{ "_id": "6a498d666d67900babdfad99", "Package": "bkmrhat", "Title": "Parallel Chain Tools for Bayesian Kernel Machine Regression", "Version": "1.1.7", "Date": "2025-11-19", "Authors@R": "person(\"Alexander\", \"Keil\", email=\"alex.keil@nih.gov\", role = c(\"aut\", \"cre\"))", "Description": "Bayesian kernel machine regression (from the 'bkmr'\npackage) is a Bayesian semi-parametric generalized linear model\napproach under identity and probit links. There are a number of\nfunctions in this package that extend Bayesian kernel machine\nregression fits to allow multiple-chain inference and\ndiagnostics, which leverage functions from the 'future',\n'rstan', and 'coda' packages. Reference: Bobb, J. F., Henn, B.\nC., Valeri, L., & Coull, B. A. (2018). Statistical software for\nanalyzing the health effects of multiple concurrent exposures\nvia Bayesian kernel machine regression. ;\n.", "License": "GPL (>= 3)", "URL": "https://github.com/alexpkeil1/bkmrhat/", "BugReports": "https://github.com/alexpkeil1/bkmrhat/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://alexpkeil1.r-universe.dev", "Date/Publication": "2025-11-24 18:35:51 UTC", "RemoteUrl": "https://github.com/alexpkeil1/bkmrhat", "RemoteRef": "HEAD", "RemoteSha": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-22 09:39:05 UTC", "User": "root" }, "Author": "Alexander Keil [aut, cre]", "Maintainer": "Alexander Keil ", "_user": "alexpkeil1", "_type": "src", "_file": "bkmrhat_1.1.7.tar.gz", "_fileid": "https://r2.ropensci.org/7e570afa96126a03be0b009e6ba640b8bb55f58bf563c58e83774d2f2e83ad42", "_filesize": 4804008, "_sha256": "7e570afa96126a03be0b009e6ba640b8bb55f58bf563c58e83774d2f2e83ad42", "_expires": "2026-10-12T22:47:00.000Z", "_created": "2026-06-22T09:39:05.000Z", "_published": "2026-07-04T22:47:02.879Z", "_jobs": [ { "job": 85173282407, "time": 231, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7788625689" }, { "job": 85173282527, "time": 269, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7788639926" }, { "job": 85173282495, "time": 246, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7788878555" }, { "job": 85173282353, "time": 254, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7788887688" }, { "job": 85173282233, "time": 278, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7788539666" }, { "job": 85173282472, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7788593280" }, { "job": 85173282347, "time": 248, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7788632025" }, { "job": 85173282384, "time": 241, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7788629689" }, { "job": 85173282345, "time": 241, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7788629626" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569", "_status": "success", "_upstream": "https://github.com/alexpkeil1/bkmrhat", "_commit": { "id": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "author": "Alex Keil ", "committer": "GitHub ", "message": "Delete .github/workflows/r-check.yml", "time": 1764009351 }, "_maintainer": { "name": "Alexander Keil", "email": "alex.keil@nih.gov", "login": "alexpkeil1gov", "twitter": "@PronouncedKeil", "description": "Public health researcher (alt account)", "uuid": 94704975 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "coda", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "bkmr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "rstan", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" } ], "_owner": "alexpkeil1", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 7 }, { "week": "2025-48", "n": 4 } ], "_tags": [ { "name": "v1.1.6", "date": "2025-11-19" } ], "_stars": 7, "_contributors": [ { "user": "alexpkeil1", "count": 112, "uuid": 5647707 } ], "_userbio": { "uuid": 5647707, "type": "user", "name": "Alex Keil", "followers": 82, "description": "Environmental and occupational epidemiologist researching the data/policy interface and improving the science behind policy." }, "_downloads": { "count": 410, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bkmrhat" }, "_devurl": "https://github.com/alexpkeil1/bkmrhat", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/bkmrhat.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/alexpkeil1/bkmrhat", "_realowner": "alexpkeil1", "_cranurl": true, "_releases": [ { "version": "0.1.16", "date": "2020-09-16" }, { "version": "1.0.0", "date": "2020-10-12" }, { "version": "1.0.1", "date": "2021-01-26" }, { "version": "1.0.2", "date": "2021-02-17" }, { "version": "1.1.1", "date": "2021-09-07" }, { "version": "1.1.2", "date": "2022-03-07" }, { "version": "1.1.3", "date": "2022-03-29" }, { "version": "1.1.7", "date": "2025-11-30" } ], "_exports": [ "comb_bkmrfits", "comb_bkmrfits_lowmem", "ExtractPIPs_parallel", "kmbayes_combine", "kmbayes_combine_lowmem", "kmbayes_continue", "kmbayes_diag", "kmbayes_diagnose", "kmbayes_parallel", "kmbayes_parallel_continue", "OverallRiskSummaries_parallel", "PredictorResponseBivar_parallel", "PredictorResponseUnivar_parallel", "SamplePred_parallel", "SingVarRiskSummaries_parallel" ], "_help": [ { "page": "as.mcmc.bkmrfit", "title": "Convert bkmrfit to mcmc object for coda MCMC diagnostics", "topics": [ "as.mcmc.bkmrfit" ] }, { "page": "as.mcmc.list.bkmrfit.list", "title": "Convert multi-chain bkmrfit to mcmc.list for coda MCMC diagnostics", "topics": [ "as.mcmc.list.bkmrfit.list" ] }, { "page": "ExtractPIPs_parallel", "title": "Posterior inclusion