{ "_id": "6aae63d13d719c1f8407c29c", "Package": "pvEBayes", "Title": "Empirical Bayes Methods for Pharmacovigilance", "Version": "0.3.0", "Authors@R": "c(\nperson(\n\"Yihao\", \"Tan\",\nemail = \"yihaotan@buffalo.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0002-9196-8166\")\n),\nperson(\n\"Marianthi\", \"Markatou\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1453-8229\")\n),\nperson(\n\"Saptarshi\", \"Chakraborty\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3121-9174\")\n),\nperson(given = \"Raktim\", family = \"Mukhopadhyay\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0009-0007-8972-6682\"))\n)", "Maintainer": "Yihao Tan ", "Description": "A suite of empirical Bayes methods to use in\npharmacovigilance. Contains various model fitting and\npost-processing functions. For more details see Tan et al.\n(2025) ,\n; Koenker and Mizera (2014)\n; Efron (2016)\n.", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE, roclets = c (\"namespace\", \"rd\",\n\"srr::srr_stats_roclet\"))", "RoxygenNote": "7.3.2", "LazyData": "true", "Config/testthat/edition": "3", "URL": "https://github.com/ropensci/pvEBayes", "BugReports": "https://github.com/ropensci/pvEBayes/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libgmp3-dev make libicu-dev libjpeg-dev\nlibpng-dev libxml2-dev libssl-dev pkg-config libclang-dev", "Repository": "https://ropensci.r-universe.dev", "Date/Publication": "2026-06-18 14:16:07 UTC", "RemoteUrl": "https://github.com/ropensci/pvEBayes", "RemoteRef": "main", "RemoteSha": "c8b5cd89255132ab198158616dedfc382be9b68b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-19 10:21:45 UTC", "User": "root" }, "Author": "Yihao Tan [aut, cre] (ORCID: ),\nMarianthi Markatou [aut] (ORCID:\n),\nSaptarshi Chakraborty [aut] (ORCID:\n),\nRaktim Mukhopadhyay [aut] (ORCID:\n)", "_user": "ropensci", "_type": "src", "_file": "pvEBayes_0.3.0.tar.gz", "_fileid": "https://r2.ropensci.org/487cc96e98765473e27ad0fe4f171f286b5167a2940204b3c9bc1a6c04104a60", "_filesize": 858713, "_sha256": "487cc96e98765473e27ad0fe4f171f286b5167a2940204b3c9bc1a6c04104a60", "_expires": "2026-12-28T10:28:31.000Z", "_created": "2026-09-19T10:21:45.000Z", "_published": "2026-09-19T10:28:33.592Z", "_jobs": [ { "job": 105881809847, "time": 204, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10582651839" }, { "job": 105881809871, "time": 208, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10582766689" }, { "job": 105881809923, "time": 161, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10583231015" }, { "job": 105881809840, "time": 191, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10582746710" }, { "job": 105881809874, "time": 120, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10582686709" }, { "job": 105881809941, "time": 254, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10582407002" }, { "job": 105881809921, "time": 156, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10582731620" }, { "job": 105881809918, "time": 240, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10583265495" }, { "job": 105881346403, "time": 212, "config": "pkgdown", "r": "4.6.0", "check": "OK", "artifact": "10582661467" }, { "job": 105881346340, "time": 231, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10583245280" }, { "job": 105881809825, "time": 158, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10582367054" }, { "job": 105881809897, "time": 346, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10582577013" }, { "job": 105881809997, "time": 193, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10583101229" }, { "job": 105881809915, "time": 144, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10582491910" }, { "job": 105881809885, "time": 223, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10582821603" }, { "job": 105881809904, "time": 130, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10582811497" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563", "_status": "success", "_upstream": "https://github.com/ropensci/pvEBayes", "_commit": { "id": "c8b5cd89255132ab198158616dedfc382be9b68b", "author": "YihaoTan ", "committer": "YihaoTan ", "message": "update badge\n", "time": 1781792167 }, "_maintainer": { "name": "Yihao Tan", "email": "yihaotan@buffalo.edu", "orcid": "0009-0002-9196-8166" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "data.table", "role": "Imports" }, { "package": "ggdist", "role": "Imports" }, { "package": "ggfittext", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "wacolors", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "CVXR", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "ropensci", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 2 }, { "week": "2025-47", "n": 7 }, { "week": "2025-48", "n": 8 }, { "week": "2025-49", "n": 4 }, { "week": "2025-50", "n": 3 }, { "week": "2025-51", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 2 }, { "week": "2026-04", "n": 1 }, { "week": "2026-09", "n": 1 }, { "week": "2026-10", "n": 14 }, { "week": "2026-11", "n": 4 }, { "week": "2026-12", "n": 2 }, { "week": "2026-13", "n": 1 }, { "week": "2026-18", "n": 6 }, { "week": "2026-21", "n": 1 }, { "week": "2026-24", "n": 7 }, { "week": "2026-25", "n": 3 } ], "_tags": [], "_topics": [ "pharmacovigilance", "cpp" ], "_stars": 0, "_contributors": [ { "user": "yihaotancn", "count": 1, "uuid": 75647584 } ], "_userbio": { "uuid": 1200269, "type": "organization", "name": "rOpenSci", "followers": 1154, "description": "Tools and R Packages for Open Science" }, "_downloads": { "count": 349, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pvEBayes" }, "_devurl": "https://github.com/ropensci/pvebayes", "_pkgdown": "https://docs.ropensci.org/pvEBayes", "_searchresults": 3, "_metadata": { "review": { "id": 760, "status": "reviewed", "version": "0.2.2", "organization": "rOpenSci Software Review", "url": "https://github.com/ropensci/software-review/issues/760" }, "ropensci_category": "stat" }, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/pvEBayes.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/ropensci/pvebayes", "_realowner": "ropensci", "_cranurl": true, "_releases": [ { "version": "0.1.1", "date": "2025-07-10" }, { "version": "0.1.2", "date": "2025-10-03" }, { "version": "0.2.0", "date": "2025-12-15" }, { "version": "0.2.1", "date": "2026-01-11" }, { "version": "0.2.2", "date": "2026-03-13" }, { "version": "0.3.0", "date": "2026-06-16" } ], "_exports": [ "%>%", "estimate_null_expected_count", "extract_all_fitted_models", "eyeplot_pvEBayes", "generate_contin_table", "get_posterior_prob", "heatmap_pvEBayes", "posterior_draws", "pvEBayes", "pvEBayes_tune", "summary_table_pvEBayes" ], "_datasets": [ { "name": "faers_opioid_mental", "title": "FDA opioid dataset with 243 mental-related adverse events", "object": "faers_opioid_mental", "class": [ "matrix", "array" ], "fields": [ "Codeine", "Fentanyl", "Oxycodone", "Pentazocine", "Tramadol", "Other_drug" ], "rows": 244, "table": true, "tojson": true }, { "name": "gbca2025", "title": "FDA GBCA dataset with 1328 adverse events", "object": "gbca2025", "class": [ "matrix", "array" ], "fields": [ "Gadobenate", "Gadobutrol", "Gadodiamide", "Gadopentetate", "Gadoterate", "Gadoteridol", "Gadoxetate", "Other_drugs" ], "rows": 1328, "table": true, "tojson": true }, { "name": "gbca2025_69", "title": "FDA GBCA dataset with 69 adverse events", "object": "gbca2025_69", "class": [ "matrix", "array" ], "fields": [ "Gadobenate", "Gadobutrol", "Gadodiamide", "Gadopentetate", "Gadoterate", "Gadoteridol", "Gadoxetate", "Other_drugs" ], "rows": 70, "table": true, "tojson": true }, { "name": "statin2025", "title": "FDA statin dataset with 5119 adverse events", "object": "statin2025", "class": [ "matrix", "array" ], "fields": [ "Atorvastatin", "Fluvastatin", "Lovastatin", "Pravastatin", "Rosuvastatin", "Simvastatin", "Other_drugs" ], "rows": 5119, "table": true, "tojson": true }, { "name": "statin2025_44", "title": "FDA statin dataset with 44 adverse events", "object": "statin2025_44", "class": [ "matrix", "array" ], "fields": [ "Atorvastatin", "Fluvastatin", "Lovastatin", "Pravastatin", "Rosuvastatin", "Simvastatin", "Other_drugs" ], "rows": 45, "table": true, "tojson": true }, { "name": "statin42", "title": "FDA statin dataset with 42 adverse events", "object": "statin42", "class": [ "matrix", "array" ], "fields": [ "Atorvastatin", "Fluvastatin", "Lovastatin", "Pravastatin", "Rosuvastatin", "Simvastatin", "Other" ], "rows": 43, "table": true, "tojson": true }, { "name": "vigi_opioid_mental", "title": "VigiBase opioid dataset with 100 mental-related adverse events", "object": "vigi_opioid_mental", "class": [ "matrix", "array" ], "fields": [ "Codeine", "Fentanyl", "Oxycodone", "Pentazocine", "Tramadol", "Other_drugs" ], "rows": 101, "table": true, "tojson": true } ], "_help": [ { "page": "pvEBayes-package", "title": "A suite of empirical Bayes methods to use in pharmacovigilance.", "topics": [ "pvEBayes-package" ] }, { "page": "AIC.pvEBayes", "title": "Obtain Akaike Information Criterion (AIC) for a pvEBayes object", "topics": [ "AIC.pvEBayes" ] }, { "page": "BIC.pvEBayes", "title": "Obtain Bayesian Information Criterion (BIC) for a pvEBayes object", "topics": [ "BIC.pvEBayes" ] }, { "page": "estimate_null_expected_count", "title": "Estimate expected null baseline count based on reference row and column", "topics": [ "estimate_null_expected_count" ] }, { "page": "extract_all_fitted_models", "title": "Extract all fitted models from a tuned pvEBayes Object", "topics": [ "extract_all_fitted_models" ] }, { "page": "eyeplot_pvEBayes", "title": "Generate an eyeplot showing the distribution of posterior draws for selected drugs and adverse events", "topics": [ "eyeplot_pvEBayes" ] }, { "page": "faers_opioid_mental", "title": "FDA opioid dataset with 243 mental-related adverse events", "topics": [ "faers_opioid_mental" ] }, { "page": "gbca2025", "title": "FDA GBCA dataset with 1328 adverse events", "topics": [ "gbca2025" ] }, { "page": "gbca2025_69", "title": "FDA GBCA dataset with 69 adverse events", "topics": [ "gbca2025_69" ] }, { "page": "generate_contin_table", "title": "Generate random contingency tables based on a reference table embedded signals,and possibly with zero inflation", "topics": [ "generate_contin_table" ] }, { "page": "get_posterior_prob", "title": "Obtain posterior probability of being a signal", "topics": [ "get_posterior_prob" ] }, { "page": "heatmap_pvEBayes", "title": "Generate a heatmap plot visualizing posterior probabilities for selected drugs and adverse events", "topics": [ "heatmap_pvEBayes" ] }, { "page": "logLik.pvEBayes", "title": "Extract log marginal likelihood for a pvEBayes object", "topics": [ "logLik.pvEBayes" ] }, { "page": "plot.pvEBayes", "title": "Plotting method for a pvEBayes object", "topics": [ "plot.pvEBayes" ] }, { "page": "posterior_draws", "title": "Generate posterior draws for each AE-drug combination", "topics": [ "posterior_draws" ] }, { "page": "print.pvEBayes", "title": "Print method for a pvEBayes object", "topics": [ "print.pvEBayes" ] }, { "page": "pvEBayes", "title": "Fit a general-gamma, GPS, K-gamma, KM or efron model for a contingency table.", "topics": [ "pvEBayes" ] }, { "page": "pvEBayes_tune", "title": "Select hyperparameter and obtain the optimal general-gamma or efron model based on AIC and BIC", "topics": [ "pvEBayes_tune" ] }, { "page": "statin2025", "title": "FDA statin dataset with 5119 adverse events", "topics": [ "statin2025" ] }, { "page": "statin2025_44", "title": "FDA statin dataset with 44 adverse events", "topics": [ "statin2025_44" ] }, { "page": "statin42", "title": "FDA statin dataset with 42 adverse events", "topics": [ "statin42" ] }, { "page": "summary_table_pvEBayes", "title": "Obtain a summary table for a pvEBayes object", "topics": [ "summary_table_pvEBayes" ] }, { "page": "summary.pvEBayes", "title": "Summary method for a pvEBayes object", "topics": [ "summary.pvEBayes" ] }, { "page": "vigi_opioid_mental", "title": "VigiBase opioid dataset with 100 mental-related adverse events", "topics": [ "vigi_opioid_mental" ] } ], "_readme": "https://github.com/ropensci/pvEBayes/raw/main/README.md", "_rundeps": [ "backports", "checkmate", "clarabel", "cli", "commonmark", "cpp11", "curl", "CVXR", "data.table", "distributional", "farver", "generics", "ggdist", "ggfittext", "ggplot2", "glue", "gmp", "gridtext", "gtable", "highs", "isoband", "jpeg", "labeling", "lattice", "lifecycle", "litedown", "magrittr", "markdown", "Matrix", "numDeriv", "osqp", "pillar", "pkgconfig", "png", "quadprog", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S7", "scales", "scs", "shades", "slam", "stringi", "stringr", "tibble", "utf8", "vctrs", "viridisLite", "wacolors", "withr", "xfun", "xml2" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "pvEBayes-introduction.Rmd", "filename": "pvEBayes-introduction.html", "title": "Introduction