Package: icmstate 0.1.1

Daniel Gomon

icmstate: Interval Censored Multi-State Models

Allows for the non-parametric estimation of transition intensities in interval-censored multi-state models using the approach of Gomon and Putter (2024) <doi:10.48550/arXiv.2409.07176> or Gu et al. (2023) <doi:10.1093/biomet/asad073>.

Authors:Daniel Gomon [aut, cre], Hein Putter [aut]

icmstate_0.1.1.tar.gz
icmstate_0.1.1.tar.gz(r-4.5-noble)icmstate_0.1.1.tar.gz(r-4.4-noble)
icmstate_0.1.1.tgz(r-4.4-emscripten)icmstate_0.1.1.tgz(r-4.3-emscripten)
icmstate.pdf |icmstate.html✨
icmstate/json (API)
NEWS

# Install 'icmstate' in R:

install.packages('icmstate', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

3.65 score 15 scripts 466 downloads 20 exports 56 dependencies

Last updated 2 months agofrom:3dafb872cd. Checks:OK: 1 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-linux-x86_64	WARNING	Nov 25 2024

Exports:direct_from_observed_intervals estimate_support_msm evalstep get_trans_intervals graphfromIntervals interpol_msfit msm_frydman npmsm plot_probtrans plot_surv probtrans_weib remove_redundant_observations sim_id_weib sim_weibmsm support_from_direct_intervals support_npmsm supportHudgens transprob visualise_data visualise_msm

Dependencies:backports checkmate cli codetools colorspace cpp11 data.table deSolve diagram digest expm fansi farver future future.apply generics ggplot2 globals glue gtable igraph isoband KernSmooth labeling lattice lava lifecycle listenv magrittr MASS Matrix mgcv msm mstate munsell mvtnorm nlme numDeriv parallelly pillar pkgconfig prodlim progressr R6 RColorBrewer Rcpp rlang scales shape SQUAREM survival tibble utf8 vctrs viridisLite withr

Comparison with known results

Rendered fromcomparison-with-known-results.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2024-10-28
Started: 2024-10-28

Overview

Rendered fromOverview.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2024-11-08
Started: 2024-10-28

Simulating Multi-state models with icmstate

Rendered fromsim_msm.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2024-11-08
Started: 2024-10-28

Citation

Readme and manuals

Help Manual

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