Package: icmstate 0.1.0

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_0.1.0.tar.gz
icmstate_0.1.0.tar.gz(r-4.5-noble)icmstate_0.1.0.tar.gz(r-4.4-noble)
icmstate_0.1.0.tgz(r-4.4-emscripten)icmstate_0.1.0.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'))

Peer review:

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.

3.32 score 14 scripts 20 exports 56 dependencies

Last updated 26 days agofrom:16798dc371. Checks:OK: 1 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-linux-x86_64WARNINGOct 29 2024

Exports:direct_from_observed_intervalsestimate_support_msmevalstepget_trans_intervalsgraphfromIntervalsinterpol_msfitmsm_frydmannpmsmplot_probtransplot_survprobtrans_weibremove_redundant_observationssim_id_weibsim_weibmsmsupport_from_direct_intervalssupport_npmsmsupportHudgenstransprobvisualise_datavisualise_msm

Dependencies:backportscheckmateclicodetoolscolorspacecpp11data.tabledeSolvediagramdigestexpmfansifarverfuturefuture.applygenericsggplot2globalsgluegtableigraphisobandKernSmoothlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixmgcvmsmmstatemunsellmvtnormnlmenumDerivparallellypillarpkgconfigprodlimprogressrR6RColorBrewerRcpprlangscalesshapeSQUAREMsurvivaltibbleutf8vctrsviridisLitewithr

Comparison with known results

Rendered fromcomparison-with-known-results.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Overview

Rendered fromOverview.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Simulating Multi-state models with icmstate

Rendered fromsim_msm.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
icmstateicmstate-package icmstate
Check if event time is larger/equal than other event timeageqb
Check if event time is larger than other event timeagreaterb
Check if event time is contained within half-open intervalainB
Check if half-open intervals intersect with event timesAintersectb
Check if closed interval is contained in half-open infinite intervalAlargerb
Check if closed interval is contained in other closed intervalAsubsetB
Translate observed transition intervals into direct transition intervalsdirect_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 timesevalstep
Get transition intervals from specified dataget_trans_intervals
Construct Graph from censoring/truncation intervalsgraphfromIntervals
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 transitionsnpmsm
Plot the transition probabilities for a fitted 'npmsm' modelplot_probtrans
Plot the transition specific survival probabilities for a fitted 'npmsm' modelplot_surv
Plot a "npmsm" objectplot.npmsm
Print a "npmsm" objectprint.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 timesprod_lambda_G_base
Remove redundant observations from supplied data frameremove_redundant_observations
Simulate panel data from an illness-death model with Weibull transition hazardssim_id_weib
Simulate multiple trajectories from an interval-censored multi-state model with Weibull transition intensitiessim_weibmsm
Estimate support of multiple transitions given direct transition intervalssupport_from_direct_intervals
Numerically find the support of the transitions from a converged npmsm algorithmsupport_npmsm
Determine the support of the NPMLE for interval censored data.supportHudgens
Wrapper for the 'probtrans' functiontransprob transprob.msfit transprob.msm transprob.npmsm
Visualise data for illness-death model, only applicable to Frydman(1995) setting.visualise_data
Visualise multi-state datavisualise_msm