.

2012-01-31 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Bug fix for models where transitions are only
	allowed from one state.  Thanks to Gavin Chan for the report.

2012-01-31 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: If user supplies an ematrix with all misclassification
	probabilities zero, the non-misclassification model is fitted.
	Thanks to Sharareh Taghipour for the report.

	* R/msm.R(msm.check.model): Bug fix for error messages when model
	inconsistent with data.

2011-11-28 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R: boot.msm and functions which use this can now use
	doSMP to parallelise calculations.

2011-11-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R: Fix of bug which affected calculation of confidence
	intervals by the "normal" method when there were fixed parameters
	or HMMs.

2011-10-27 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Bug fix: Subset function "[.msm.est" was labelling
	columns wrong for objects with no SE component (pmatrix.msm,
	pnext.msm).

2011-09-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.1 released

2011-07-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: New function "[.msm.est" to extract specific rows
	and columns of the output from, e.g., qmatrix.msm() in a more
	intuitive way.

2011-07-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: New function "pnext.msm" to compute a matrix of
	probabilities for the next state of the process.

2011-07-07 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/msm.Rd: Doc clarifies that "death" is overridden by
	"obstype" and "exacttimes", and "exacttimes" is overridden
	by "obstype".

2011-06-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/msm.Rd: Correct documentation for factor levels of
	"timeperiod".

	* R/outputs.R(qematrix.msm): Fix CIs for diagonal entries when
	first state is absorbing.

	* R/msm.R(msm.check.model): Refer to observation numbers, not
	transition numbers, in "data inconsistent with model" error
	message.

2011-05-26 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 1.0.1 released

2011-05-20 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(msm.fill.pci.covs): Bug fix, pmatrix.msm would break
	for models with non-integer time change points "pci". Thanks to
	Christos Argyropoulos for the report.

	* man/prevalence.msm.Rd: Clarify that "piecewise.times" is not
	needed for models fitted with "pci". Thanks to Christos
	Argyropoulos.

	* R/msm.R(msm): Warning if initcovariates is supplied but the
	model is not hidden Markov. Thanks to Christos Argyropoulos.

2011-05-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R(dtnorm): Return -Inf when log=TRUE and x outside
	truncation bounds.  Thanks to William Leeds for the report.

2011-02-08 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/msm.Rd: Help page clarified to say that "state" is also used
	for the observed outcome in a HMM. Thanks to Ricardo Antunes.

2010-11-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Line types, colours and widths can be configured in
	plotprog.msm, plot.survfit.msm and plot.prevalence.msm.

	* DESCRIPTION: Version 1.0 finally released to accompany the
	forthcoming paper on msm in Journal of Statistical Software.

2010-11-12 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/msm.Rd: Documentation for the return value of msm corrected
	to state that the "logbaseline" components of result matrices are
	evaluated with covariates set to zero if center=FALSE, and at
	their means if center=TRUE.  Previously it stated that
	"logbaseline" was evaluated at the mean covariate values.

	* R/msm.R(msm), R/outputs.R(print.msm): Return the "baseline" and
	"sojourn" components of result matrices at covariate values of 0
	if center=0.  Thanks to Kenneth Gundersen for the report.

2010-11-01 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R(bootdata.trans.msm): Fix for bootstrapping when some
	levels of a factor do not appear in a bootstrapped dataset.
	Thanks to Gale Bravener for the report.

2010-10-29 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.check.times): Fixed a bug in comparing small floating
	point numbers to zero, and added "may be" to warning about data
	inconsistent with transition matrix, due to uncertainty about
	these comparisons.

2010-09-22 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.check.times): Added warning for multiple observations
	at the same time on the same person with different states, which
	leads to zero likelihood and "cannot be evaluated at initial
	values" message.

2010-05-18 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 0.9.7 released

2010-05-07 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Ematrices and ematrix.msm for models with all
	"fixedpars" returned correctly.

2010-05-04 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R: Bug fixes.  "end" argument wasn't included in
	totlos.ci.msm and totlos.normci.msm, bootstrapping broke with
	covariates on HMM outcomes, and "fixedpars" weren't accounted for
	in normboot.msm.  Thanks to Li Su for these reports.

2010-02-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Fix for "NA in probability vector" error caused by
	floating point comparisons in empiricaldists(), which were still
	happening.  Thanks to Wen-Wen Yang for the report.

	* DESCRIPTION: Version 0.9.6 released

2010-01-29 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/pijt.c(Pmat): Don't round extreme likelihood contributions
	to 0 and 1 for models with "exacttimes", since they are not
	probabilities.  Fixes occasional wrong likelihood calculations.

2010-01-14 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: The "pci" element of fitted model objects now excludes
	values which are outside the time range of the data.  Allows
	pmatrix.msm to be used on such models without error.  Also give a
	warning when any "pci" cut points equal the min/max time point in
	the data.  Thanks to Matt Cowperthwaite.

