# msm v1.6.7

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

Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. 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.

## Functions in msm

Name | Description | |

efpt.msm | Expected first passage time | |

qcmodel.object | Developer documentation: model for covariates on transition intensities | |

boot.msm | Bootstrap resampling for multi-state models | |

msm.object | Fitted msm model objects | |

psor | Psoriatic arthritis data | |

msm2Surv | Convert data for `msm' to data for `survival', `mstate' or `flexsurv' analysis | |

pexp | Exponential distribution with piecewise-constant rate | |

ematrix.msm | Misclassification probability matrix | |

plotprog.msm | Kaplan Meier estimates of incidence | |

pearson.msm | Pearson-type goodness-of-fit test | |

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

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

hmmMV | Multivariate hidden Markov models | |

hmodel.object | Developer documentation: hidden Markov model structure object | |

emodel.object | Developer documentation: misclassification model structure object | |

fev | FEV1 measurements from lung transplant recipients | |

statetable.msm | Table of transitions | |

logLik.msm | Extract model log-likelihood | |

lrtest.msm | Likelihood ratio test | |

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

plot.prevalence.msm | Plot of observed and expected prevalences | |

tnorm | Truncated Normal distribution | |

ecmodel.object | Developer documentation: model for covariates on misclassification probabilities | |

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

pmatrix.msm | Transition probability matrix | |

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

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

simfitted.msm | Simulate from a Markov model fitted using msm | |

msm.form.qoutput | Extract msm model parameter estimates in compact format | |

plot.survfit.msm | Plot empirical and fitted survival curves | |

qmodel.object | Developer documentation: transition model structure object | |

surface.msm | Explore the likelihood surface | |

msm | Multi-state Markov and hidden Markov models in continuous time | |

paramdata.object | Developer documentation: internal msm parameters object | |

hmm-dists | Hidden Markov model constructors | |

ppass.msm | Passage probabilities | |

model.frame.msm | Extract original data from msm objects. | |

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

msm.summary | Summarise a fitted multi-state model | |

prevalence.msm | Tables of observed and expected prevalences | |

pnext.msm | Probability of each state being next | |

qratio.msm | Estimated ratio of transition intensities | |

totlos.msm | Total length of stay, or expected number of visits | |

medists | Measurement error distributions | |

qmatrix.msm | Transition intensity matrix | |

phasemeans.msm | Parameters of phase-type models in mixture form | |

printold.msm | Print a fitted msm model object | |

plot.msm | Plots of multi-state models | |

qgeneric | Generic function to find quantiles of a distribution | |

recreate.olddata | Convert data stored in msm object to old format | |

print.msm | Print a fitted msm model object | |

scoreresid.msm | Score residuals | |

updatepars.msm | updatepars.msm | |

transient.msm | Transient and absorbing states | |

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

coef.msm | Extract model coefficients | |

cmodel.object | Developer documentation: censoring model object | |

crudeinits.msm | Calculate crude initial values for transition intensities | |

deltamethod | The delta method | |

2phase | Coxian phase-type distribution with two phases | |

aneur | Aortic aneurysm progression data | |

MatrixExp | Matrix exponential | |

bos | Bronchiolitis obliterans syndrome after lung transplants | |

cav | Heart transplant monitoring data | |

No Results! |

## Vignettes of msm

## Last month downloads

## Details

Date | 2019-03-15 |

License | GPL (>= 2) |

URL | https://github.com/chjackson/msm |

BugReports | https://github.com/chjackson/msm/issues |

LazyData | yes |

NeedsCompilation | yes |

Packaged | 2019-03-18 17:15:16 UTC; chris |

Repository | CRAN |

Date/Publication | 2019-03-18 21:10:03 UTC |

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