{ "_id": "6a2292abcd65a98ecbd55fb5", "Package": "regmedint", "Title": "Regression-Based Causal Mediation Analysis with Interaction and\nEffect Modification Terms", "Version": "1.0.1", "Authors@R": "c( \nperson(\"Kazuki\", \"Yoshida\",\nemail = \"kazukiyoshida@mail.harvard.edu\",\nrole = c(\"ctb\",\"aut\"),\ncomment = c(ORCID = \"0000-0002-2030-3549\")),\nperson(\"Yi\", \"Li\",\nemail = \"yi.li10@mail.mcgill.ca\",\nrole = c(\"cre\",\"aut\"),\ncomment = c(ORCID = \"0000-0002-9359-210X\")),\nperson(\"Maya\", \"Mathur\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-6698-2607\"))\n)", "Description": "This is an extension of the regression-based causal\nmediation analysis first proposed by Valeri and VanderWeele\n(2013) and Valeri and VanderWeele (2015)\n). It supports including\neffect measure modification by covariates(treatment-covariate\nand mediator-covariate product terms in mediator and outcome\nregression models) as proposed by Li et al (2023)\n. It also accommodates the\noriginal 'SAS' macro and 'PROC CAUSALMED' procedure in 'SAS'\nwhen there is no effect measure modification. Linear and\nlogistic models are supported for the mediator model. Linear,\nlogistic, loglinear, Poisson, negative binomial, Cox, and\naccelerated failure time (exponential and Weibull) models are\nsupported for the outcome model.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "URL": "https://kaz-yos.github.io/regmedint/", "BugReports": "https://github.com/kaz-yos/regmedint/issues", "Repository": "https://kaz-yos.r-universe.dev", "Date/Publication": "2026-03-06 04:23:06 UTC", "RemoteUrl": "https://github.com/kaz-yos/regmedint", "RemoteRef": "HEAD", "RemoteSha": "78a14701a49954aabd236810339a6a77850c01c9", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 09:06:48 UTC", "User": "root" }, "Author": "Kazuki Yoshida [ctb, aut] (ORCID:\n),\nYi Li [cre, aut] (ORCID: ),\nMaya Mathur [ctb] (ORCID: )", "Maintainer": "Yi Li ", "MD5sum": "fb62d0f7c652baaad2eeb14dc7d61ef6", "_user": "kaz-yos", "_type": "src", "_file": "regmedint_1.0.1.tar.gz", "_fileid": "62451faa8960a6f60d85af858bc11ff9fd1a68e87931def482a724ae2bdc2228", "_filesize": 629877, "_sha256": "62451faa8960a6f60d85af858bc11ff9fd1a68e87931def482a724ae2bdc2228", "_created": "2026-06-05T09:06:48.000Z", "_published": "2026-06-05T09:11:07.144Z", "_distro": "noble", "_jobs": [ { "job": 79697764214, "time": 158, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7432948258" }, { "job": 79697764218, "time": 177, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7432954390" }, { "job": 79697764216, "time": 107, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7432931820" }, { "job": 79697764255, "time": 128, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7432940066" }, { "job": 79697102450, "time": 258, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7432897638" }, { "job": 79697764198, "time": 138, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7432942303" }, { "job": 79697764289, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7432943383" }, { "job": 79697764269, "time": 134, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7432940751" }, { "job": 79697764245, "time": 210, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7432965015" } ], "_buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/kaz-yos/regmedint", "_commit": { "id": "78a14701a49954aabd236810339a6a77850c01c9", "author": "Kazuki Yoshida ", "committer": "GitHub ", "message": "Merge pull request #21 from li-ruijie/main\n\nmerge", "time": 1772770986 }, "_maintainer": { "name": "Yi Li", "email": "yi.li10@mail.mcgill.ca", "login": "einsley1993", "description": "Epidemiology and biostatistics researcher", "uuid": 