probabilities by chain", "topics": [ "ExtractPIPs_parallel" ] }, { "page": "kmbayes_combine", "title": "Combine multiple BKMR chains", "topics": [ "comb_bkmrfits", "kmbayes_combine" ] }, { "page": "kmbayes_combine_lowmem", "title": "Combine multiple BKMR chains in lower memory settings", "topics": [ "comb_bkmrfits_lowmem", "kmbayes_combine_lowmem" ] }, { "page": "kmbayes_continue", "title": "Continue sampling from existing bkmr fit", "topics": [ "kmbayes_continue" ] }, { "page": "kmbayes_diagnose", "title": "MCMC diagnostics using rstan", "topics": [ "kmbayes_diag", "kmbayes_diagnose" ] }, { "page": "kmbayes_parallel", "title": "Run multiple BKMR chains in parallel", "topics": [ "kmbayes_parallel" ] }, { "page": "kmbayes_parallel_continue", "title": "Continue sampling from existing bkmr_parallel fit", "topics": [ "kmbayes_parallel_continue" ] }, { "page": "OverallRiskSummaries_parallel", "title": "Overall summary by chain", "topics": [ "OverallRiskSummaries_parallel" ] }, { "page": "predict.bkmrfit", "title": "Posterior mean/sd predictions", "topics": [ "predict.bkmrfit" ] }, { "page": "PredictorResponseBivar_parallel", "title": "Bivariate predictor response by chain", "topics": [ "PredictorResponseBivar_parallel" ] }, { "page": "PredictorResponseUnivar_parallel", "title": "Univariate predictor response summary by chain", "topics": [ "PredictorResponseUnivar_parallel" ] }, { "page": "SamplePred_parallel", "title": "Posterior samples of E(Y|h(Z),X,beta) by chain", "topics": [ "SamplePred_parallel" ] }, { "page": "SingVarRiskSummaries_parallel", "title": "Single variable summary by chain", "topics": [ "SingVarRiskSummaries_parallel" ] } ], "_readme": "https://github.com/alexpkeil1/bkmrhat/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "bkmr", "callr", "checkmate", "cli", "coda", "codetools", "cpp11", "data.table", "desc", "digest", "distributional", "dotCall64", "dplyr", "farver", "fields", "future", "generics", "ggplot2", "globals", "glue", "gmm", "gridExtra", "gtable", "inline", "isoband", "labeling", "lattice", "lifecycle", "listenv", "loo", "magrittr", "maps", "MASS", "Matrix", "matrixStats", "mvtnorm", "nlme", "numDeriv", "otel", "parallelly", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "purrr", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "S7", "sandwich", "scales", "spam", "StanHeaders", "stringi", "stringr", "tensorA", "tibble", "tidyr", "tidyselect", "tmvtnorm", "truncnorm", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "bkmrhat-vignette.Rmd", "filename": "bkmrhat-vignette.html", "title": "The bkmrhat package: diagnostics and multi-chain inference in Bayesian kernel machine regression", "author": "Alexander Keil", "engine": "knitr::knitr", "headings": [ "Introduction to bkmr and bkmrhat", "How to use the bkmrhat package", "Example 1: single vs multi-chains", "Example 2: Diagnostics", "Example 3: Posterior summaries", "Example 4: diagnostics and inference when variable selection is used (Bayesian model averaging over the scale parameters of the kernel function)", "Example 5: Parallel posterior summaries as diagnostics", "Example 6: Continuing a fit", "Acknowledgments" ], "created": "2020-08-30 01:22:18", "modified": "2025-11-17 16:49:12", "commits": 17 } ], "_score": 4.924279286061882, "_indexed": true, "_nocasepkg": "bkmrhat", "_universes": [ "alexpkeil1", "alexpkeil1gov" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.7", "date": "2026-06-22T09:41:19.000Z", "distro": "noble", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/8ce019fc43fccbfe95f214d9d8a39eacede1b8e46195fd25da155e748ca93079", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.6.0", "os": "linux", "version": "1.1.7", "date": "2026-06-22T09:41:52.000Z", "distro": "noble", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/abc7de5713dff559a351e018e145a2a7f327391dc07a4830d9b87770490c1aea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.5.3", "os": "mac", "version": "1.1.7", "date": "2026-06-22T09:53:26.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/354796ef5c419e3c0b5265127025cffea388d4e4312226213f28c074dc2d65dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.6.0", "os": "mac", "version": "1.1.7", "date": "2026-06-22T09:53:36.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/1fc8b52ae99b5b818de41cf427826500c34a49481b4b599954ecf056275ff1aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.7", "date": "2026-06-22T09:41:48.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/6529089caa345bc5ea63205b4fec7fe21a15e0ff4d6ff3858a0db7e039443203", "status": "success", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.7.0", "os": "win", "version": "1.1.7", "date": "2026-06-22T09:40:53.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/ce109b4f6ab465e4dc2d0e67a1e758dde12331c3bea833c4cd51e4fa728356c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.5.3", "os": "win", "version": "1.1.7", "date": "2026-06-22T09:40:48.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/669e0c4e73bf48b274069f92a311e1229be41f466d72060c4501c490a5a780c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" }, { "r": "4.6.0", "os": "win", "version": "1.1.7", "date": "2026-06-22T09:40:46.000Z", "commit": "6b5ea188a9be71fd8b9213050727feafcb475e3b", "fileid": "https://r2.ropensci.org/a85a75a0074a5416279bf0f3b902a5c84b62cdb4aff3adcf33efd6b10b01a6c6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexpkeil1/actions/runs/27943344569" } ] }