{ "_id": "6a15629cacfb0bcc41d61304", "Package": "postpack", "Title": "Utilities for Processing Posterior Samples Stored in\n'mcmc.lists'", "Version": "0.5.4.9000", "Authors@R": "person(\"Ben\", \"Staton\", email = \"statonbe@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2342-3482\"))", "Description": "The aim of 'postpack' is to provide the infrastructure for\na standardized workflow for 'mcmc.list' objects. These objects\ncan be used to store output from models fitted with Bayesian\ninference using 'JAGS', 'WinBUGS', 'OpenBUGS', 'NIMBLE',\n'Stan', or even custom MCMC algorithms. Although the 'coda' R\npackage provides some methods for these objects, it is somewhat\nlimited in easily performing post-processing tasks for specific\nnodes. Models are ever increasing in their complexity and the\nnumber of tracked nodes, and oftentimes a user may wish to\nsummarize/diagnose sampling behavior for only a small subset of\nnodes at a time for a particular question or figure. Thus, many\n'postpack' functions support performing tasks on a subset of\nnodes, where the subset is specified with regular expressions.\nThe functions in 'postpack' streamline the extraction,\nsummarization, and diagnostics of specific monitored nodes\nafter model fitting. Further, because there is rarely only ever\none model under consideration, 'postpack' scales efficiently to\nperform the same tasks on output from multiple models\nsimultaneously, facilitating rapid assessment of model\nsensitivity to changes in assumptions.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.1", "Roxygen": "list(markdown = TRUE)", "URL": "https://bstaton1.github.io/postpack/", "BugReports": "https://github.com/bstaton1/postpack/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfftw3-dev make libicu-dev libuv1-dev", "Repository": "https://bstaton1.r-universe.dev", "Date/Publication": "2022-12-21 23:43:14 UTC", "RemoteUrl": "https://github.com/bstaton1/postpack", "RemoteRef": "HEAD", "RemoteSha": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 09:03:12 UTC", "User": "root" }, "Author": "Ben Staton [aut, cre] (ORCID: )", "Maintainer": "Ben Staton ", "MD5sum": "15215408c311506d0e0e8a9dcef12fe0", "_user": "bstaton1", "_type": "src", "_file": "postpack_0.5.4.9000.tar.gz", "_fileid": "c95cfd46695e6f0861f6e0ee56a3edc0761bec0a57ed3e468adb6c4449d9a13c", "_filesize": 840499, "_sha256": "c95cfd46695e6f0861f6e0ee56a3edc0761bec0a57ed3e468adb6c4449d9a13c", "_created": "2026-05-26T09:03:12.000Z", "_published": "2026-05-26T09:06:36.345Z", "_distro": "noble", "_jobs": [ { "job": 77841666305, "time": 153, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7213040075" }, { "job": 77841666557, "time": 158, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7213041965" }, { "job": 77841666324, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7213031829" }, { "job": 77841666351, "time": 133, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7213023096" }, { "job": 77840981046, "time": 244, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7212986746" }, { "job": 77841666275, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7213035593" }, { "job": 77841666306, "time": 124, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7213032420" }, { "job": 77841666356, "time": 129, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7213034026" }, { "job": 77841666320, "time": 102, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7213023105" } ], "_buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bstaton1/postpack", "_commit": { "id": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "author": "Ben ", "committer": "Ben ", "message": "Rebuild pkgdown site\n", "time": 1671666194 }, "_maintainer": { "name": "Ben Staton", "email": "statonbe@gmail.com", "login": "bstaton1", "description": "", "uuid": 42722538, "orcid": "0000-0002-2342-3482" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "stringr", "version": ">= 1.3.1", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "mcmcse", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "rstan", "role": "Suggests" }, { "package": "R2WinBUGS", "role": "Suggests" }, { "package": "R2jags", "role": "Suggests" }, { "package": "R2OpenBUGS", "role": "Suggests" }, { "package": "nimble", "role": "Suggests" }, { "package": "rjags", "role": "Suggests" }, { "package": "jagsUI", "role": "Suggests" } ], "_owner": "bstaton1", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "bstaton1", "count": 