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CIMEHR: Longitudinal EHR Analysis with Informative Visits and Recording

Longitudinal outcomes in electronic health records (EHR) are seen only when a patient visits and the outcome is recorded at that visit, and both processes can depend on the patient's latent health. The package fits the CIMEHR estimator for this setting, a three-stage procedure linked by a shared latent factor: a frailty partial likelihood for the visiting process, a pairwise likelihood for the recording (observation) process, and an estimating equation for the outcome. Spline and higher-order Laplace variants are included, together with comparison methods (summary statistics, linear mixed models, Lin-Ying, Liang, pairwise likelihood, joint models, inverse intensity rate ratio weighting and balancing, multiple imputation, linear increments and EHRJoint) behind one common interface. Methods are described in Yang, Shi, and Mukherjee (2026) <doi:10.48550/arXiv.2602.15374>.

Version: 0.2.0
Depends: R (≥ 4.1.0)
Imports: nlme, parallel, Rcpp, splines, stats, tools, utils
LinkingTo: Rcpp
Suggests: ggplot2 (≥ 3.4.0), knitr, mice, pan, rmarkdown
Published: 2026-10-22
DOI: 10.32614/CRAN.package.CIMEHR
Author: Cheng-Han Yang ORCID iD [aut, cre], Yiren Hou ORCID iD [aut]
Maintainer: Cheng-Han Yang <chenghanyang728 at gmail.com>
BugReports: https://github.com/ysph-dsde/CIMEHR/issues
License: MIT + file LICENSE
Copyright: See file inst/COPYRIGHTS.
CIMEHR copyright details
URL: https://github.com/ysph-dsde/CIMEHR
NeedsCompilation: yes
Citation: CIMEHR citation info
Materials: README, NEWS
CRAN checks: CIMEHR results [issues need fixing before 2026-11-21]

Documentation:

Reference manual: CIMEHR.html , CIMEHR.pdf
Vignettes: From EHR visit records to fitted biomarker trajectories (source, R code)

Downloads:

Package source: CIMEHR_0.2.0.tar.gz
Windows binaries: r-devel: CIMEHR_0.2.0.zip, r-release: CIMEHR_0.2.0.zip, r-oldrel: CIMEHR_0.2.0.zip
macOS binaries: r-release (arm64): CIMEHR_0.2.0.tgz, r-oldrel (arm64): CIMEHR_0.2.0.tgz, r-release (x86_64): CIMEHR_0.2.0.tgz, r-oldrel (x86_64): CIMEHR_0.2.0.tgz
Old sources: CIMEHR archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=CIMEHR to link to this page.

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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