{ "_id": "6a22a93e0ef520ea2f58b04c", "Package": "BSET", "Type": "Package", "Title": "A Bayesian Surrogate Evaluation Test", "Version": "1.0", "Date": "2026-05-15", "Authors@R": "c(\nperson(\"Pietro\", \"Carlotti\", role = c(\"aut\", \"cre\"),\nemail = \"pietro.carlotti@utexas.edu\"),\nperson(\"Layla\", \"Parast\", role = \"aut\",\nemail = \"parast@austin.utexas.edu\"))", "Description": "An implementation of the Bayesian Surrogate Evaluation\nTest (BSET) for assessing the validity of surrogate markers in\nclinical trials. Provides hypothesis testing tools to evaluate\nwhether a surrogate can reliably estimate the causal effect of\na treatment on a primary outcome. Implements the\nimputation-based Bayesian methodology of Carlotti and Parast\n(2026) , extending the\nfrequentist rank-based approach of Parast et al. (2024)\n. Addresses key limitations of the\nfrequentist method, including the lack of causal\ninterpretability and the inability to adjust for covariates in\nthe estimation process.", "License": "GPL-3", "URL": "https://pietrocarlotti.github.io/BSET/,\nhttps://github.com/PietroCarlotti/BSET", "BugReports": "https://github.com/PietroCarlotti/BSET/issues", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "RdMacros": "Rdpack", "VignetteBuilder": "knitr, bookdown", "Config/pak/sysreqs": "make", "Repository": "https://pietrocarlotti.r-universe.dev", "Date/Publication": "2026-05-29 20:05:36 UTC", "RemoteUrl": "https://github.com/pietrocarlotti/bset", "RemoteRef": "HEAD", "RemoteSha": "5977ba8a59547383447ea2b8fd06473186cd663f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 10:43:59 UTC", "User": "root" }, "Author": "Pietro Carlotti [aut, cre],\nLayla Parast [aut]", "Maintainer": "Pietro Carlotti ", "MD5sum": "f39fa6bc030920202802d94c90396366", "_user": "pietrocarlotti", "_type": "src", "_file": "BSET_1.0.tar.gz", "_fileid": "cf33762698a2dfe18b584d200c25c564ebfcfd1f0ab295405c42c02ff0c8114f", "_filesize": 8377281, "_sha256": "cf33762698a2dfe18b584d200c25c564ebfcfd1f0ab295405c42c02ff0c8114f", "_created": "2026-06-05T10:43:59.000Z", "_published": "2026-06-05T10:47:26.793Z", "_distro": "noble", "_jobs": [ { "job": 79712131862, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7434725090" }, { "job": 79712131897, "time": 157, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7434722980" }, { "job": 79712131889, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7434721504" }, { "job": 79712131837, "time": 171, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7434725888" }, { "job": 79711643013, "time": 208, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7434678871" }, { "job": 79712131863, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7434716303" }, { "job": 79712131895, "time": 123, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7434713325" }, { "job": 79712131953, "time": 138, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7434717574" }, { "job": 79712131896, "time": 109, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7434709343" } ], "_buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/pietrocarlotti/bset", "_commit": { "id": "5977ba8a59547383447ea2b8fd06473186cd663f", "author": "PietroCarlotti ", "committer": "PietroCarlotti ", "message": "update\n", "time": 1780085136 }, "_maintainer": { "name": "Pietro Carlotti", "email": "pietro.carlotti@utexas.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "rstan", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "SurrogateRank", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" } ], "_owner": "pietrocarlotti", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-15", "n": 51 }, { "week": "2026-16", "n": 22 }, { "week": "2026-17", "n": 58 }, { "week": "2026-18", "n": 24 }, { "week": "2026-19", "n": 40 }, { "week": "2026-20", "n": 7 }, { "week": "2026-21", "n": 2 }, { "week": "2026-22", "n": 1 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "pietrocarlotti", "count": 210, "uuid": 91976479 } ], "_userbio": { "uuid": 91976479, "type": "user", "name": "PietroCarlotti" }, "_downloads": { "count": 212, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BSET" }, "_devurl": "https://github.com/pietrocarlotti/bset", "_pkgdown": "https://pietrocarlotti.github.io/BSET/", "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/BSET.