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CIMEHR: Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data

Fits semiparametric joint models for longitudinal electronic health record (EHR) data that addresses two-stage hierarchical missingness mechanism. The first stage is the visiting process, and the second stage is the observation process. The core CIMEHR method (Clinical Informative Missingness for Electronic Health Records) uses a three-stage procedure: partial likelihood with log-normal frailty for visit intensity, probit regression with shared latent factor-linked random effects for observation, and weighted least squares with risk-set centering for the outcome. These three stages are connected through a shared latent factor that induces dependence across all three processes. A data simulator and implementations of common benchmark methods (linear mixed models, multiple imputation, and others) are included for comparative studies. Detailed methods are described in Yang, Shi, and Mukherjee (2026) <doi:10.48550/arXiv.2602.15374>.

Version: 0.1.0
Depends: R (≥ 3.5)
Imports: MASS, Rcpp, nleqslv, pbivnorm, numDeriv, stats, utils, data.table, mice, nlme, slim
LinkingTo: Rcpp
Suggests: tibble, dplyr, tidyr, knitr, rmarkdown
Published: 2026-06-08
DOI: 10.32614/CRAN.package.CIMEHR (may not be active yet)
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
URL: https://github.com/ysph-dsde/CIMEHR
NeedsCompilation: yes
Citation: CIMEHR citation info
Materials: README, NEWS
CRAN checks: CIMEHR results

Documentation:

Reference manual: CIMEHR.html , CIMEHR.pdf
Vignettes: Getting Started with CIMEHR (source, R code)

Downloads:

Package source: CIMEHR_0.1.0.tar.gz
Windows binaries: r-devel: not available, r-release: CIMEHR_0.1.0.zip, r-oldrel: not available
macOS binaries: r-release (arm64): CIMEHR_0.1.0.tgz, r-oldrel (arm64): CIMEHR_0.1.0.tgz, r-release (x86_64): CIMEHR_0.1.0.tgz, r-oldrel (x86_64): CIMEHR_0.1.0.tgz

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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