{ "_id": "6ad70d00d556c3a3418a6646", "Package": "survregVB", "Title": "Variational Bayesian Analysis of Survival Data", "Version": "0.0.2", "Authors@R": "c(\nperson(\"Alison\", \"Zhang\", , \"alisonxzhang@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Chengqian\", \"Xian\", , \"cxian3@uwo.ca\", role = c(\"aut\"))\n)", "Description": "Implements Bayesian inference in accelerated failure time\n(AFT) models for right-censored survival times assuming a\nlog-logistic distribution. Details of the variational Bayes\nalgorithms, with and without shared frailty, are described in\nXian et al. (2024) and Xian et\nal. (2024) , respectively.", "URL": "https://github.com/chengqianxian/survregVB", "License": "MIT + file LICENSE | LGPL-2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "LazyData": "true", "Repository": "https://chengqianxian.r-universe.dev", "Date/Publication": "2025-06-22 20:06:22 UTC", "RemoteUrl": "https://github.com/chengqianxian/survregvb", "RemoteRef": "HEAD", "RemoteSha": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-20 06:36:33 UTC", "User": "root" }, "Author": "Alison Zhang [aut, cre],\nChengqian Xian [aut]", "Maintainer": "Alison Zhang ", "_user": "chengqianxian", "_type": "src", "_file": "survregVB_0.0.2.tar.gz", "_fileid": "https://r2.ropensci.org/91a237e2cdd4d76c4ab9cf3a0d7a9b218d238d9df5c69cf2638f7d87f30b1c9c", "_filesize": 265323, "_sha256": "91a237e2cdd4d76c4ab9cf3a0d7a9b218d238d9df5c69cf2638f7d87f30b1c9c", "_expires": "2027-01-28T06:41:02.000Z", "_created": "2026-10-20T06:36:33.000Z", "_published": "2026-10-20T06:41:04.066Z", "_upstream": "https://github.com/chengqianxian/survregvb", "_status": "success", "_maintainer": { "name": "Alison Zhang", "email": "alisonxzhang@gmail.com", "login": "azhan92", "description": "", "uuid": 118318226 }, "_jobs": [ { "job": 118491108878, "time": 114, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12245710769" }, { "job": 118491108892, "time": 140, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12244719230" }, { "job": 118491108789, "time": 223, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12245043347" }, { "job": 118491108862, "time": 148, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12245975579" }, { "job": 118488960890, "time": 408, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12244619742" }, { "job": 118491108812, "time": 131, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12245655968" }, { "job": 118491108813, "time": 78, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12245935794" }, { "job": 118491109021, "time": 78, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12244774077" }, { "job": 118491108829, "time": 136, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12245134593" } ], "_buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530", "_commit": { "id": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "author": "azhan92 ", "committer": "azhan92 ", "message": "Update author's list\n", "time": 1750622782 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "bayestestR", "role": "Imports" }, { "package": "invgamma", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "survival", "role": "Suggests" } ], "_owner": "chengqianxian", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "azhan92", "count": 47, "uuid": 118318226 } ], "_userbio": { "uuid": 48890743, "type": "user", "name": "chengqianxian", "followers": 2 }, "_downloads": { "count": 208, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/survregVB" }, "_devurl": "https://github.com/chengqianxian/survregvb", "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/survregVB.html", "LICENSE" ], "_homeurl": "https://github.com/chengqianxian/survregvb", "_realowner": "chengqianxian", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2025-05-29" }, { "version": "0.0.2", "date": "2025-06-22" } ], "_exports": [ "survregVB", "survregVB.fit", "survregVB.frailty.fit" ], "_datasets": [ { "name": "dnase", "title": "Subset of 'rhDNase' from the 'survival' package", "object": "dnase", "class": [ "data.frame" ], "fields": [ "trt", "fev", "infect", "time" ], "rows": 645, "table": true, "tojson": true }, { "name": "lung_cancer", "title": "Subset of GSE102287: African American (AA) Patients", "object": "lung_cancer", "class": [ "data.frame" ], "fields": [ "patient", "time", "status", "age", "gender", "smoking", "Stage" ], "rows": 60, "table": true, "tojson": true }, { "name": "simulation_frailty", "title": "Simulated data incorporating shared frailty effects to model clustered time-to-event data.", "object": "simulation_frailty", "class": [ "data.frame" ], "fields": [ "x1", "x2", "Time", "Time.15", "delta", "delta.15", "cluster" ], "rows": 75, "table": true, "tojson": true }, { "name": "simulation_nofrailty", "title": "Simulated data without shared frailty effects to model unclustered time-to-event data.", "object": "simulation_nofrailty", "class": [ "data.frame" ], "fields": [ "x1", "x2", "Time", "Time.10", "Time.30", "delta", "delta.10", "delta.30" ], "rows": 300, "table": true, "tojson": true } ], "_help": [ { "page": "alpha_star", "title": "Calculates parameter alpha^* of q^*(b) to optimize the evidence based lower bound (ELBO) in 'survregVB.fit' and 'survregVB.frailty.fit'.", "topics": [ "alpha_star" ] }, { "page": "dnase", "title": "Subset of 'rhDNase' from the 'survival' package", "topics": [ "dnase" ] }, { "page": "elbo", "title": "Calculates the variational Bayes convergence criteria, evidence lower bound (ELBO), optimized in 'survregVB.fit'.", "topics": [ "elbo" ] }, { "page": "elbo_cluster", "title": "Calculates the variational Bayes convergence criteria, evidence lower bound (ELBO), optimized in 'survregVB.frailty.fit'.", "topics": [ "elbo_cluster" ] }, { "page": "eta_star", "title": "Calculates parameter