# Interval Censored Multi-State Models

## Documentation for package ‘icmstate’ version 0.2.0

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

## Help Pages

icmstate-package | icmstate
ageqb | Check if event time is larger/equal than other event time
agreaterb | Check if event time is larger than other event time
ainB | Check if event time is contained within half-open interval
Aintersectb | Check if half-open intervals intersect with event times
Alargerb | Check if closed interval is contained in half-open infinite interval
AsubsetB | Check if closed interval is contained in other closed interval
direct_from_observed_intervals | Translate observed transition intervals into direct transition intervals
estimate_support_msm | Estimate the support of a general Markov interval-censored Multi-state model without loops.
evalstep | Sample from a markov chain multi state model with exactly observed transition times
extend_msfit | Given a 'msfit' object, extend the times considered in the object
get_trans_intervals | Get transition intervals from specified data
graphfromIntervals | Construct Graph from censoring/truncation intervals
icmstate | icmstate
interpol_msfit | Given a 'msfit' object, linearly interpolate the cumulative hazard taking into account the support sets for 'msfit' objects.
msm_frydman | Determine NPMLE for Multi State illness death Markov model using Frydman (1995)
npmsm | NPMLE for general multi-state model with interval censored transitions
plot.npmsm | Plot a "npmsm" object
plot.probtrans.subjects | Plot an object of class '"probtrans.subjects"'
plot.smoothmsm | Plot a "smoothmsm" object
plot_probtrans | Plot the transition probabilities for a fitted 'npmsm' model
plot_surv | Plot the transition specific survival probabilities for a fitted 'npmsm' model
predict_tp | Calculate subject specific transition probabilities from a multi-state proportional hazards model.
print.npmsm | Print a "npmsm" object
print.summary.probtrans.subjects | Print method for a summary.probtrans.subjects object
probtrans_coxph | Calculate subject specific transition probabilities from a multi-state 'coxph' model.
probtrans_weib | Determine transition probabilities for a multi-state model with Weibull hazards for the transitions.
prod_lambda_G_base | Calculate the product of intensities over interval decided by failure times
remove_redundant_observations | Remove redundant observations from supplied data frame
sim_id_weib | Simulate panel data from an illness-death model with Weibull transition hazards
sim_weibmsm | Simulate multiple trajectories from an interval-censored multi-state model with Weibull transition intensities
smoothmsm | Smooth hazard estimation for general multi-state model with interval censored transitions
summary.probtrans.subjects | Summary method for a probtrans.subjects object
supportHudgens | Determine the support of the NPMLE for interval censored data.
support_from_direct_intervals | Estimate support of multiple transitions given direct transition intervals
support_npmsm | Numerically find the support of the transitions from a converged npmsm algorithm
transprob | Wrapper for the 'probtrans' function
transprob.msfit | Wrapper for the 'probtrans' function
transprob.msm | Wrapper for the 'probtrans' function
transprob.npmsm | Wrapper for the 'probtrans' function
visualise_data | Visualise data for illness-death model, only applicable to Frydman(1995) setting.
visualise_msm | Visualise multi-state data