Function reference • msmbayes

Exploratory data analysis

msmhist(): Illustrate the empirical distribution of states against time in intermittently-observed multistate data

msmhist_bardata(): Estimate state occupation probabilities to be illustrated by a bar plot in msmhist

Fitting models

msmbayes(): Bayesian multi-state models for intermittently-observed data

msmprior(): Constructor for a prior distribution in msmbayes

Getting results from fitted models

qdf(): Transition intensities from an msmbayes model, presented as a tidy data frame

qmatrix(): Transition intensity matrix from an msmbayes model

pmatrixdf(): Transition probabilities from an msmbayes model, presented as a tidy data frame

pmatrix(): Transition probability matrix from an msmbayes model

loghr(): Log hazard ratios for covariates on transition intensities

hr(): Hazard ratios for covariates on transition intensities

mean_sojourn(): Mean sojourn times from an msmbayes model

totlos(): Total length of stay in each state over an interval

edf(): Misclassification probabilities from an msmbayes model

summary(<msmbayes>): Summarise basic parameter estimates from an msmbayes model

standardise_to() standardize_to(): Constructor for a standardising population used for model outputs

Datasets

infsim infsim2: Simulated infection testing data

bigdat: A simulated multistate dataset with lots of observations and covariates

infsim_model infsim_modelc cav_misc: Example fitted model objects used for testing msmbayes

Package overview

msmbayes-package: The 'msmbayes' package for Bayesian multi-state modelling of intermittently-observed data