eta^* of q^*(sigma^2_{gamma}) to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "eta_star" ] }, { "page": "lambda_star", "title": "Calculates parameter lambda^* of q^*(sigma^2_{gamma}) to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "lambda_star" ] }, { "page": "lung_cancer", "title": "Subset of GSE102287: African American (AA) Patients", "topics": [ "lung_cancer" ] }, { "page": "mu_star", "title": "Calculates parameter mu^* of q^*(beta) to optimize the evidence based lower bound (ELBO) in 'survregVB.fit'.", "topics": [ "mu_star" ] }, { "page": "mu_star_cluster", "title": "Calculates parameter mu^* of q^*(beta) to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "mu_star_cluster" ] }, { "page": "omega_star", "title": "Calculates parameter omega^* of q^*(b) to optimize the evidence based lower bound (ELBO) in 'survregVB.fit'.", "topics": [ "omega_star" ] }, { "page": "omega_star_cluster", "title": "Calculates parameter omega^* of q^*(b) to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "omega_star_cluster" ] }, { "page": "sigma_squared_star", "title": "Calculates parameter sigma^{2*}_i of q^*(gamma_i) for i=1,...,K clusters to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "sigma_squared_star" ] }, { "page": "sigma_star", "title": "Calculates parameter Sigma^* of q^*(beta) to optimize the evidence based lower bound (ELBO) in 'survregVB.fit'.", "topics": [ "Sigma_star" ] }, { "page": "Sigma_star_cluster", "title": "Calculates parameter Sigma^* of q^*(beta) to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "Sigma_star_cluster" ] }, { "page": "simulation_frailty", "title": "Simulated data incorporating shared frailty effects to model clustered time-to-event data.", "topics": [ "simulation_frailty" ] }, { "page": "simulation_nofrailty", "title": "Simulated data without shared frailty effects to model unclustered time-to-event data.", "topics": [ "simulation_nofrailty" ] }, { "page": "summary.survregVB", "title": "Summary for Variational Bayes log-logistic AFT models.", "topics": [ "print.summary.survregVB", "summary.survregVB" ] }, { "page": "survregVB", "title": "Variational Bayesian Analysis of Survival Data Using a Log-Logistic Accelerated Failure Time Model", "topics": [ "survregVB" ] }, { "page": "survregVB.fit", "title": "Variational Bayesian Analysis of Survival Data Using a Log-Logistic Accelerated Failure Time Model", "topics": [ "survregVB.fit" ] }, { "page": "survregVB.frailty.fit", "title": "Variational Bayesian Analysis of Correlated Survival Data Using a Log-Logistic Accelerated Failure Time Model", "topics": [ "survregVB.frailty.fit" ] }, { "page": "survregVB.object", "title": "Variational Bayes Accelererated Failure Time Survival Model Object", "topics": [ "print.survregVB", "survregVB.object" ] }, { "page": "tau_star", "title": "Calculates parameter tau^*_i of q^*(gamma_i) for i=1,...,K clusters to optimize the evidence based lower bound (ELBO) in 'survregVB.frailty.fit'.", "topics": [ "tau_star" ] } ], "_readme": "https://github.com/chengqianxian/survregvb/raw/HEAD/README.md", "_rundeps": [ "bayestestR", "datawizard", "insight", "invgamma" ], "_vignettes": [ { "source": "survregVB.Rmd", "filename": "survregVB.html", "title": "Using the survregVB Package", "engine": "knitr::rmarkdown", "headings": [ "Overview of survregVB", "The AFT Model", "The AFT Model With Shared Frailty", "Getting Started using survregVB", "Fitting the Model", "Fitting a Model with Shared Frailty", "Session info", "References" ], "created": "2025-01-22 22:00:06", "modified": "2025-05-02 16:48:12", "commits": 19 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "survregvb", "_universes": [ "chengqianxian", "azhan92" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.2", "date": "2026-10-20T06:38:27.000Z", "distro": "resolute", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/c155563026e22b2ca379fdca0a474d9755fd5a7f4e47c5295b9b5a6222f32cd0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.6.1", "os": "linux", "version": "0.0.2", "date": "2026-10-20T06:38:54.000Z", "distro": "resolute", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/ba11942da75ac8afa32e251303018d75e69262ff28f0b05f6b7b12c852824f53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.5.3", "os": "mac", "version": "0.0.2", "date": "2026-10-20T06:39:43.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/b8ac1503ea1a6985cb7cc3c59262ee872131601a22e6eed12841fdbf0ac6db47", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.6.1", "os": "mac", "version": "0.0.2", "date": "2026-10-20T06:38:34.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/caad61b4b42e83ca7a3f16dc215112784f2ebc3b9267b2d5ebaa592bc5d2ec13", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.2", "date": "2026-10-20T06:39:02.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/ac3f8d6f6495a735d39efc73871b35db23d23b620e5e65224ef7cc844de8d4f9", "status": "success", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.7.0", "os": "win", "version": "0.0.2", "date": "2026-10-20T06:37:40.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/2921093762dfbb89fd4b05ef9252d2818323a8e440c03140f1b511a0fc7cd05f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.5.3", "os": "win", "version": "0.0.2", "date": "2026-10-20T06:37:42.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/ed33391e41893d228db65d8c925a1cfd4c074052451c20c2411e361a2f062378", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" }, { "r": "4.6.1", "os": "win", "version": "0.0.2", "date": "2026-10-20T06:38:39.000Z", "commit": "85f5ebe5b323ea3b5e9f6ec55d30c723271e544e", "fileid": "https://r2.ropensci.org/98f411167ba04644b723db4c0d5760d48fb34845d031715a5a35550084e092d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/chengqianxian/actions/runs/39380679530" } ] }