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
Packaged: 2026-10-22 01:31:31 UTC; yh785
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>
Repository: CRAN
Date/Publication: 2026-10-22 13:30:38 UTC
Built: R 4.5.2; x86_64-apple-darwin20; 2026-10-22 15:29:19 UTC; unix
Archs: CIMEHR.so.dSYM