194, "uuid": 42722538 }, { "user": "henryjhershey", "count": 2, "uuid": 34039859 }, { "user": "hadley", "count": 1, "uuid": 4196 } ], "_userbio": { "uuid": 42722538, "type": "user", "name": "Ben Staton" }, "_downloads": { "count": 206, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/postpack" }, "_devurl": "https://github.com/bstaton1/postpack", "_pkgdown": "https://bstaton1.github.io/postpack/", "_searchresults": 232, "_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/postpack.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/bstaton1/postpack", "_realowner": "bstaton1", "_cranurl": true, "_releases": [ { "version": "0.5.2", "date": "2020-09-17" }, { "version": "0.5.3", "date": "2021-06-02" }, { "version": "0.5.4", "date": "2022-12-21" } ], "_exports": [ "array_format", "diag_plots", "get_params", "match_params", "post_bind", "post_convert", "post_dim", "post_remove", "post_subset", "post_summ", "post_thin", "vcov_decomp", "write_model" ], "_datasets": [ { "name": "cjs", "title": "Example mcmc.list 1", "object": "cjs", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "cjs_no_rho", "title": "Example mcmc.list 2", "object": "cjs_no_rho", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "array_format", "title": "Convert a vector to the array structure used in model", "topics": [ "array_format" ] }, { "page": "cjs", "title": "Example mcmc.list 1", "topics": [ "cjs" ] }, { "page": "cjs_no_rho", "title": "Example mcmc.list 2", "topics": [ "cjs_no_rho" ] }, { "page": "density_plot", "title": "Create a density plot for a single desired node", "topics": [ "density_plot" ] }, { "page": "diag_plots", "title": "Create MCMC diagnostic plots for nodes of interest", "topics": [ "diag_plots" ] }, { "page": "drop_index", "title": "Extract the base node name of a parameter", "topics": [ "drop_index" ] }, { "page": "get_params", "title": "Obtain the names of all nodes", "topics": [ "get_params" ] }, { "page": "id_mat", "title": "Extract chain and iteration IDs for each sample", "topics": [ "id_mat" ] }, { "page": "ins_regex_bracket", "title": "Insert escapes on regex brackets", "topics": [ "ins_regex_bracket" ] }, { "page": "ins_regex_lock", "title": "Insert the symbols to lock in a string for matching", "topics": [ "ins_regex_lock" ] }, { "page": "list_out", "title": "List vector elements in a nice format", "topics": [ "list_out" ] }, { "page": "match_params", "title": "Find matching node names", "topics": [ "match_params" ] }, { "page": "mytitle", "title": "Add a title between two figures", "topics": [ "mytitle" ] }, { "page": "post_bind", "title": "Combine two objects containing posterior samples", "topics": [ "post_bind" ] }, { "page": "post_convert", "title": "Convert MCMC samples to mcmc.list format", "topics": [ "post_convert" ] }, { "page": "post_dim", "title": "Obtain MCMC dimensions from an mcmc.list", "topics": [ "post_dim" ] }, { "page": "post_remove", "title": "Remove nodes from mcmc.list", "topics": [ "post_remove" ] }, { "page": "post_subset", "title": "Extract samples from specific nodes", "topics": [ "post_subset" ] }, { "page": "post_summ", "title": "Obtain posterior summaries and diagnostics of specific nodes", "topics": [ "post_summ" ] }, { "page": "post_thin", "title": "Perform post-MCMC thinning", "topics": [ "post_thin" ] }, { "page": "postpack", "title": "Utilities for Processing Posterior Samples Stored in mcmc.lists", "topics": [ "postpack" ] }, { "page": "rm_regex_bracket", "title": "Remove escapes on regex brackets", "topics": [ "rm_regex_bracket" ] }, { "page": "rm_regex_lock", "title": "Remove the symbols that lock in a string for matching", "topics": [ "rm_regex_lock" ] }, { "page": "trace_plot", "title": "Create a trace plot for a single desired node", "topics": [ "trace_plot" ] }, { "page": "vcov_decomp", "title": "Decompose the posterior of a variance-covariance node", "topics": [ "vcov_decomp" ] }, { "page": "write_model", "title": "Export BUGS/JAGS model from function