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msm (version 0.5.2)

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. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates. A variety of observation schemes are supported, including processes observed at arbitrary times, completely-observed processes, and censored states.

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Version

Install

install.packages('msm')

Monthly Downloads

19,748

Version

0.5.2

License

GPL version 2 or newer

Maintainer

Christopher H Jackson

Last Published

October 4th, 2024

Functions in msm (0.5.2)

prevalence.msm

Tables of observed and expected prevalences
qratio.msm

Estimated ratio of transition intensities
simmulti.msm

Simulate multiple trajectories from a multi-state Markov model with arbitrary observation times
aneur

Aortic aneurysm progression data
bos

Bronchiolitis obliterans syndrome after lung transplants
MatrixExp

Matrix exponential
heart

Heart transplant monitoring data
medists

Measurement error distributions
odds.msm

Calculate tables of odds ratios for covariates on misclassification probabilities
psor

Psoriatic arthritis data
hazard.msm

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

Total length of stay
deltamethod

The delta method
viterbi.msm

Calculate the most likely path through underlying stages
pmatrix.piecewise.msm

Transition probability matrix for processes with piecewise-constant intensities
hmm-dists

Hidden Markov model constructors
ematrix.msm

Misclassification probability matrix
fev

FEV1 measurements from lung transplant recipients
pexp

Exponential distribution with piecewise-constant rate
msm

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

Extract model log-likelihood
sojourn.msm

Mean sojourn times from a multi-state model
tnorm

Truncated Normal distribution
plot.msm

Plots of multi-state models
qmatrix.msm

Transition intensity matrix
pmatrix.msm

Transition probability matrix
msm.summary

Summarise a fitted multi-state model
crudeinits.msm

Calculate crude initial values for transition intensities
coef.msm

Extract model coefficients
transient.msm

Transient and absorbing states
statetable.msm

Table of transitions
sim.msm

Simulate one individual trajectory from a continuous-time Markov model