{ "_id": "6a27d88724555f66ed546b58", "Package": "CIMEHR", "Title": "Gaussian Clinically Informative Visiting and Observation\nProcesses in Electronic Health Record (EHR) Data", "Version": "0.1.0", "Authors@R": "c(\nperson(given = \"Cheng-Han\", family = \"Yang\",\nemail = \"chenghanyang728@gmail.com\",\nrole = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0002-4161-3140\")),\nperson(given = \"Yiren\", family = \"Hou\",\nemail = \"yiren.hou@yale.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0005-0422-4268\"))\n)", "Description": "Fits semiparametric joint models for longitudinal\nelectronic health record (EHR) data that addresses two-stage\nhierarchical missingness mechanism. The first stage is the\nvisiting process, and the second stage is the observation\nprocess. The core CIMEHR method (Clinical Informative\nMissingness for Electronic Health Records) uses a three-stage\nprocedure: partial likelihood with log-normal frailty for visit\nintensity, probit regression with shared latent factor-linked\nrandom effects for observation, and weighted least squares with\nrisk-set centering for the outcome. These three stages are\nconnected through a shared latent factor that induces\ndependence across all three processes. A data simulator and\nimplementations of common benchmark methods (linear mixed\nmodels, multiple imputation, and others) are included for\ncomparative studies. Detailed methods are described in Yang,\nShi, and Mukherjee (2026) .", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/ysph-dsde/CIMEHR", "BugReports": "https://github.com/ysph-dsde/CIMEHR/issues", "VignetteBuilder": "knitr", "LazyData": "true", "Config/pak/sysreqs": "cmake make libicu-dev libx11-dev zlib1g-dev", "Repository": "https://ysph-dsde.r-universe.dev", "Date/Publication": "2026-06-02 14:58:53 UTC", "RemoteUrl": "https://github.com/ysph-dsde/cimehr", "RemoteRef": "HEAD", "RemoteSha": "62c978710930a7248d2849aed64dbc15a27cba3b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-09 09:04:09 UTC", "User": "root" }, "Author": "Cheng-Han Yang [aut, cre] (ORCID:\n),\nYiren Hou [aut] (ORCID: )", "Maintainer": "Cheng-Han Yang ", "MD5sum": "62b13a84135487bf55053a46aadefd9b", "_user": "ysph-dsde", "_type": "src", "_file": "CIMEHR_0.1.0.tar.gz", "_fileid": "35e0d3b4571ad6ba86b36fc756770d5a56f33e05ebad0424f6da8a22a68fc605", "_filesize": 1214825, "_sha256": "35e0d3b4571ad6ba86b36fc756770d5a56f33e05ebad0424f6da8a22a68fc605", "_created": "2026-06-09T09:04:09.000Z", "_published": "2026-06-09T09:10:31.018Z", "_distro": "noble", "_jobs": [ { "job": 80286479658, "time": 148, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7503249913" }, { "job": 80286479641, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7503243176" }, { "job": 80286479685, "time": 150, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7503251271" }, { "job": 80286479639, "time": 141, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7503246498" }, { "job": 80286479753, "time": 205, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7503260767" }, { "job": 80286479661, "time": 239, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7503276372" }, { "job": 80286479680, "time": 211, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7503259898" }, { "job": 80286479779, "time": 326, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7503297116" }, { "job": 80285600621, "time": 285, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7503190544" }, { "job": 80286479603, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7503238405" }, { "job": 80286479645, "time": 112, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7503234971" }, { "job": 80286479699, "time": 110, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7503234052" }, { "job": 80286479648, "time": 108, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7503233583" } ], "_buildurl": "https://github.com/r-universe/ysph-dsde/actions/runs/27195384280", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ysph-dsde/cimehr", "_commit": { "id": "62c978710930a7248d2849aed64dbc15a27cba3b", "author": "yirenhou2001 ", "committer": "yirenhou2001 ", "message": "Updates before first submission to CRAN\n", "time": 1780412333 }, "_maintainer": { "name": "Cheng-Han Yang", "email": "chenghanyang728@gmail.com", "login": "cyang728", "description": "I am an Associate Research Sciesntist in Biostatistics program at Yale university. My research interests lie in EHR data analysis and survival analysis. 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Input data format", "1.1 Converting short/wide data to long data", "2. Example dataset", "3. Method comparison", "Methods implemented in CIMEHR", "Outcome-only", "IP-only", "Imputation + IP-only", "IP+IO", "4. Simpler benchmark methods first", "4.1 Summary-statistic regression", "4.2 Linear mixed model", "4.3 Pairwise likelihood", "5. Visiting-process and joint methods", "5.1 Inverse intensity rate ratio weighting", "5.2 Inverse intensity rate ratio balancing", "5.3 Liang--Lu--Ying joint visiting/outcome model", "5.4 EHRJoint", "6. Primary CIMEHR methods", "6.1 Base CIMEHR", "6.1.1 Stage-specific summaries and coefficient extraction", "6.2 CIMEHR with Gauss--Hermite quadrature", "6.3 CIMEHR with OU pairwise composite likelihood", "7. Comparing methods with method_comparisons()", "8. Simulation study", "9. Bootstrap inference", "10. 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