2009-11-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Fix for problem revealed by different handling of
	factors in R-2.10.0, which caused all expected values to be
	returned as zero.  Thanks to Brian Tom for the report.

	* DESCRIPTION: Version 0.9.5 released.

2009-11-13 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.form.data): Bug fix for handling missing subject ID.

	* DESCRIPTION: Version 0.9.4 released.

2009-11-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(pmatrix.msm, pmatrix.piecewise.msm): Allow options
	to MatrixExp to be passed through.

	* R/msm.R(crudeinits.msm): Don't break with missing values.

2009-09-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/likderiv.msm: Bug fix: Use obstype.obs when calculating score
	residuals, not obstype. Also fixed misplaced for loop initialising
	patient derivatives to zero in src/lik.c(derivsimple_subj). Thanks
	to Aidan O'Keeffe for the report.

2009-08-26 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Fix for "replacement has 0 rows" error - don't add
	covariates column to internal data when there are no covariates.

 	* R/pearson.R: timeinterval rounded in empiricaldists to avoid "NA
	in probability vector" errors in R-devel arising from floating
	point fuzz.

2009-08-20 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: fix of previous bug fix from 06-24 for derivatives with
	respect to fixed parameters.  Thanks to Aidan O'Keeffe for the
	report.

	* DESCRIPTION: Version 0.9.3 released.

2009-07-27 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R(msm.form.output): Bug fix - estimates of covariate
	effects were being ordered wrongly in matrices outputted by msm in
	models with "qconstraint". Thanks to Brian Tom for the report.

2009-06-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 0.9.2 released.

2009-06-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Bug fix - don't return derivatives with respect to
	fixed parameters - this was causing "gradient in optim evaluated
	to wrong length" error for models with fixed parameters fitted
	using BFGS. Thanks to Isaac Dinner for the report.

2009-06-12 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* tests/simple.R: Removed a couple of tests which fail due to
	floating point fuzz on Fedora/Red Hat PPC Linux.

	* DESCRIPTION: Version 0.9.1 released.

2009-06-09 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Covariate grouping fixed to 1 for pci models with
	no other covariates, as the covariate group is equivalent to the
	time group.

	* DESCRIPTION: Version 0.9 released.

2009-06-05 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Licence altered from GPLv2 to GPL v2 or later.
	Licence text removed from src/pijt.c.

	* R/msm.R(msm): Default changed to use.deriv=TRUE.

	* R/msm.R(msm.pci): Don't impute observations for pci models at
	times when there is already an observation.  This fixes "times not
	ordered" errors when bootstrap resampling for Pearson test.

2009-04-29 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(factorcov2numeric.msm): Extractor functions now set
	unspecified covariate values in covariate lists to 0, and ignore
	unknown covariates.

	* R/outputs.R(factorcov2numeric.msm): All extractor functions can
	now accept covariate values as numeric contrasts as well as factor
	levels.

	* R/outputs.R(plot.survfit.msm): Call to survfit fixed for
	compatibility with R version 2.9.0.

	* R/outputs.R(pmatrix.msm): Adapted to automatically handle "pci"
	models with piecewise constant intensities, with new "t1" argument
	representing start time.  New internal function
	"msm.fill.pci.covs" to enable time-constant covariates to be
	passed through this facility properly.  Arguments of all calls to
	pmatrix.msm changed.  As a result, functions which call
	pmatrix.msm (prevalence.msm, expected.msm, totlos.msm,
	plot.survfit.msm) now handle time-inhomogeneous models specified
	using "pci".

	* R/msm.R(msm.pci): Bug fix - covmeans calculated wrong in pci
	models with other covariates, leading to error in qmatrix.msm for
	covariates=0.

2009-04-29 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: Bug fix - score residuals were being calculated
	wrongly for models with covariates.

2009-04-24 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Fixed "second argument must be a list" bug.

	* R/outputs.R: Order of effects in hazard.msm and odds.msm changed
	to read across rows of the transition/misclassification
	matrix. This is for consistency with, e.g. fixedpars.

2009-04-08 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* man/msm.Rd: Documentation for qconstraint clarified.

	* R/outputs.R: Bug fix - interactions now expanded properly when
	calling extractor functions for models with interactions between
	covariates.

	* R/msm.R: Bug fix which affected bootstrap refitting in
	pearson.msm, giving "Error in `$<-.data.frame`(`*tmp*`,
	"pci.imp"..."

	* DESCRIPTION: Version 0.8.2 released.

2009-04-03 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	*  LaTeX sources for PDF manual included in src/doc to enable
	msm to be approved as a Debian package.

2008-07-25 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: Bug fix, maxtimes was producing negative censoring
	times.

	* DESCRIPTION: Version 0.8.1 released.

2008-07-23 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: New option "pci" to msm, which automatically constructs
	a model with piecewise-constant transition intensities which
	change at the supplied times.

	* R/boot.R: Give an informative error in normal theory CIs when
	SEs not available from fitted model.