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pietrocarlotti/bset", "_realowner": "pietrocarlotti", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2026-05-22" } ], "_exports": [ "Bayesian_test", "BSET", "compute_BF_distribution", "compute_delta", "compute_estimands_Carlotti_and_Parast_2026", "compute_estimands_Parast_et_al_2024", "compute_theta", "compute_V_S_star", "DGP_no_X", "DGP_X_binary", "DGP_X_Gaussian", "frequentist_test" ], "_datasets": [ { "name": "Carlotti_and_Parast_2026_simulations_grid", "title": "Simulation grid for Carlotti and Parast (2026)", "object": "Carlotti_and_Parast_2026_simulations_grid", "class": [ "data.frame" ], "fields": [ "setting", "simulation", "Bayesian_epsilon", "Bayesian_CI_upper", "Bayesian_coverage", "Bayesian_power", "frequentist_epsilon", "frequentist_CI_upper", "frequentist_coverage", "frequentist_power", "n_sample", "n_chains", "n_iterations", "n_simulations", "BF_alternative", "timestamp", "seed" ], "rows": 1000, "table": true, "tojson": true }, { "name": "estimands_Carlotti_and_Parast_2026", "title": "True estimands for Carlotti and Parast (2026)", "object": "estimands_Carlotti_and_Parast_2026", "class": [ "data.frame" ], "fields": [ "setting", "U_Y_MC", "U_S_MC", "delta_MC", "V_Y_MC", "V_S_MC", "theta_MC" ], "rows": 2, "table": true, "tojson": true }, { "name": "estimands_Parast_et_al_2024", "title": "True estimands for Parast et al. (2024)", "object": "estimands_Parast_et_al_2024", "class": [ "data.frame" ], "fields": [ "setting", "U_Y_MC", "U_S_MC", "delta_MC", "V_Y_MC", "V_S_MC", "theta_MC" ], "rows": 4, "table": true, "tojson": true }, { "name": "Parast_et_al_2024_simulations_grid", "title": "Simulation grid for Parast et al. (2024)", "object": "Parast_et_al_2024_simulations_grid", "class": [ "data.frame" ], "fields": [ "setting", "simulation", "Bayesian_epsilon", "Bayesian_CI_upper", "Bayesian_coverage", "Bayesian_power", "frequentist_epsilon", "frequentist_CI_upper", "frequentist_coverage", "frequentist_power", "n_sample", "n_chains", "n_iterations", "n_simulations", "BF_alternative", "timestamp", "seed" ], "rows": 2000, "table": true, "tojson": true } ], "_help": [ { "page": "Bayesian_test", "title": "Bayesian Test from Carlotti and Parast (2026)", "topics": [ "Bayesian_test" ] }, { "page": "BSET", "title": "Bayesian Surrogate Evaluation Test from Carlotti and Parast (2026)", "topics": [ "BSET" ] }, { "page": "Carlotti_and_Parast_2026_simulations_grid", "title": "Simulation grid for Carlotti and Parast (2026)", "topics": [ "Carlotti_and_Parast_2026_simulations_grid" ] }, { "page": "compute_BF_distribution", "title": "Compute the Distribution of the Bayes Factor from Carlotti and Parast (2026)", "topics": [ "compute_BF_distribution" ] }, { "page": "compute_delta", "title": "Monte Carlo Computation of the Parameter delta from Parast et al. (2024)", "topics": [ "compute_delta" ] }, { "page": "compute_estimands_Carlotti_and_Parast_2026", "title": "Monte Carlo Computation of the Estimands for the Simulation Study in Carlotti and Parast (2026)", "topics": [ "compute_estimands_Carlotti_and_Parast_2026" ] }, { "page": "compute_estimands_Parast_et_al_2024", "title": "Monte Carlo Computation of the Estimands for the Simulation Study in Parast et al. (2024)", "topics": [ "compute_estimands_Parast_et_al_2024" ] }, { "page": "compute_theta", "title": "Monte Carlo Computation of the Parameter theta from Carlotti and Parast (2026)", "topics": [ "compute_theta" ] }, { "page": "compute_V_S_star", "title": "Compute v_S from Carlotti and Parast (2026)", "topics": [ "compute_V_S_star" ] }, { "page": "DGP_no_X", "title": "Data Generating Process without Baseline Covariates", "topics": [ "DGP_no_X" ] }, { "page": "DGP_X_binary", "title": "Data Generating Process with a Binary Covariate", "topics": [ "DGP_X_binary" ] }, { "page": "DGP_X_Gaussian", "title": "Data Generating Process with a Gaussian Covariate", "topics": [ "DGP_X_Gaussian" ] }, { "page": "estimands_Carlotti_and_Parast_2026", "title": "True estimands for Carlotti and Parast (2026)", "topics": [ "estimands_Carlotti_and_Parast_2026" ] }, { "page": "estimands_Parast_et_al_2024", "title": "True estimands for Parast et al. (2024)", "topics": [ "estimands_Parast_et_al_2024" ] }, { "page": "frequentist_test", "title": "Frequentist Test from Parast et al. (2024)", "topics": [ "frequentist_test" ] }, { "page": "Parast_et_al_2024_simulations_grid", "title": "Simulation grid for Parast et al. (2024)", "topics": [ "Parast_et_al_2024_simulations_grid" ] } ], "_pkglogo": "https://github.com/pietrocarlotti/bset/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/pietrocarlotti/bset/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "codetools", "cpp11", "desc", "digest", "distributional", "dplyr", "farver", "future", "generics", "ggplot2", "globals", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lifecycle", "listenv", "loo", "magrittr", "matrixStats", "mvtnorm", "numDeriv", "parallelly", "pbmcapply", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "QuickJSR", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "Rdpack", "rlang", "rstan", "S7", "scales", "StanHeaders", "SurrogateRank", "tensorA", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "BSET_tutorial.Rmd", "filename": "BSET_tutorial.html", "title": "BSET Tutorial", "author": "Pietro Carlotti", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick Start", "Computing the true values of the discrepancy parameters", "Computing the validation threshold", "Running the BSET procedure", "BSET with no covariates", "BSET with covariates", "References" ], "created": "2026-04-09 15:09:37", "modified": "2026-05-04 19:46:52", "commits": 22 } ], "_score": 4.6020599913279625, "_indexed": true, "_nocasepkg": "bset", "_universes": [ "pietrocarlotti" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0", "date": "2026-06-05T10:46:36.000Z", "distro": "noble", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "d0da77354deba616bcc2b6d1f8b58143ff478cf4e7ad5ee1a25bc6d6ffabb6ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.6.0", "os": "linux", "version": "1.0", "date": "2026-06-05T10:46:29.000Z", "distro": "noble", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "57294b29af72565587826fe3d224e08348f0be08e7db21ed90c6bf1a119169dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.5.3", "os": "mac", "version": "1.0", "date": "2026-06-05T10:46:18.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "60f3fc36e5747b07459da866e07cf25fe6a85d6e35e9cb8ea48f0f941ba1d5e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.6.0", "os": "mac", "version": "1.0", "date": "2026-06-05T10:46:29.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "3736f0c694d255b00eda1711aedacc6ebf6e5db5010c8054cedca57594bb2d6f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.6.0", "os": "wasm", "version": "1.0", "date": "2026-06-05T10:46:31.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "4a07f1e8c505ba4457d4080c602f896304638dd81caaa7f4d8bfd751226c929e", "status": "success", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.7.0", "os": "win", "version": "1.0", "date": "2026-06-05T10:45:45.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "6764db69122bf65950cde577515377a2aee85f50d0f2489cfa7255ce3d67710b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.5.3", "os": "win", "version": "1.0", "date": "2026-06-05T10:45:52.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "1fcc4a40f7e097f0be9f306a79447f7ecc6ebea3915fb72e51441d531666b2fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" }, { "r": "4.6.0", "os": "win", "version": "1.0", "date": "2026-06-05T10:45:30.000Z", "commit": "5977ba8a59547383447ea2b8fd06473186cd663f", "fileid": "f6e7e392b76b829802b5051170d6cef48f2be61a4fd4d795584c46881511d7c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/pietrocarlotti/actions/runs/27010186207" } ] }