62157377, "orcid": "0000-0002-9359-210X" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Deriv", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "sandwich", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "boot", "role": "Suggests" }, { "package": "furrr", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "geepack", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "mice", "role": "Suggests" }, { "package": "mitools", "role": "Suggests" }, { "package": "modelr", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "magic", "role": "Suggests" }, { "package": "formattable", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" } ], "_owner": "kaz-yos", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-46", "n": 1 }, { "week": "2026-10", "n": 1 } ], "_tags": [], "_topics": [ "causal-inference", "mediation-analysis" ], "_stars": 36, "_contributors": [ { "user": "kaz-yos", "count": 940, "uuid": 2884877 }, { "user": "einsley1993", "count": 118, "uuid": 62157377 }, { "user": "li-ruijie", "count": 7, "uuid": 1547237 } ], "_userbio": { "uuid": 2884877, "type": "user", "name": "Kazuki Yoshida", "description": "Father in Training | Rheumatology & Immunology Clinical Development" }, "_downloads": { "count": 922, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/regmedint" }, "_mentions": 2, "_devurl": "https://github.com/kaz-yos/regmedint", "_pkgdown": "https://kaz-yos.github.io/regmedint/", "_searchresults": 50, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/regmedint.html", "manual.pdf" ], "_homeurl": "https://github.com/kaz-yos/regmedint", "_realowner": "kaz-yos", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2020-05-11" }, { "version": "0.2.0", "date": "2020-11-16" }, { "version": "0.2.1", "date": "2021-05-12" }, { "version": "1.0.0", "date": "2022-04-06" }, { "version": "1.0.1", "date": "2024-01-13" }, { "version": "1.0.2", "date": "2026-03-06" } ], "_exports": [ "fit_mreg", "regmedint" ], "_datasets": [ { "name": "vv2015", "title": "Example dataset from Valeri and VanderWeele 2015.", "object": "vv2015", "class": [ "spec_tbl_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "id", "x", "m", "y", "cens", "c", "event" ], "rows": 100, "table": true, "tojson": true } ], "_help": [ { "page": "beta_hat", "title": "Create a vector of coefficients from the mediator model (mreg)", "topics": [ "beta_hat" ] }, { "page": "calc_myreg", "title": "Return mediation analysis functions given mediator and outcome models specifications.", "topics": [ "calc_myreg" ] }, { "page": "calc_myreg_mreg_linear_yreg_linear", "title": "Create calculators for effects and se (mreg linear / yreg linear)", "topics": [ "calc_myreg_mreg_linear_yreg_linear" ] }, { "page": "calc_myreg_mreg_linear_yreg_logistic", "title": "Create calculators for effects and se (mreg linear / yreg logistic)", "topics": [ "calc_myreg_mreg_linear_yreg_logistic" ] }, { "page": "calc_myreg_mreg_logistic_yreg_linear", "title": "Create calculators for effects and se (mreg logistic / yreg linear)", "topics": [ "calc_myreg_mreg_logistic_yreg_linear" ] }, { "page": "calc_myreg_mreg_logistic_yreg_logistic", "title": "Create calculators for effects and se (mreg logistic / yreg logistic)", "topics": [ "calc_myreg_mreg_logistic_yreg_logistic" ] }, { "page": "coef.regmedint", "title": "Extract point estimates.", "topics": [ "coef.regmedint" ] }, { "page": "coef.summary_regmedint", "title": "Extract the result matrix from a summary_regmedint object.", "topics": [ "coef.summary_regmedint" ] }, { "page": "confint.regmedint", "title": "Confidence intervals for mediation prameter estimates.", "topics": [ "confint.regmedint" ] }, { "page": "fit_mreg", "title": "Fit a model for the mediator given the treatment and covariates.", "topics": [ "fit_mreg" ] }, { "page": "fit_yreg", "title": "Fit a model for the outcome given