2008-07-22 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c (GetOutcomeProb): HMM now applies to censored
	outcomes, unless obstrue = 1.  Thanks to Norm Good for the
	suggestion.

2008-04-15 Chris Jackson  <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: deriv.test argument to msm removed.

	* src/lik.c: Bug fix in liksimple/derivsimple - the P matrix was
	not being recalculated when the obstype changed between 1 and 2.
	Thanks to Peter Jepsen for uncovering this.

2008-03-31 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: totlos.msm now computes total length of stay for
	all states, not just transient states. New argument "end" added.

	* R/outputs.R: xlim argument added to plotprog.msm.

	* R/outputs.R: legend added to plot.prevalence.msm.

2008-03-28 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 0.8 released.

2008-03-18 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/pearson.R: New file for the Pearson-type goodness-of-fit
	test. Thanks to Andrew Titman for his work on this.

	* data/heart.txt: Data "heart" renamed to "cav".

	* R/simul.R: any() bugs in simmisc.msm for simulating
	misclassification models fixed

2008-03-11 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: logLik.msm degrees of freedom corrected for models
	with parameter constraints.

	* R/outputs.R: New function "plot.survfit.msm" to plot
	  Kaplan-Meier estimate of survival probabilty compared with the
	  fitted survival probability from a model.

	* R/outputs.R: Allow customisable axis titles and line widths in
	all plot functions.

2008-03-03 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: New function "plotprog.msm" to plot Kaplan-Meier
	estimates of time to first occurrence of each state.  Added
	"survfit" and "Surv" imports from the "survival" package.

	* R/outputs.R: New likelihood ratio test function
	"lrtest.msm".

2008-03-03 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: logLik method returns the log-likelihood, not the
	minus log-likelihood. Thanks to Jay Rotella for the report.

2008-02-27 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: Transformation bug fixed which caused rtnorm to hang
	for extreme means. Thanks to Björn Bornkamp.

2008-02-18 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R: Simulate normal CIs using unreplicated parameters, so
	that they work with the new release of mvtnorm.  Thanks to Peter
	Jepsen for the report.

2007-12-12 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R,src/lik.c: Score residuals implemented.

2007-12-10 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: Quantile functions: uniroot() convergence tolerance
	tightened to solve problems with obtaining quantiles for small
	arguments.  Thanks to Barbara Bredner for the report.

	* DESCRIPTION: Version 0.7.6 released.

2007-11-21 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/simul.R: Bug fix, "cur.t not found" error.

	* R/simul.R: Allow covariates on misclassification probabilities
	in simulations

2007-11-20 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Don't give no-SEs warning when hessian=FALSE

	* R/simul.R: Handle only one observation per subject.

	* R/outputs.R: New internal function intervaltrans.msm to
	determine set of allowed transitions in an interval.

	* DESCRIPTION: Version 0.7.5 released.

2007-11-08 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(qratio.se.msm): Bug fix for factor
	covariates. Thanks to Peter Jepsen.

2007-11-05 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R (bootdata.trans.msm,bootdata.subject.msm), R/msm.R
	(msm.form.data,msm.form.covdata): Handle factor covariates
	properly when bootstrap refitting, by retaining the original
	covariates (not the numeric contrasts) in the data.  Thanks to
	Peter Jepsen.

	* R/outputs.R: qmatrix.msm, ematrix.msm, sojourn.msm and
	qratio.msm can now be called with ci="none", returning just the
	matrix of estimates, with no CI.

2007-11-02 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: MatrixExp now accepts a vector of t, in which case it
	only needs to calculate the eigensystem once.

2007-10-30 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: Bug fix in ppexp. Thanks to Mike Murphy.

	* msm-manual: More explanation of censored states versus censored
	event times.

2007-10-25 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/hmm.c: New beta HMM outcome distribution.

	* src/lik.c: Ignore initprobs in HMMs if the true state is known
	at the initial observation.

2007-10-24 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/lik.c: Handle censoring properly in Viterbi algorithm.

2007-10-22 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/boot.R(bootdata.subject.msm): Bug fix, wrong covariate matrix
	was being read.  Thanks to Peter Jepsen for the report.

	* msm-manual.pdf: Correction of algebraic typos in Viterbi
	algorithm.

	* src/lik.c: Account for obstrue in Viterbi algorithm.

	* R/outputs.R: Allow Viterbi algorithm to be used to impute
	censored states in data with censored states but no HMM.

2007-10-18 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(prevalence.msm,plot.prevalence.msm): Account for
	arguments supplied to prevalence.msm when doing the plot.  Thanks
	to Peter Jepsen for the report.

2007-10-01 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/Makevars: CR endings removed to satisfy R CMD CHECK in R 2.6.0

	* R/outputs.R(print.msm.est): test for CI using is.list(), since $
	on an atomic object fails in R 2.7.0 instead of returning NULL.

	* DESCRIPTION: Version 0.7.4 released.  Use standardised license string.

2007-08-15 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 0.7.3 released.

