# Multi-state Markov and hidden Markov models in continuous time

## Documentation for package ‘msm’ version 1.1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

absorbing.msm | Transient and absorbing states
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
coef.msm | Extract model coefficients
contour.msm | Explore the likelihood surface
crudeinits.msm | Calculate crude initial values for transition intensities
deltamethod | The delta method
dmenorm | Measurement error distributions
dmeunif | Measurement error distributions
dpexp | Exponential distribution with piecewise-constant rate
dtnorm | Truncated Normal distribution
ematrix.msm | Misclassification probability matrix
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
hmmBeta | Hidden Markov model constructors
hmmBinom | Hidden Markov model constructors
hmmCat | Hidden Markov model constructors
hmmExp | Hidden Markov model constructors
hmmGamma | Hidden Markov model constructors
hmmIdent | Hidden Markov model constructors
hmmLNorm | Hidden Markov model constructors
hmmMETNorm | Hidden Markov model constructors
hmmMEUnif | Hidden Markov model constructors
hmmNBinom | Hidden Markov model constructors
hmmNorm | Hidden Markov model constructors
hmmPois | Hidden Markov model constructors
hmmT | Hidden Markov model constructors
hmmTNorm | Hidden Markov model constructors
hmmUnif | Hidden Markov model constructors
hmmWeibull | Hidden Markov model constructors
image.msm | Explore the likelihood surface
logLik.msm | Extract model log-likelihood
lrtest.msm | Likelihood ratio test
MatrixExp | Matrix exponential
medists | Measurement error distributions
msm | Multi-state Markov and hidden Markov models in continuous time
odds.msm | Calculate tables of odds ratios for covariates on misclassification probabilities
pearson.msm | Pearson-type goodness-of-fit test
persp.msm | Explore the likelihood surface
pexp | Exponential distribution with piecewise-constant rate
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
pmenorm | Measurement error distributions
pmeunif | Measurement error distributions
pnext.msm | Probability of each state being next
ppexp | Exponential distribution with piecewise-constant rate
prevalence.msm | Tables of observed and expected prevalences
print.summary.msm | Summarise a fitted multi-state model
psor | Psoriatic arthritis data
ptnorm | Truncated Normal distribution
qmatrix.msm | Transition intensity matrix
qmenorm | Measurement error distributions
qmeunif | Measurement error distributions
qpexp | Exponential distribution with piecewise-constant rate
qratio.msm | Estimated ratio of transition intensities
qtnorm | Truncated Normal distribution
rmenorm | Measurement error distributions
rmeunif | Measurement error distributions
rpexp | Exponential distribution with piecewise-constant rate
rtnorm | Truncated Normal distribution
scoreresid.msm | Score residuals
sim.msm | Simulate one individual trajectory from a continuous-time Markov model
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
tnorm | Truncated Normal distribution
totlos.msm | Total length of stay
transient.msm | Transient and absorbing states
viterbi.msm | Calculate the most likely path through underlying states