the treatment, mediator, and covariates.", "topics": [ "fit_yreg" ] }, { "page": "grad_prop_med_yreg_linear", "title": "Calculate the gradient of the proportion mediated for yreg linear.", "topics": [ "grad_prop_med_yreg_linear" ] }, { "page": "grad_prop_med_yreg_logistic", "title": "Calculate the gradient of the proportion mediated for yreg logistic.", "topics": [ "grad_prop_med_yreg_logistic" ] }, { "page": "new_regmedint", "title": "Low level constructor for a regmedint S3 class object.", "topics": [ "new_regmedint" ] }, { "page": "print.regmedint", "title": "print method for regmedint object", "topics": [ "print.regmedint" ] }, { "page": "print.summary_regmedint", "title": "Print method for summary objects from 'summary.regmedint'", "topics": [ "print.summary_regmedint" ] }, { "page": "prop_med_yreg_linear", "title": "Calculate the proportion mediated for yreg linear.", "topics": [ "prop_med_yreg_linear" ] }, { "page": "prop_med_yreg_logistic", "title": "Calculate the proportion mediated for yreg logistic.", "topics": [ "prop_med_yreg_logistic" ] }, { "page": "regmedint", "title": "Conduct regression-based causal mediation analysis", "topics": [ "regmedint" ] }, { "page": "report_missing", "title": "Report variables with missing data", "topics": [ "report_missing" ] }, { "page": "summary.regmedint", "title": "summary method for regmedint object", "topics": [ "summary.regmedint" ] }, { "page": "summary.regmedint_mod_poisson", "title": "Summary with robust sandwich variance estimator for modified Poisson", "topics": [ "summary.regmedint_mod_poisson" ] }, { "page": "theta_hat", "title": "Create a vector of coefficients from the outcome model (yreg)", "topics": [ "theta_hat" ] }, { "page": "validate_args", "title": "Validate arguments to regmedint before passing to other functions", "topics": [ "validate_args" ] }, { "page": "validate_regmedint", "title": "Validate soundness of a regmedint object.", "topics": [ "validate_regmedint" ] }, { "page": "vcov.regmedint", "title": "Extract variance estimates in the vcov form.", "topics": [ "vcov.regmedint" ] }, { "page": "vcov.regmedint_mod_poisson", "title": "Robust sandwich variance estimator for modified Poisson", "topics": [ "vcov.regmedint_mod_poisson" ] }, { "page": "vv2015", "title": "Example dataset from Valeri and VanderWeele 2015.", "topics": [ "vv2015" ] } ], "_readme": "https://github.com/kaz-yos/regmedint/raw/HEAD/README.md", "_rundeps": [ "assertthat", "Deriv", "lattice", "MASS", "Matrix", "sandwich", "survival", "zoo" ], "_vignettes": [ { "source": "vig_05_emm.Rmd", "filename": "vig_05_emm.html", "title": "Implementation of extended formulas when there are effect measure modifiers", "author": "Yi Li, Kazuki Yoshida", "engine": "knitr::rmarkdown", "headings": [ "No EMM by covariates", "EMM by covariates", "There is $A\\times C$ term in mediator model", "There is $A\\times C$ term in both mediator and outcome models", "There are $A\\times C$ term in both mediator and outcome models, and $M\\times C$ term in outcome model" ], "created": "2022-02-03 21:24:46", "modified": "2022-02-18 17:28:07", "commits": 3 }, { "source": "vig_02_formulas.Rmd", "filename": "vig_02_formulas.html", "title": "Implementation of formulas", "author": "Kazuki Yoshida", "engine": "knitr::rmarkdown", "headings": [ "mreg linear yreg linear (V2015 p466 Proposition 2.3)", "Point estimates", "Standard error estimates", "mreg linear yreg non-linear (V2015 p468 Proposition 2.4)", "mreg logistic yreg linear (V2015 p471 Proposition 2.5)", "mreg logistic yreg non-linear (V2015 p473 Proposition 2.6)", "Bibliography" ], "created": "2020-04-26 09:39:49", "modified": "2021-05-11 12:25:12", "commits": 3 }, { "source": "vig_01_introduction.Rmd", "filename": "vig_01_introduction.html", "title": "Introduction