2007-08-14 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

        * R/boot.R: Handle obstype and obsmisc in bootstrap refitting, and
	handle refitting of msm models where obstype, obsmisc and subject
	vectors are calculated within the argument to msm.  Thanks to
	Peter Jepsen for the report.

	* R/boot.R, R/outputs.R: Add bootstrap handlers (both
	nonparametric and normal-theory) for qmatrix.msm, ematrix.msm,
	sojourn.msm, qratio.msm, pmatrix.piecewise.msm, totlos.msm,
	prevalence.msm.

2007-07-27 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* src/analyticp.c: Bug fix: exponential of certain degenerate 5
	state intensity matrices was not being calculated properly. Thanks
	to Ross Boylan for the report.

	* man/msm.Rd: Make clear that the initial values for constrained
	parameters are taken from the first of the multiple initial values
	supplied.  Thanks to Ross Boylan.

2007-06-30 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(surface.msm): Bug fix: don't include auxiliary
	parameters in HMMs. Thanks to Michael Sweeting.

2007-06-29 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R(MatrixExp), src/pijt.c(MatrixExp): Bug fix. When there
	are complex eigenvalues, don't use the eigensystem method of
	calculating the matrix exponential. Thanks to Véronique Bouchard.

2007-06-05 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R(expected.msm): Bug fix, wrong risk set was being
	calculated for user-specified "times".

	* R/outputs.R(observed.msm): Allow interpolation of observed
	states using the midpoint of an interval.

	* R/outputs.R(pmatrix.msm), R/boot.R: Confidence intervals for P
	matrix can now be calculated by simulating from multivariate
	normal distribution of MLEs.

	* R/outputs.R(plot.prevalence.msm),man/plot.prevalence.msm.Rd: new
	function for prevalence plots.

	* man/pmatrix.piecewise.msm.Rd: Example corrected to use four sets
	of covariates. Thanks to Qing Wang.

	* DESCRIPTION,NAMESPACE: Added rmvnorm import from "mvtnorm" package.

2007-05-31 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* DESCRIPTION: Version 0.7.2 released.

2007-05-29 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/outputs.R: Functions to calculate SEs and CIs for ematrix.msm
	adapted to deal with multinomial logistic regression.  CIs for
	probabilities are calculated using delta method approximation to
	variance of logit p, instead of log p as previously.

2007-05-26 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/utils.R: Truncated normal random sampling algorithm
	improved to use the rejection method by Christian Robert.
	Thanks to Vivek Roy for the suggestion.

2007-05-25 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Constraints on intensity covariate effects that some
	effects are equal to other effects multiplied by -1 are now
	allowed.

	* R/msm.R: Structural zeroes are allowed for initial state
	occupancy probabilities.

	* inst/doc/msm-manual.pdf: Misclassification examples on heart
	data changed so that individuals' first observations are not
	misclassified.

2007-05-21 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/lik.c: Serious bug fix. Effects of covariates on outcome
	probabilities in misclassification models (categorical HMMs) are
	now estimated using multinomial logistic regressions, instead of
	(incorrectly) independent univariate logistic regressions for each
	probability.

	* R/msm.R, R/lik.c: Effects of covariates on initial state
	probabilities in HMMs can now be estimated through multinomial
	logistic regression.

2007-05-13 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

        * R/outputs.R, R/boot.R: New option "ci.boot" to prevalence.msm, a
	helper to calculate bootstrap confidence limits for the expected
	prevalences using "boot.msm".

	* R/msm.R, src/lik.c: New argument "obstrue" to msm, to allow some
	observations to be observed without error in misclassification models.

2007-05-11 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

        * R/msm.R: Return derivatives in $deriv component of the msm
	object after optimisation. Thanks to Ole Rummel.

2007-04-18 Chris Jackson   <chris.jackson@mrc-bsu.cam.ac.uk>

	* R/msm.R: Don't drop covariates on transition process which are
	missing at the last observation for a patient, because they are
	not used in the analysis.  This has the consequences that output
	from prevalence.msm may be different from earlier versions (0.7 or
	earlier) if there are missing values in the data.  Users are
	advised to drop missing values from their data (if statistically
	appropriate!)  before using msm.

	* DESCRIPTION: Maintainer email address changed.

	* DESCRIPTION: Version 0.7.1 released.

2007-04-05 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(viterbi.msm): Bug fix for models with
	covariates. Thanks to Hongjie Wang.

	* R/outputs.R(prevalence.msm): Can now calculate expected
	prevalences for models with piecewise-constant intensities, in the
	same manner as pmatrix.piecewise.msm.

2007-04-04 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(prevalence.msm): Bug fix, initstates was being
	ignored. Thanks to Peter Jensen.

	* R/msm.R: Give a warning when the standard errors cannot be
	calculated.

	* R/msm.R(msm.form.houtput): Bug fix for initprobs display with
	only two states.

