CIMEHR
Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data
Description
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>.
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Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
Code
Structure
Lines of code
14,034
Files
89
Compiled share
0.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
23
Internal functions
74
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-06-08
Latest release
2026-06-08
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–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.