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clusteredMSM: Nonparametric Analysis of Clustered Multistate Processes

Nonparametric estimation of population-averaged transition probabilities, with cluster-bootstrap pointwise confidence intervals, simultaneous confidence bands, and two-sample Kolmogorov-Smirnov-type tests for clustered or independent multistate process data. Estimation follows Bakoyannis (2021) <doi:10.1111/biom.13327>; two-sample inference for the cluster-randomized and independent-samples designs follows Bakoyannis and Bandyopadhyay (2022) <doi:10.1007/s10463-021-00819-x>. Both methods use the working-independence Aalen-Johansen estimator. The package supports both progressive (acyclic) and non-monotone (e.g., illness-death with recovery) multistate processes, right censoring, left truncation, and informative cluster size. The user supplies data in interval format (one row per mutually-exclusive time interval per subject) and interacts with the package through a single formula-based function, patp().

Version: 0.1.0
Depends: R (≥ 3.5.0)
Imports: survival, stats, utils
Suggests: mstate, testthat (≥ 3.0.0), knitr, rmarkdown
Published: 2026-05-27
DOI: 10.32614/CRAN.package.clusteredMSM
Author: Giorgos Bakoyannis ORCID iD [aut, cre]
Maintainer: Giorgos Bakoyannis <gbakogia at iu.edu>
BugReports: https://github.com/gbakoyannis/clusteredMSM/issues
License: GPL-3
URL: https://github.com/gbakoyannis/clusteredMSM
NeedsCompilation: no
Citation: clusteredMSM citation info
Materials: README, NEWS
CRAN checks: clusteredMSM results

Documentation:

Reference manual: clusteredMSM.html , clusteredMSM.pdf
Vignettes: Getting started with clusteredMSM (source, R code)

Downloads:

Package source: clusteredMSM_0.1.0.tar.gz
Windows binaries: r-devel: clusteredMSM_0.1.0.zip, r-release: clusteredMSM_0.1.0.zip, r-oldrel: clusteredMSM_0.1.0.zip
macOS binaries: r-release (arm64): clusteredMSM_0.1.0.tgz, r-oldrel (arm64): clusteredMSM_0.1.0.tgz, r-release (x86_64): clusteredMSM_0.1.0.tgz, r-oldrel (x86_64): clusteredMSM_0.1.0.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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