# Multi-State Markov and Hidden Markov Models in Continuous Time

## Documentation for package ‘msm’ version 1.8.2

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

## Help Pages

A B C D E F H I L M O P Q R S T U V

msm-package | Multi-State Markov and Hidden Markov Models in Continuous Time

## -- A --

absorbing.msm | Transient and absorbing states
aneur | Aortic aneurysm progression data

## -- B --

boot.msm | Bootstrap resampling for multi-state models
bos | Bronchiolitis obliterans syndrome after lung transplants
bos3 | Bronchiolitis obliterans syndrome after lung transplants
bos4 | Bronchiolitis obliterans syndrome after lung transplants

## -- C --

cav | Heart transplant monitoring data
cmodel.object | Developer documentation: censoring model object
coef.msm | Extract model coefficients
contour.msm | Explore the likelihood surface
crudeinits.msm | Calculate crude initial values for transition intensities

## -- D --

d2phase | Coxian phase-type distribution with two phases
deltamethod | The delta method
dmenorm | Measurement error distributions
dmeunif | Measurement error distributions
dpexp | Exponential distribution with piecewise-constant rate
draic.msm | Criteria for comparing two multi-state models with nested state spaces
drlcv.msm | Criteria for comparing two multi-state models with nested state spaces
dtnorm | Truncated Normal distribution

## -- E --

ecmodel.object | Developer documentation: model for covariates on misclassification probabilities
efpt.msm | Expected first passage time
ematrix.msm | Misclassification probability matrix
emodel.object | Developer documentation: misclassification model structure object
envisits.msm | Total length of stay, or expected number of visits

## -- F --

fev | FEV1 measurements from lung transplant recipients

## -- H --

h2phase | Coxian phase-type distribution with two phases
hazard.msm | Calculate tables of hazard ratios for covariates on transition intensities
hmm-dists | Hidden Markov model constructors
hmmBeta | Hidden Markov model constructors
hmmBetaBinom | 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
hmmMV | Multivariate hidden Markov models
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
hmodel.object | Developer documentation: hidden Markov model structure object
hmodel2list | Convert a hmodel object to HMM constructor function calls

## -- I --

image.msm | Explore the likelihood surface

## -- L --

logLik.msm | Extract model log-likelihood
lrtest.msm | Likelihood ratio test

## -- M --

MatrixExp | Matrix exponential
medists | Measurement error distributions
model.frame.msm | Extract original data from 'msm' objects.
model.matrix.msm | Extract original data from 'msm' objects.
msm | Multi-state Markov and hidden Markov models in continuous time
msm.form.eoutput | Extract msm model parameter estimates in compact format
msm.form.qoutput | Extract msm model parameter estimates in compact format
msm.object | Fitted msm model objects
msm2Surv | Convert data for 'msm' to data for 'survival', 'mstate' or 'flexsurv' analysis

## -- O --

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

## -- P --

p2phase | Coxian phase-type distribution with two phases
paramdata.object | Developer documentation: internal msm parameters object
pearson.msm | Pearson-type goodness-of-fit test
persp.msm | Explore the likelihood surface
pexp | Exponential distribution with piecewise-constant rate
phasemeans.msm | Parameters of phase-type models in mixture form
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
ppass.msm | Passage probabilities
ppexp | Exponential distribution with piecewise-constant rate
prevalence.msm | Tables of observed and expected prevalences
print.msm | Print a fitted msm model object
print.summary.msm | Summarise a fitted multi-state model
printnew.msm | Print a fitted msm model object
printold.msm | Print a fitted msm model object
psor | Psoriatic arthritis data
ptnorm | Truncated Normal distribution

## -- Q --

q2phase | Coxian phase-type distribution with two phases
qcmodel.object | Developer documentation: model for covariates on transition intensities
qgeneric | Generic function to find quantiles of a distribution
qmatrix.msm | Transition intensity matrix
qmenorm | Measurement error distributions
qmeunif | Measurement error distributions
qmodel.object | Developer documentation: transition model structure object
qpexp | Exponential distribution with piecewise-constant rate
qratio.msm | Estimated ratio of transition intensities
qtnorm | Truncated Normal distribution

## -- R --

r2phase | Coxian phase-type distribution with two phases
recreate.olddata | Convert data stored in msm object to old format
rmenorm | Measurement error distributions
rmeunif | Measurement error distributions
rpexp | Exponential distribution with piecewise-constant rate
rtnorm | Truncated Normal distribution

## -- S --

scoreresid.msm | Score residuals
sim.msm | Simulate one individual trajectory from a continuous-time Markov model
simfitted.msm | Simulate from a Markov model fitted using msm
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

## -- T --

tidy.msm | Tidy the parameter estimates from an msm model
tidy.msm.est | Tidy the output of pmatrix.msm and similar functions
tidy.msm.estbystate | Tidy the output of totlos.msm and similar functions
tidy.msm.prevalence | Tidy the output of prevalence.msm
tnorm | Truncated Normal distribution
totlos.msm | Total length of stay, or expected number of visits
transient.msm | Transient and absorbing states
twophase | Coxian phase-type distribution with two phases

## -- U --

updatepars.msm | Update the maximum likelihood estimates in a fitted model object.

## -- V --

viterbi.msm | Calculate the probabilities of underlying states and the most likely path through them