2007-03-02 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(print.msm, qematrix.msm): Bug fix: When
	center=FALSE, reported baseline intensity matrix should be
	labelled as with covariates set to zero, not at their means.
	Thanks to Ross Boylan.

2007-02-09 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/lik.c: Return likelihood of zero for individuals with only
	one observation in censoring and hidden models. Thanks to Jonathan
	Williams for discovering the bug.

	* data/heart.txt: Age at transplant date corrected.  Thanks to
	Jonathan Williams.

2006-11-21 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R: Initial state occupancy probabilities can now be
	estimated. See new argument "est.initprobs" to msm.

	* DESCRIPTION: Version 0.7 released.

2006-11-20 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R(sim.msm): Transpose error in bug fix from 0.6.4
	corrected.

	* R/outputs.R: Values of factor covariates are now supplied to
	extractor functions in a sensible way, at last.	 Reordering bug
	fixed with named covariate lists.

2006-11-19 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/boot.R: New file. Implements bootstrap resampling for fitted
	msm models.

	* R/outputs.R: Bootstrap confidence intervals available for
	pmatrix.msm and totlos.msm.

	* R/outputs.R: pmatrix.msm now defaults to one time unit, instead
	of forcing time unit to be explicitly given.

	* R/outputs.R: observed.msm function rewritten. Fixes bug in
	calculating observed prevalence for state at maximum observed
	time, reported by Jeremy Penn.  It is also now much faster.

	* R/outputs.R: prevalence.msm is also adapted sensibly to handle
	data where not all individuals start at a common time.

2006-09-29 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* man/deltamethod.Rd: Example fixed to use correct covariance
	matrix. Thanks to Andreas Beyerlein.

2006-09-21 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/Makevars: PKG_LIBS fix to pass R CMD CHECK in R 2.4.0

	* DESCRIPTION: Version 0.6.4 released.

2006-09-12 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R(sim.msm) Bug fix: multiply covariates by baseline
	intensities in the correct order.  Also convert vector beta to
	matrix. Thanks to Stephan Lenz for the report.

2006-09-08 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/utils.R(rtnorm) Bug fix: use the correct components of
	parameters which are vectors.  Thanks to Jean-Baptiste Denis
	for the report.

2006-07-16 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* Rd/msm.Rd, inst/doc/msm-manual.pdf: Documentation correction -
	the initial values of the qmatrix are with covariates at their
	means in the data, not with the covariates at zero.  This bug
	has existed since version 0.5.

2006-07-16 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R: Row and column names of crudeinits output retained from
	qmatrix input.

2006-06-29 Chris Jackson   <chris.jackson@imperial.ac.uk>

	*  Definition of initprobs corrected on manual p31.

2006-06-28 Chris Jackson   <chris.jackson@imperial.ac.uk>

	*  References reinstated in the PDF manual.

	* DESCRIPTION: Version 0.6.3 released.

2006-06-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* DESCRIPTION: Version 0.6.2 released.

2006-06-21 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.obs.to.fromto,msm.check.times: Support character subject
	variables.  Thanks to Danstan Bagenda for the report.

2006-06-21 Chris Jackson   <chris.jackson@imperial.ac.uk>

	*  Analytically-calculated transition probability matrices
	implemented for selected 3, 4 and 5 state models. These are
	calculated in new file src/analyticp.c.  New option "analyticp" in
	msm() to revert to the old matrix exponential method.
	Update to msm-manual.pdf describing this method.

2006-06-20 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R(getobs.msm): Bug fix - Keep only one observation in
	the absorbing state when absorbing state is not the highest state.

2006-05-29 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* man/logLik.Rd: help page fixed to explain that this returns the
	minus log likelihood. Thanks to Ole Rummel.

	* msm.R (likderiv.msm): bug fix - transformation of the
	derivatives when all parameters are fixed was returning all NAs.

2006-03-26 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* lik.c(Viterbi): Bug fix - don't ignore initprobs.  Thanks to
	Melanie Wall for reporting this.

	* DESCRIPTION: Version 0.6.1 released.

2006-03-15 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* NAMESPACE: Import persp, plot and contour in from graphics.

	* msm.R (msm.check.times): Bug fix for factor subjects with empty
	levels. Thanks to Jacques Gautrais.

2006-01-04 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.R (msm.form.data): use match(, unique()) to convert subject
	to ordinal, not factor.  Also do msm.check.times after dropping
	missing data. Plus fix for missing obstime.

2005-11-25 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* DESCRIPTION: Version 0.6 released.

2005-11-17 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R: New function surface.msm for surface plots of
	likelihoods.

2005-11-16 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* lik.c,pijt.c, etc.: Analytic derivatives of the likelihood
	implemented for all models, apart from hidden Markov models or
	models with censoring.  New argument "use.deriv" to tell msm to
	use these where appropriate.  Thanks to Andrew Titman for the
	debugging help.

	*  The Dennis and Schnabel algorithm in the R function "nlm" can
	now also be used to maximise the likelihood, as an alternative to
	the algorithms in "optim".