to pvEBayes", "engine": "knitr::rmarkdown", "headings": [ "spontaneous reporting systems data mining", "Analyzing FDA statin SRS data with pvEBayes", "Fit the general-gamma model", "Extracting results", "Hyperparameter tuning", "Visualization", "References" ], "created": "2025-11-19 15:54:33", "modified": "2026-05-03 18:21:54", "commits": 12 } ], "_score": 4.954242509439325, "_indexed": true, "_nocasepkg": "pvebayes", "_universes": [ "ropensci" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-09-19T10:24:54.000Z", "distro": "resolute", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/1db0612ee4bbb32fb0118c33561214c1535e58c9da2436e069dda3c9faf29a05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.7.0", "os": "linux", "version": "0.3.0", "date": "2026-09-19T10:24:41.000Z", "distro": "resolute", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/cd33c76abdd8d76e42465ec3d344348aed1768e79bb391252479e1718aebd748", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "linux", "version": "0.3.0", "date": "2026-09-19T10:24:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/0bcf844f8b19a170aa4bb279306131e6b607ba665578d2b6e4163ece16f9dc5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "linux", "version": "0.3.0", "date": "2026-09-19T10:24:32.000Z", "distro": "resolute", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/37086662cb196f508974dfe1c6ecdeda00c98e064148d9e7ebdee630445779ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-09-19T10:23:31.000Z", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/7a7c646d525b01af2f2a823796a41d1a07d14fbdfde5268dcbbb472e318049c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.5.3", "os": "mac", "version": "0.3.0", "date": "2026-09-19T10:24:59.000Z", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/2902f62acb41075c3b229d1fc74c30014a3a080edff4e5ddcace8a85741ea60c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "mac", "version": "0.3.0", "date": "2026-09-19T10:23:57.000Z", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/79c583ff25a45266d686915e7799e7b920f9f3a391919eef369881175b6993a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "mac", "version": "0.3.0", "date": "2026-09-19T10:24:55.000Z", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/8b24dc01d24a2d59a487b7b303b519ff831d8100f3fce42d2e32fb44eeab50b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.0", "date": "2026-09-19T10:24:39.000Z", "arch": "emscripten", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/8904ffd64c96c73f787581b6b9541e84abb3b14bb7f0bff3b58a9e47601093fe", "status": "success", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-09-19T10:26:55.000Z", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/f29c1d2e0013ac2980e540bb7d7cd70150644a922d84ea6990c11a6974ad1291", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.7.0", "os": "win", "version": "0.3.0", "date": "2026-09-19T10:23:07.000Z", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/9f7fa559136c054df6961d50d683f805e918e6a3ca649acbcdf1773c5166b71b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.5.3", "os": "win", "version": "0.3.0", "date": "2026-09-19T10:23:11.000Z", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/ba6f50860701cca369e5e3c48a9efd77fdb5289826fb472792953dded04415ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "win", "version": "0.3.0", "date": "2026-09-19T10:24:56.000Z", "arch": "aarch64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/a3f7b9b35bb9fa82850de3fd8ed6d5e6d27d6a560876bc9757e42c9982cdc86f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" }, { "r": "4.6.1", "os": "win", "version": "0.3.0", "date": "2026-09-19T10:23:03.000Z", "arch": "x86_64", "commit": "c8b5cd89255132ab198158616dedfc382be9b68b", "fileid": "https://r2.ropensci.org/5c5ed4d16aeaa1d9650dd5634ba9357a819e8cf18daa4027b9ca06b8d5b85a08", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/ropensci/actions/runs/35437016563" } ] }