Package: icmstate 0.2.0

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_0.2.0.tar.gz
icmstate_0.2.0.tar.gz(r-4.7-arm64)icmstate_0.2.0.tar.gz(r-4.7-x86_64)icmstate_0.2.0.tar.gz(r-4.6-arm64)icmstate_0.2.0.tar.gz(r-4.6-x86_64)
icmstate_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
icmstate/json (API)

# 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

On CRAN:

Conda:

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

cpp

3.48 score 20 scripts 290 downloads 26 exports 78 dependencies

Last updated from:27bbed73e0. Checks:4 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING205
linux-devel-x86_64WARNING211
source / vignettesOK290
linux-release-arm64WARNING236
linux-release-x86_64WARNING241
wasm-releaseOK173

Exports:bbase_Dbbase_singletimedirect_from_observed_intervalsestimate_support_msmevalstepextend_msfitget_trans_intervalsgraphfromIntervalsinterpol_msfitmsm_frydmannpmsmplot_probtransplot_survpredict_tpprobtrans_coxphprobtrans_weibremove_redundant_observationssim_id_weibsim_weibmsmsmoothmsmsupport_from_direct_intervalssupport_npmsmsupportHudgenstransprobvisualise_datavisualise_msm

Dependencies:ashbackportsbitopsbootcheckmatecliclustercodetoolscolorspacecpp11data.tabledeSolvediagramdigestdotCall64expmfarverfdsfieldsFNNfuturefuture.applygenericsggplot2globalsgluegtablehdrcdeigraphisobandJOPSkernlabKernSmoothkslabelinglatticelavalifecyclelistenvlocfitmagrittrmapsMASSMatrixmclustmgcvmsmmstatemulticoolmvtnormnlmenumDerivparallellypcaPPpillarpkgconfigpracmaprodlimprogressrR6rainbowRColorBrewerRcppRCurlrlangrpartS7scalesshapespamSpATSSQUAREMsurvivaltibbleutf8vctrsviridisLitewithr

Overview
Introduction | Interval-censoring | Multi-state modelling | Panel data | Estimation | Methods | Key functions | Examples | Simple interval-censoring | Time homogeneous example | Time homogeneous example - exact observation times | Time inhomogeneous example | Initial estimates
Rendered fromOverview.Rmdusingknitr::rmarkdown

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

Simulating Multi-state models with icmstate
Simulating data | The transition matrix (tmat) | Choosing Weibull transition parameters (shape, scale) | Choosing/generating observation times (data, n_subj, obs_pars) | Manually choosing observation times (data) | Automatically generating an observation grid (n_subj, obs_pars) | Additional possibilities (startprobs, exact, censoring) | Starting state probabilities (startprobs) | Exactly observed states (exact) | Weibull censoring | True trajectories | Compare simulated data with true intensities | Interval-censored trajectories
Rendered fromsim_msm.Rmdusingknitr::rmarkdown

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

Comparison with known results
Known results | Frydman (1995) non-parametric estimator | Comparison with the icmstate package | Survival in state 1 | Transition to death | Not catching illness | Dying after illness
Rendered fromcomparison-with-known-results.Rmdusingknitr::rmarkdown

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
Given a 'msfit' object, extend the times considered in the objectextend_msfit
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
Plot an object of class '"probtrans.subjects"'plot.probtrans.subjects
Plot a "smoothmsm" objectplot.smoothmsm
Calculate subject specific transition probabilities from a multi-state proportional hazards model.predict_tp
Print a "npmsm" objectprint.npmsm
Print method for a summary.probtrans.subjects objectprint.summary.probtrans.subjects
Calculate subject specific transition probabilities from a multi-state 'coxph' model.probtrans_coxph
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
Smooth hazard estimation for general multi-state model with interval censored transitionssmoothmsm
Summary method for a probtrans.subjects objectsummary.probtrans.subjects
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