2005-11-11 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm-manual.pdf: definition of initial state probability f
	corrected in hidden likelihood, equation 13.  Thanks to Andrew
	Titman.

2005-11-08 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* man/deltamethod.Rd: Documentation of deltamethod clarified to
	explain how to use user-defined variables within the formula.

2005-10-11 Chris Jackson   <chris.jackson@imperial.ac.uk>

	*  Negative binomial hidden Markov model output distribution added.

	* DESCRIPTION: Version 0.5.2 released.

2005-10-10 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* lik.c(Viterbi): Bug fix, wasn't handling Markov chains with
	progressive and regressive states properly.  Thanks to Rochelle
	Watkins.

	* msm.R(msm.form.covdata): further fix for missing data.

2005-10-1 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.form.qmodel: Bug fix with gen.inits==TRUE and
	censoring. Thanks to Jacques Gautrais.

2005-07-27 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* sim.msm: collapse.covs fixed to handle covariate matrices with
	one observation time.

	* msm.R(msm.form.covdata): bug fix for covariates in global
	environment, not a data frame. This bug produced the error "Error
	in 1:n : NA/NaN argument".

2005-05-27 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* sim.msm: sample replaced by resample as in ?sample, to fix
	simulations with small models.

	* msm.R: Fix for one-parameter models. (drop=FALSE in subsetting covmat)

2005-05-25 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* utils.R: New functions (dpqr)pexp for the exponential
	distribution with piecewise-constant rate.

	* utils.R: Bug fix: arguments lower.tail and log.p implemented for
	truncated normal and measurement error distributions.

	* DESCRIPTION: Version 0.5.1 released.

2005-05-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* tests/*: Tests are now fully automated. Outputs are compared
	against known results using stopifnot().

	* outputs.R(hazard.msm, odds.msm) Names "L95", "U95" changed to
	"L","U" for generality.

2005-05-20 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.R: Data reorganised so that covariates are stored in a
	matrix throughout.  These are available from the model output as
	cov for one per observation time, and covmat for one per time
	difference.  This fixes a bug which prevented covariates with
	names such as "state", "time", "subject", among others, from being
	used.

2005-05-16 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* simul.R(sim.msm) Re-written. Fixes a bug in simulating from
	models with time-dependent covariates, where not every covariate
	change was accounted for.  Uses new function rpexp to simulate
	from the exponential distribution with piecewise-constant rate.
	Thanks to Mike Sweeting for the bug report.

	* simul.R(sim.msm) Simulations now contain a censoring time at
	maxtime, instead of the future absorption time.

	* simul.R(getobs.msm) Re-written, replacing ugly loops with
	vectorised code.

2005-04-11 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* man/simul.Rd: clarified that qmatrix is with covariates set to
	zero.  Thanks to Anne Presanis.

2005-04-11 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* outputs.R(pmatrix.piecewise.msm): Bug fix for times of length 1.
	Thanks to Anne Presanis.

2005-03-09 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* pijt.c(Pmat): Don't recalculate pii within j loop.

2005-03-08 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* pijt.c: New function Eigen. MatrixExp merged into one function.

2005-03-07 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.R(msm): Argument "hessian" added to msm.  Covariance matrix
	is set to NULL instead of a string when SEs not available.

	* msm.R(msm): Confidence limits of fixed parameters set to NA, not
	zero width.

2005-03-06 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* DESCRIPTION: Version 0.5 released.  This is a major re-write, so
	instead of a detailed change log, the NEWS entry is reproduced
	below.

Version 0.5 (2005-03-06)
-----------

* Major update. Much of the internal R and C code has been re-written.

* General continuous-time hidden Markov models can now be fitted with
  msm, as well as misclassification models.  Allowed response
  distributions conditionally on the hidden state include categorical,
  normal, Poisson, exponential and others.  See the new "hmodel"
  argument. Misclassification models can either be fitted in the old
  style using an ematrix, or using a general HMM with a categorical
  response distribution.  Covariates can be fitted to many of the new
  hidden response processes via generalized regressions.  See
  "hcovariates", "hcovinits" arguments.

* Per-observation observation schemes, generalising the "exacttimes"
  and "death" concepts.  An optional new variable in the data can
  specify whether each observation is a snapshot of the process, an
  exactly-observed transition time, or a death state.  Observations
  are allowed to be at identical times, for example, a snapshot
  followed instantly by an exact transition time.

* Various syntax changes for cleaner moder specification.

  - Instead of 0/1 indicators, qmatrix and ematrix should contain the
  initial values for the transition intensity / misclassification
  matrix.  These matrices can be named with names for the states of
  the Markov chain.

  - The inits argument is abolished.  Initial values are estimated
  automatically if the new argument to msm "gen.inits = TRUE" is
  supplied.  This uses the initial values calculated by
  crudeinits.msm.

  - misc no longer needs to be specified if an ematrix is supplied.