to file", "topics": [ "write_model" ] } ], "_pkglogo": "https://raw.githubusercontent.com/bstaton1/postpack/master/man/figures/postpack-social-media-image.png", "_readme": "https://github.com/bstaton1/postpack/raw/HEAD/readme.md", "_rundeps": [ "abind", "brio", "callr", "cli", "coda", "crayon", "desc", "diffobj", "ellipse", "evaluate", "fftwtools", "fs", "glue", "jsonlite", "lattice", "lifecycle", "magrittr", "mcmcse", "pkgbuild", "pkgload", "praise", "processx", "ps", "R6", "Rcpp", "RcppArmadillo", "rlang", "rprojroot", "stringi", "stringr", "testthat", "vctrs", "waldo", "withr" ], "_vignettes": [ { "source": "example-mcmclists.Rmd", "filename": "example-mcmclists.html", "title": "Example mcmc.lists", "engine": "knitr::rmarkdown", "headings": [ "The Context", "The Model" ], "created": "2020-08-28 22:42:34", "modified": "2020-08-31 16:03:47", "commits": 2 }, { "source": "feature-overview.Rmd", "filename": "feature-overview.html", "title": "Feature Overview", "engine": "knitr::rmarkdown", "headings": [ "Prequisites", "Getting Started", "Query MCMC Attributes", "Extracting Posterior Summaries", "Extracting MCMC Diagnostics", "Extracting Posterior Samples", "Matrix/Array Nodes", "array_format()", "vcov_decomp()", "Manipulate Samples", "post_thin()", "post_bind()", "Two mcmc.lists", "One mcmc.list and one matrix" ], "created": "2020-08-28 22:42:34", "modified": "2020-09-28 02:39:05", "commits": 4 }, { "source": "multiple-models.Rmd", "filename": "multiple-models.html", "title": "Multiple Models", "engine": "knitr::rmarkdown", "headings": [], "created": "2020-08-28 22:42:34", "modified": "2022-12-20 23:44:08", "commits": 2 }, { "source": "pattern-matching.Rmd", "filename": "pattern-matching.html", "title": "Pattern Matching", "engine": "knitr::rmarkdown", "headings": [ "match_params()", "Automatic Escape of Brackets", "Wild Cards", "Anchors", "Repetition", "More resources" ], "created": "2020-08-28 22:42:34", "modified": "2020-08-31 16:07:37", "commits": 2 } ], "_score": 6.268577971882843, "_indexed": true, "_nocasepkg": "postpack", "_universes": [ "bstaton1" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.5.4.9000", "date": "2026-05-26T09:05:53.000Z", "distro": "noble", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "c5deafb3151c7a99e6f6756f27394acdc974fe5c784d06c19c4dc3233929e1ac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.6.0", "os": "linux", "version": "0.5.4.9000", "date": "2026-05-26T09:06:00.000Z", "distro": "noble", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "1c21e2e0fafde6b6906f96cbbdb9dde38cafd7981897d0b03dedca921d0796a0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.5.3", "os": "mac", "version": "0.5.4.9000", "date": "2026-05-26T09:05:33.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "624e8d2d241d1e2c8d65f65e1a90dbf71a87f24a0ffc1adf74f33c01dd32625c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.6.0", "os": "mac", "version": "0.5.4.9000", "date": "2026-05-26T09:05:08.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "b06fe3de09e22dbefd823c3ba1ac599b87ad6a111fec9915d845c248215310c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.6.0", "os": "wasm", "version": "0.5.4.9000", "date": "2026-05-26T09:05:54.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "db7e1dd8b6007a9f2a9f1eff2a1072f4e2c809e82e0e6dbdd955a227b0887d52", "status": "success", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.7.0", "os": "win", "version": "0.5.4.9000", "date": "2026-05-26T09:05:26.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "cbd209d016363e0858f1a6c4a87f446708b24fe909fd2e1337f9a81d3a01cb79", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.5.3", "os": "win", "version": "0.5.4.9000", "date": "2026-05-26T09:05:32.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "df2d66b6c55808bd474faf4b4a772980256651705124c2b155f342b75e5246a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" }, { "r": "4.6.0", "os": "win", "version": "0.5.4.9000", "date": "2026-05-26T09:04:58.000Z", "commit": "eddf9dbf6ec8a70845f9edcf60b3aaa4efc9fa46", "fileid": "ae40a0d354bc8c0dcf5a03484413af04a4ddbae9f73849d665e36f6cd35f1518", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bstaton1/actions/runs/26442700156" } ] }