R Observatory: Metrics for CIMEHR version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CIMEHR

0.1.0

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

0packages depend

557downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Cheng-Han YangFirst published 2026-06-081 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("CIMEHR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ysph-dsde/CIMEHR")

Development version from ysph-dsde/CIMEHR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-cimehr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-CIMEHR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-CIMEHR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.4 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 2,209 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 24%

Downloads

557

CRAN downloads in the past year

Rank #19,750 · ~2/day · ~46/mo

Releases R versions

Daily download trend is not available in this view yet.

16530 days

55790 days

5571 year

Compare downloads with other packages →

Also on57 r2u2 autocran

Repository

GitHub ↗ ysph-dsde/cimehr

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-06-02

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ysph-dsde/cimehr on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (11)

MASSRcpp nleqslv pbivnorm numDerivstatsutilsdata.table micenlmeslim

LinkingTo (1)

Rcpp

Suggests (5)

tibble dplyr tidyr knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Cheng-Han Yang

Author, Maintainer

Authors (2)

Cheng-Han Yang

Author, Maintainer

Yiren Hou

Author

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-06-08 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-08
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 270 KB / 1 file
Download size: 779 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CIMEHR")

Format

Yang, C., & Hou, Y. (2026). CIMEHR: Gaussian Clinically Informative Visiting and Observation Processes in Electronic Health Record (EHR) Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CIMEHR

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for CIMEHR version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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