  - fixedpars=TRUE fixes all parameters, or specific parameters can
  be fixed as before.

  - crudeinits.msm takes a state ~ time formula instead of two
  separate state, time arguments, for consistency with the msm
  function.

  - Initial values for covariate effects on transition rates /
  misclassification probabilities are assumed to be zero unless
  otherwise specified by the new "covinits" / "misccovinits" argument.

* Support for 'from-to' style data has been withdrawn. Storing data in
  this format is inadvisable as it destroys the longitudinal nature of
  the data.

* Speed improvements.  The algorithm for calculating the likelihood
  for non-hidden multi-state models has changed so that the matrix
  exponential of the Q matrix is only calculated once for each time
  difference / covariate combination.  Therefore, users should see
  speed improvements for data where the same from-state, to-state,
  time difference, covariates combination appears many times.

* Confidence intervals are now presented instead of standard errors
  for uncertainty in parameter estimates.

* New method of calculating matrix exponentials when the eigenvector
  matrix is not invertible.  It now uses the more robust method of
  Pade approximants with scaling and squaring, instead of power
  series.  Faster LAPACK routines are now used for matrix inversion.

* covmatch argument to msm has been abolished.  To take a
  time-dependent covariate value from the end of the relevant
  transition instead of the default start, users are expected to
  manipulate their data accordingly before calling msm, shifting the
  positions of the covariate back by one within each subject.

* Syntax changes for simmulti.msm.

Bug fixes
---------

* The likelihood is now calculated correctly for individuals with
   censored intermediate states, as well as censored initial and final states.
   Thanks to Michael Sweeting for reporting this.

* hazard.scale and odds.scale were interpreted wrongly in hazard.msm
  and odds.msm respectively.

* time-dependent covariate values now taken from the start instead of
  end of the transition under hidden Markov models.


2005-01-28 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/lik.c (GetCensoredPObsTrue): Censored outcomes are now
	assumed to be not misclassified.

	* msm.R(msm.form.censor): Bug fix - transient states were detected
	incorrectly.

	* src/pijt.c: Bug fix. P matrix calculation for misclassification
	models was ignoring exacttimes.

	* src/lik.c: Bug fix. Ignore death when exacttimes = TRUE.

	* DESCRIPTION: Version 0.4.1 released.

2005-01-07 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* DESCRIPTION: Version 0.4 released.

2005-01-06 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm/R/msm.process.covs: Bug fix - covariates were not being
	centered. Thanks to Andrew Titman.

2004-12-29  Chris Jackson  <chris.jackson@imperial.ac.uk>

	Support added for censored observations.

	* src/lik.c: Bug fix. Don't ignore exacttimes for
	misclassification models.

	Fixes in documentation. Thanks to Ross Boylan.

2004-09-18 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* man: Rd syntax errors fixed to pass R CMD CHECK under 2.0.0 *

	* msm-manual: Reference to the PDF manual for msm made more
	prominent.

	* DESCRIPTION: Version 0.3.3 released.

2004-06-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm.R(msm.process.covs): Bug fix, constraints were not being
	calculated properly when some covariates were constrained and some
	were not.  Thanks to Mike Sweeting.

2004-06-01 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm-manual: Correction - heartmiscsex.msm is actually run using
	default Nelder-Mead optimization, not BFGS.

2004-05-13 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R: plot.msm now plots survival curves in different
	colours as well as different line types.

2004-05-11 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R: simmulti.msm now returns a data frame, as it should
	do.

2004-04-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* New argument "start" in simmulti.msm to give the starting state
	for each individual. Thanks to Stephan Lenz for the suggestion.


2004-03-25 Chris Jackson   <chris.jackson@imperial.ac.uk>

	*  NEWS file moved to inst directory, so that it ends up in the
	root directory of binary installs. Leave ChangeLog in the source
	package.

	* DESCRIPTION: Version 0.3.2 released.

2004-03-24 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(print.msm): Bug fix - only say "covariates set to
	their means" in the output if there actually are any covariates.

	* msm-manual.pdf: Hidden Markov model theory moved to straight
	after general model theory, general cleanups.

2004-03-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* msm-manual.pdf: R code examples rewritten using Sweave.
	Examples run again with different death assumption, most estimates
	are negligibly different.  Misclassification model examples
	corrected to include death.  Example of plot.msm added. This is
	not distributed as a vignette, as the msm model examples take a
	long time to fit.

2004-03-22 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R(simmulti.msm, getobs.msm): tunit argument abolished
	and death times assumed to be known exactly.

	* src/lik.c(fillparvec): Bug fix. Bounds checking on vector of
	indices of fixed parameters. Thanks to Ross Boylan.

2004-03-21 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R, src/lik.c: tunit argument is now abolished (with
	warning given).  Death states are assumed to have exact entry
	times, not within one day.  This is cleaner and more logical, as
	in longitudinal studies all observations are usually accurate to
	one basic time unit, not just deaths.

