Package: CIMEHR
Type: Package
Title: Longitudinal EHR Analysis with Informative Visits and Recording
Version: 0.2.0
Authors@R: c(
    person(given = "Cheng-Han", family = "Yang",
           email = "chenghanyang728@gmail.com",
           role = c("aut","cre"),
           comment = c(ORCID = "0000-0002-4161-3140")),
    person(given = "Yiren", family = "Hou",
           email = "yiren.hou@yale.edu",
           role = "aut",
           comment = c(ORCID = "0009-0005-0422-4268"))
  )
Description: 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>.
License: MIT + file LICENSE
Copyright: See file inst/COPYRIGHTS.
URL: https://github.com/ysph-dsde/CIMEHR
BugReports: https://github.com/ysph-dsde/CIMEHR/issues
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: nlme, parallel, Rcpp, splines, stats, tools, utils
LinkingTo: Rcpp
Suggests: ggplot2 (>= 3.4.0), knitr, mice, pan, rmarkdown
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
Collate: 'RcppExports.R' 'cimehr_shared.R' 'cimehr.R' 'cimehr_hl.R'
        'cimehr_hl_moments.R' 'cimehr_identification.R'
        'cimehr_numerics.R' 'cimehr_prediction.R' 'cimehr_spline.R'
        'cimehr_spline_hl.R' 'cimehr_zero.R' 'curve_bootstrap.R'
        'curve_refit.R' 'dispatch.R' 'ehrjoint.R'
        'ehrjoint_prediction.R' 'iirr_balancing_marker.R'
        'iirr_balancing_visit.R' 'iirr_weighting_marker.R'
        'iirr_weighting_visit.R' 'input_data.R' 'jmvl_g_marker.R'
        'jmvl_g_visit.R' 'li_iirr.R' 'li_liang.R' 'li_lmm.R'
        'li_reconstruction.R' 'liang_completed_followup.R'
        'liang_marker.R' 'liang_trajectory.R' 'liang_visit.R'
        'lin_ying_marker.R' 'lin_ying_visit.R' 'lmm.R' 'meanfit.R'
        'mi_iirr.R' 'mi_liang.R' 'mi_lmm.R' 'native_adapter.R'
        'oa_lmm.R' 'outcome_summary.R' 'pairlik.R' 'registry.R'
        'stages.R' 'stages_spline.R' 'summary_max.R' 'summary_mean.R'
        'summary_median.R' 'summary_min.R' 'trajectory_api.R'
        'va_lmm.R'
Config/roxygen2/version: 8.1.1
Repository: https://ysph-dsde.r-universe.dev
Date/Publication: 2026-10-22 01:29:32 UTC
RemoteUrl: https://github.com/ysph-dsde/cimehr
RemoteRef: HEAD
RemoteSha: 94144caa6c96988d4b94d8a84930e4c99f43f459
Packaged: 2026-10-22 05:13:28 UTC; root
Author: Cheng-Han Yang [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4161-3140>),
  Yiren Hou [aut] (ORCID: <https://orcid.org/0009-0005-0422-4268>)
Maintainer: Cheng-Han Yang <chenghanyang728@gmail.com>