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msm (version 1.2)

Multi-state Markov and hidden Markov models in continuous time

Description

Functions for fitting general continuous-time Markov and hidden Markov multi-state models to longitudinal data. A variety of observation schemes are supported, including processes observed at arbitrary times (panel data), continuously-observed processes, and censored states. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.

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Version

Install

install.packages('msm')

Monthly Downloads

18,399

Version

1.2

License

GPL (>= 2)

Maintainer

Christopher Jackson

Last Published

May 15th, 2013

Functions in msm (1.2)

hazard.msm

Calculate tables of hazard ratios for covariates on transition intensities
surface.msm

Explore the likelihood surface
boot.msm

Bootstrap resampling for multi-state models
cav

Heart transplant monitoring data
msm.summary

Summarise a fitted multi-state model
MatrixExp

Matrix exponential
simmulti.msm

Simulate multiple trajectories from a multi-state Markov model with arbitrary observation times
lrtest.msm

Likelihood ratio test
medists

Measurement error distributions
deltamethod

The delta method
totlos.msm

Total length of stay
qmatrix.msm

Transition intensity matrix
pexp

Exponential distribution with piecewise-constant rate
transient.msm

Transient and absorbing states
pnext.msm

Probability of each state being next
pmatrix.piecewise.msm

Transition probability matrix for processes with piecewise-constant intensities
psor

Psoriatic arthritis data
hmm-dists

Hidden Markov model constructors
logLik.msm

Extract model log-likelihood
pearson.msm

Pearson-type goodness-of-fit test
prevalence.msm

Tables of observed and expected prevalences
sim.msm

Simulate one individual trajectory from a continuous-time Markov model
msm

Multi-state Markov and hidden Markov models in continuous time
efpt.msm

Expected first passage time
coef.msm

Extract model coefficients
plot.msm

Plots of multi-state models
odds.msm

Calculate tables of odds ratios for covariates on misclassification probabilities
pmatrix.msm

Transition probability matrix
qratio.msm

Estimated ratio of transition intensities
statetable.msm

Table of transitions
fev

FEV1 measurements from lung transplant recipients
plotprog.msm

Kaplan Meier estimates of incidence
crudeinits.msm

Calculate crude initial values for transition intensities
simfitted.msm

Simulate from a Markov model fitted using msm
scoreresid.msm

Score residuals
bos

Bronchiolitis obliterans syndrome after lung transplants
aneur

Aortic aneurysm progression data
plot.survfit.msm

Plot empirical and fitted survival curves
plot.prevalence.msm

Plot of observed and expected prevalences
ematrix.msm

Misclassification probability matrix
tnorm

Truncated Normal distribution
sojourn.msm

Mean sojourn times from a multi-state model
viterbi.msm

Calculate the most likely path through underlying states