	* R/msm.R, src/lik.c: More than one death state is now supported.
	A death state has exact entry time, with an unknown transient
	state at the previous instant. Thanks to Jean-Luc Bulliard for
	suggesting this.

	* R/msm.R(msm.check.times): Just give a warning if a subject only
	has one observation, no need to die.

	* R/msm.R(lik.msm): Bug fix. set diagonal to 0 when calculating
	number of misclassified states nms, in case user has given non
	zero diagonal entries in ematrix.

	* (various) Changes made so that R CMD CHECK passes with R 1.9.0
	alpha: codoc mismatches and PACKAGE argument in .C()

2003-10-14 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/pijt.c(MatrixExpSeries): Bug fix. Don't overwrite the matrix
	A, as it is needed after the function exits. This had led to wrong
	results when exacttimes = TRUE and the intensity matrix had
	repeated eigenvalues.

	* src/lik.c(liksimple, liksimple_fromto, UpdateLik): Don't ignore
	death argument when exacttimes = TRUE.

	* R/msm.R(msm.check.times): Use table instead of tapply to count
	the number of observations per subject. Fixes further problems
	with running out of memory.

	* DESCRIPTION: Version 0.3.1 released.

2003-09-29 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R: Debugging print statements removed from
	pmatrix.piecewise.msm

	* msm-manual.pdf: Version number added.

	* DESCRIPTION: Version 0.3 released.

2003-09-26 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/lik.c, src/pijt.c: Allocate memory using S_alloc, not
	Calloc. Solves the problem of running out of memory for large
	datasets.

	* R/outputs.R(observed.msm): Fixed a bug with looping over a
	factor patient ID, which caused prevalence.msm to fail.

2003-09-25 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(print.msm) Don't draw ASCII underlines under
	"Multi-state Markov models" banner - looks ugly in proportional
	font.

	* R/msm.R: nmiscs model attribute (number of misclassification
	probabilities) changed to nmisc for compatibility with C code.

	* src/lik.c(liksimple, liksimple_fromto): Bug fixed in the
	likelhood calculation for non-misclassified reversible models with
	death time known within one day.  The error assumed the unobserved
	states on the day before death could only be states greater or
	equal than the previously observed state. This is not true for
	reversible models.

	* man/summary.msm.Rd: usage and argument lists made consistent,
	satisfying new R CMD CHECK.

2003-09-24 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R, R/outputs.R, src/lik.c: A new argument "qconstraint" to
	msm now allow equality constraints between baseline transition
	intensities. A similar argument "econstraint" allows equality
	constraints between misclassification probabilities. Thanks to
	Mike Sweeting and Ross Boylan for suggesting this.

2003-09-23 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* src/pijt.c(pijt): Bug fixed in the likelihood calculation for
	exact transition times with reversible models.  The error assumed
	Prr(t) was always equal to exp(-qrr t), when this is only
	satisfied for a state r which is only visited once.

2003-06-30 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R(qematrix.msm): Didn't work when the baseline rates
	or probabilities were fixed to zero, bug fixed (now uses
	x$model$qvector to test whether a transition is allowed, not
	x$Qmatrices$logbaseline).

	* R/outputs.R: New function - pmatrix.piecewise.msm, for
	calculating P-matrices for processes with non-homogeneous but
	piecewise-constant intensities. Thanks to Mike Sweeting for
	suggesting this.

	* DESCRIPTION: Version 0.2.2 released

2003-06-25 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R (msm.check.model): Bug fix - was reporting the wrong
	subject numbers when there were disallowed transitions in the
	data. Thanks to Stephan Lenz for spotting this.

2003-06-20 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/outputs.R: Covariates argument is now checked that it is a
	list, to avoid ugly warnings in R 1.7.0

2003-06-16 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/msm.R (msm.form.output): Died when only one parameter in the
	model, fixed by coercing covmat to matrix.

2003-06-03 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* inst/doc/msm-manual.pdf: Edits to manual, e.g. correction of
	covariates formulae to include baseline intensity, lots of typos
	corrected.

	* DESCRIPTION: Version 0.2.1 released

2003-04-29 Chris Jackson   <chris.jackson@imperial.ac.uk>

	* R/simul.R: Bug fix in simmulti.msm: didn't work for one
	covariate. Thanks to Mike Sweeting for spotting this.

	* R/msm.R: Subject identification variable is now allowed to be
	factor or character. Thanks to Pablo Emilio Verde for the
	suggestion.

	* R/msm.R: msm.check.times also checks whether all the
	observations on a subject are adjacent in the data set.

2003-03-20  Chris Jackson  <chris.jackson@imperial.ac.uk>

	* R/R: Bug fix in msm.check.times. Thanks to Pablo Emilio Verde
	for helping to find this.

2003-02-20  Chris Jackson  <chris.jackson@imperial.ac.uk>

	* R/simul.R: Bug fix in getobs.msm: exact death times were
	ignored. (obstimes[i] replaced by sim$times[j+1]).

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