MatrixExp               Matrix exponential
aneur                   Aortic aneurysm progression data
boot.msm                Bootstrap resampling for multi-state models
bos                     Bronchiolitis obliterans syndrome after lung
                        transplants
cav                     Heart transplant monitoring data
cmodel.object           Developer documentation: censoring model object
coef.msm                Extract model coefficients
crudeinits.msm          Calculate crude initial values for transition
                        intensities
deltamethod             The delta method
draic.msm               Criteria for comparing two multi-state models
                        with nested state spaces
ecmodel.object          Developer documentation: model for covariates
                        on misclassification probabilities
efpt.msm                Expected first passage time
ematrix.msm             Misclassification probability matrix
emodel.object           Developer documentation: misclassification
                        model structure object
fev                     FEV1 measurements from lung transplant
                        recipients
hazard.msm              Calculate tables of hazard ratios for
                        covariates on transition intensities
hmm-dists               Hidden Markov model constructors
hmmMV                   Multivariate hidden Markov models
hmodel.object           Developer documentation: hidden Markov model
                        structure object
hmodel2list             Convert a hmodel object to HMM constructor
                        function calls
logLik.msm              Extract model log-likelihood
lrtest.msm              Likelihood ratio test
medists                 Measurement error distributions
model.frame.msm         Extract original data from 'msm' objects.
msm                     Multi-state Markov and hidden Markov models in
                        continuous time
msm-package             Multi-State Markov and Hidden Markov Models in
                        Continuous Time
msm.form.qoutput        Extract msm model parameter estimates in
                        compact format
msm.object              Fitted msm model objects
msm2Surv                Convert data for 'msm' to data for 'survival',
                        'mstate' or 'flexsurv' analysis
odds.msm                Calculate tables of odds ratios for covariates
                        on misclassification probabilities
paramdata.object        Developer documentation: internal msm
                        parameters object
pearson.msm             Pearson-type goodness-of-fit test
pexp                    Exponential distribution with
                        piecewise-constant rate
phasemeans.msm          Parameters of phase-type models in mixture form
plot.msm                Plots of multi-state models
plot.prevalence.msm     Plot of observed and expected prevalences
plot.survfit.msm        Plot empirical and fitted survival curves
plotprog.msm            Kaplan Meier estimates of incidence
pmatrix.msm             Transition probability matrix
pmatrix.piecewise.msm   Transition probability matrix for processes
                        with piecewise-constant intensities
pnext.msm               Probability of each state being next
ppass.msm               Passage probabilities
prevalence.msm          Tables of observed and expected prevalences
print.msm               Print a fitted msm model object
printold.msm            Print a fitted msm model object
psor                    Psoriatic arthritis data
qcmodel.object          Developer documentation: model for covariates
                        on transition intensities
qgeneric                Generic function to find quantiles of a
                        distribution
qmatrix.msm             Transition intensity matrix
qmodel.object           Developer documentation: transition model
                        structure object
qratio.msm              Estimated ratio of transition intensities
recreate.olddata        Convert data stored in msm object to old format
scoreresid.msm          Score residuals
sim.msm                 Simulate one individual trajectory from a
                        continuous-time Markov model
simfitted.msm           Simulate from a Markov model fitted using msm
simmulti.msm            Simulate multiple trajectories from a
                        multi-state Markov model with arbitrary
                        observation times
sojourn.msm             Mean sojourn times from a multi-state model
statetable.msm          Table of transitions
summary.msm             Summarise a fitted multi-state model
surface.msm             Explore the likelihood surface
tidy.msm                Tidy the parameter estimates from an msm model
tidy.msm.est            Tidy the output of pmatrix.msm and similar
                        functions
tidy.msm.estbystate     Tidy the output of totlos.msm and similar
                        functions
tidy.msm.prevalence     Tidy the output of prevalence.msm
tnorm                   Truncated Normal distribution
totlos.msm              Total length of stay, or expected number of
                        visits
transient.msm           Transient and absorbing states
twophase                Coxian phase-type distribution with two phases
updatepars.msm          Update the maximum likelihood estimates in a
                        fitted model object.
viterbi.msm             Calculate the probabilities of underlying
                        states and the most likely path through them
