Multi-state Markov and hidden Markov models in continuous time


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Documentation for package ‘msm’ version 1.1

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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
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