1. Prepare the participant and visit data | 2. State the designs and fit the four variants | 3. Inspect estimates and uncertainty by stage | 4. Construct baseline and population trajectories | 5. Request pointwise 95% intervals explicitly | 6. Locate the included results or export your own
Package: CIMEHR 0.2.0
Cheng-Han Yang
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>.
Authors:
CIMEHR_0.2.0.tar.gz
CIMEHR_0.2.0.zip(r-4.7-x86_64)CIMEHR_0.2.0.zip(r-4.7-arm64)CIMEHR_0.2.0.zip(r-4.6-x86_64)CIMEHR_0.2.0.zip(r-4.6-arm64)CIMEHR_0.2.0.zip(r-4.5-x86_64)
CIMEHR_0.2.0.tgz(r-4.6-x86_64)CIMEHR_0.2.0.tgz(r-4.6-arm64)CIMEHR_0.2.0.tgz(r-4.5-x86_64)CIMEHR_0.2.0.tgz(r-4.5-arm64)
CIMEHR_0.2.0.tar.gz(r-4.7-arm64)CIMEHR_0.2.0.tar.gz(r-4.7-x86_64)CIMEHR_0.2.0.tar.gz(r-4.6-arm64)CIMEHR_0.2.0.tar.gz(r-4.6-x86_64)
CIMEHR_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CIMEHR/json (API)
| # Install 'CIMEHR' in R: |
| install.packages('CIMEHR', repos = c('https://ysph-dsde.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ysph-dsde/cimehr/issues
Datasets:
- cimehr_example - Simulated Participant and Biomarker Visit Records
Last updated from:94144caa6c. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 196 | ||
| linux-devel-x86_64 | OK | 221 | ||
| source / vignettes | OK | 480 | ||
| linux-release-arm64 | OK | 200 | ||
| linux-release-x86_64 | OK | 241 | ||
| macos-release-arm64 | OK | 217 | ||
| macos-release-x86_64 | OK | 415 | ||
| macos-oldrel-arm64 | OK | 176 | ||
| macos-oldrel-x86_64 | OK | 430 | ||
| windows-devel-arm64 | OK | 316 | ||
| windows-devel-x86_64 | OK | 328 | ||
| windows-release-arm64 | OK | 349 | ||
| windows-release-x86_64 | OK | 215 | ||
| windows-oldrel-x86_64 | OK | 279 | ||
| wasm-release | OK | 144 |
Exports:available_comparison_methodsbaseline_meanCIMEHRCIMEHR_HLcimehr_methodsCIMEHR_splineCIMEHR_spline_HLcoef_stageEHRJointextract_coefficientfit_methodIIRRIIRR_balancingInverse_intensity_rate_ratio_balancingInverse_intensity_rate_ratio_weightingJMVL_GJoint_modeling_visiting_and_longitudinal_LiangLiangLin_YingLinear_increment_IPLinear_mixed_modelLMMmeanfitmethod_comparisonsMultiple_imputation_IPPairwise_likelihoodpopulation_trajectorysummary_observationsummary_outcomeSummary_statsummary_visiting
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Longitudinal Analysis of Electronic Health Records with Informative Visiting and Recording | CIMEHR-package |
| Evaluate Baseline and Population Mean Curves | baseline_mean plot.cimehr_fit population_trajectory predict.cimehr_fit |
| CIMEHR Three-Stage Estimator for Informative Visiting and Recording | CIMEHR CIMEHR_HL |
| Simulated Participant and Biomarker Visit Records | cimehr_example |
| Methods for Fitted CIMEHR and Comparison-Method Objects | cimehr_fit-methods coef.cimehr_fit confint.cimehr_fit print.cimehr_fit summary.cimehr_fit vcov.cimehr_fit |
| CIMEHR with a Spline Baseline and Spline Trajectories | CIMEHR_spline CIMEHR_spline_HL predict.cimehr_spline_fit |
| Named Wrappers for the Comparison Methods | comparison_methods EHRJoint IIRR IIRR_balancing Inverse_intensity_rate_ratio_balancing Inverse_intensity_rate_ratio_weighting JMVL_G Joint_modeling_visiting_and_longitudinal_Liang Liang Linear_increment_IP Linear_mixed_model Lin_Ying LMM Multiple_imputation_IP Pairwise_likelihood Summary_stat |
| Fit CIMEHR or a Comparison Method Through the Common Interface | available_comparison_methods cimehr_methods fit_method method_comparisons |
| Construct and Plot Fitted Longitudinal Mean Curves | as.data.frame.cimehr_meanfit cimehr_meanfit meanfit meanfit.cimehr_fit plot.cimehr_meanfit print.cimehr_meanfit summary.cimehr_meanfit |
| Stage-Specific Parameter Tables | coef_stage extract_coefficient stage_summaries summary_observation summary_outcome summary_visiting |