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msm (version 1.4)

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

19,748

Version

1.4

License

GPL (>= 2)

Maintainer

Christopher Jackson

Last Published

July 8th, 2014

Functions in msm (1.4)

aneur

Aortic aneurysm progression data
odds.msm

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

Misclassification probability matrix
fev

FEV1 measurements from lung transplant recipients
ecmodel.object

Developer documentation: model for covariates on misclassification probabilities
logLik.msm

Extract model log-likelihood
plotprog.msm

Kaplan Meier estimates of incidence
draic.msm

Criteria for comparing two multi-state models with nested state spaces
prevalence.msm

Tables of observed and expected prevalences
pearson.msm

Pearson-type goodness-of-fit test
MatrixExp

Matrix exponential
ppass.msm

Passage probabilities
efpt.msm

Expected first passage time
bos

Bronchiolitis obliterans syndrome after lung transplants
emodel.object

Developer documentation: misclassification model structure object
coef.msm

Extract model coefficients
hmodel.object

Developer documentation: hidden Markov model structure object
msm2Surv

Convert data for `msm' to data for `survival' and `mstate' analysis
medists

Measurement error distributions
msm.object

Fitted msm model objects
hazard.msm

Calculate tables of hazard ratios for covariates on transition intensities
paramdata.object

Developer documentation: internal msm parameters object
plot.prevalence.msm

Plot of observed and expected prevalences
msm

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

Extract msm model parameter estimates in compact format
print.msm

Print a fitted msm model object
cmodel.object

Developer documentation: censoring model object
crudeinits.msm

Calculate crude initial values for transition intensities
recreate.olddata

Convert data stored in msm object to old format
plot.survfit.msm

Plot empirical and fitted survival curves
pexp

Exponential distribution with piecewise-constant rate
qmodel.object

Developer documentation: transition model structure object
cav

Heart transplant monitoring data
model.frame.msm

Extract original data from msm objects.
deltamethod

The delta method
pnext.msm

Probability of each state being next
boot.msm

Bootstrap resampling for multi-state models
psor

Psoriatic arthritis data
plot.msm

Plots of multi-state models
qcmodel.object

Developer documentation: model for covariates on transition intensities
scoreresid.msm

Score residuals
simmulti.msm

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

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

Simulate from a Markov model fitted using msm
qgeneric

Generic function to find quantiles of a distribution
tnorm

Truncated Normal distribution
msm.summary

Summarise a fitted multi-state model
transient.msm

Transient and absorbing states
statetable.msm

Table of transitions
qratio.msm

Estimated ratio of transition intensities
qmatrix.msm

Transition intensity matrix
pmatrix.msm

Transition probability matrix
surface.msm

Explore the likelihood surface
lrtest.msm

Likelihood ratio test
hmm-dists

Hidden Markov model constructors
sojourn.msm

Mean sojourn times from a multi-state model
pmatrix.piecewise.msm

Transition probability matrix for processes with piecewise-constant intensities
viterbi.msm

Calculate the most likely path through underlying states
printold.msm

Print a fitted msm model object
totlos.msm

Total length of stay, or expected number of visits