to user interface functions", "author": "Kazuki Yoshida, Yi Li", "engine": "knitr::rmarkdown", "headings": [ "Data preparation", "regmedint object", "regemedint() object constructor", "summary() for regmedint", "coef() for regmedint", "vcov() for regmedint", "confint() for regmedint", "print() for regmedint", "Methods for summary_regmedint", "coef() for summary_regmedint", "print() for summary_regmedint" ], "created": "2020-04-26 09:39:49", "modified": "2022-02-03 21:24:46", "commits": 5 }, { "source": "vig_03_bootstrap.Rmd", "filename": "vig_03_bootstrap.html", "title": "Using bootstrapping with regemedint", "author": "Kazuki Yoshida", "engine": "knitr::rmarkdown", "headings": [ "Bootstrapping support", "boot package", "modelr package", "Comparison to the delta method confidence intervals" ], "created": "2020-04-26 09:39:49", "modified": "2021-05-11 12:25:12", "commits": 5 }, { "source": "vig_04_mi.Rmd", "filename": "vig_04_mi.html", "title": "Using multiple imputation with regmedint", "author": "Kazuki Yoshida", "engine": "knitr::rmarkdown", "headings": [ "Missing data generation", "Truth fit", "Naive complete case analysis", "Multiple imputation", "Comparison" ], "created": "2020-04-26 09:39:49", "modified": "2021-05-11 12:25:12", "commits": 4 }, { "source": "vig_06_delta_boot.Rmd", "filename": "vig_06_delta_boot.html", "title": "Validation of extended formuals with effect modification using bootstrap", "author": "Yi Li, Kazuki Yoshida", "engine": "knitr::rmarkdown", "headings": [ "About this document", "Parallel computing setup", "Simulated data generating process", "Generate datasets", "Model fit", "1. Linear mediator model, linear outcome model", "2. Logistic mediator model, linear outcome model", "3. Linear mediator model, logistic outcome model", "4. Logistic mediator model, logistic outcome model", "Results comparison" ], "created": "2022-02-03 21:24:46", "modified": "2022-03-11 20:57:47", "commits": 7 } ], "_score": 7.635483746814912, "_indexed": true, "_nocasepkg": "regmedint", "_universes": [ "kaz-yos", "einsley1993" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-06-05T09:09:08.000Z", "distro": "noble", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "19e158e88aa357e7183f05b6f6c34b4cc34d64faf3fa7eaecd76e6c5f5a36283", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-06-05T09:09:22.000Z", "distro": "noble", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "19d92de35cf4a442f03b13d17fee0256dcc02b651d728b03542d72e960ae1d81", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-06-05T09:08:28.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "43c75ccffb4623108b8b4438f7fcc935ffc9d353add6bff4b8edd20bb8f015f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-06-05T09:08:52.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "452a81242eba177f4883996a04000326f5d60ae634c8e53e18f5d9adcc036cee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-06-05T09:09:30.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "b66467e1ba462c8e2de4a71f379165cd9bf2f53fe2dbf03b188cfd9d93f61953", "status": "success", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-06-05T09:08:28.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "00f82d4d048b11b12bfd2e9df2d4430b0ab59f6c1db3376e8696049e944d4f07", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-06-05T09:08:20.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "c6b88316f7ffd0c3372c3ce5b7969edbdaab61dba38692cc86aa3b94a7f97174", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-06-05T09:09:33.000Z", "commit": "78a14701a49954aabd236810339a6a77850c01c9", "fileid": "5bab1f244540fa760194008b7c5931205d4ae9439802952889bf3c65499ab33e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kaz-yos/actions/runs/27005834485" } ] }