{ "_id": "6a21be31cd65a98ecbd3d999", "Package": "jagshelper", "Type": "Package", "Title": "Extracting and Visualizing Output from 'jagsUI'", "Version": "0.4.1", "Date": "2024-11-07", "Author": "Matt Tyers [aut, cre]", "Authors@R": "person(\"Matt\", \"Tyers\", email = \"matttyersstat@gmail.com\",\nrole = c(\"aut\", \"cre\"))", "Maintainer": "Matt Tyers ", "Description": "Tools are provided to streamline Bayesian analyses in\n'JAGS' using the 'jagsUI' package. Included are functions for\nextracting output in simpler format, functions for streamlining\nassessment of convergence, and functions for producing summary\nplots of output. Also included is a function that provides a\nsimple template for running 'JAGS' from 'R'. Referenced\nmaterials can be found at .", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "URL": "https://github.com/mbtyers/jagshelper", "BugReports": "https://github.com/mbtyers/jagshelper/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "jags", "Repository": "https://mbtyers.r-universe.dev", "Date/Publication": "2026-06-04 16:04:59 UTC", "RemoteUrl": "https://github.com/mbtyers/jagshelper", "RemoteRef": "HEAD", "RemoteSha": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-04 18:00:25 UTC", "User": "root" }, "MD5sum": "78fb77e7ee5e3148da272927bae20ad4", "_user": "mbtyers", "_type": "src", "_file": "jagshelper_0.4.1.tar.gz", "_fileid": "8855813e4df89bb71365f3aafed368f52b49eb72a5babe95a7b0b22360295105", "_filesize": 6231405, "_sha256": 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"artifact": "7419220054" }, { "job": 79582514986, "time": 99, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7419213061" }, { "job": 79582515015, "time": 114, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7419219352" } ], "_buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/mbtyers/jagshelper", "_commit": { "id": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "author": "Matt Tyers ", "committer": "Matt Tyers ", "message": "added horizontal= and xorder= to caterpillar, fixed many bugs!\n", "time": 1780589099 }, "_maintainer": { "name": "Matt Tyers", "email": "matttyersstat@gmail.com", "login": "mbtyers", "description": "", "uuid": 16109393 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "jagsUI", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "mbtyers", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-23", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "mbtyers", "count": 81, "uuid": 16109393 }, { "user": "olivroy", "count": 1, "uuid": 52606734 } ], "_userbio": { "uuid": 16109393, "type": "user", "name": "Matt Tyers" }, "_downloads": { "count": 592, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/jagshelper" }, "_devurl": "https://github.com/mbtyers/jagshelper", "_searchresults": 104, "_topics": [ "jags", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/jagshelper.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/mbtyers/jagshelper", "_realowner": "mbtyers", "_cranurl": true, "_releases": [ { "version": "0.1.6", "date": "2022-10-14" }, { "version": "0.1.8", "date": "2022-10-21" }, { "version": "0.1.9", "date": "2022-11-01" }, { "version": "0.1.11", "date": "2022-11-08" }, { "version": "0.2.0", "date": "2023-11-23" }, { "version": "0.2.1", "date": "2024-01-18" }, { "version": "0.2.2", "date": "2024-03-19" }, { "version": "0.2.3", "date": "2024-04-30" }, { "version": "0.2.4", "date": "2024-07-01" }, { "version": "0.3.0", "date": "2024-07-23" }, { "version": "0.3.1", "date": "2024-07-30" }, { "version": "0.3.2", "date": "2024-08-19" }, { "version": "0.4.0", "date": "2024-10-21" }, { "version": "0.4.1", "date": "2024-11-07" } ], "_exports": [ "caterpillar", "chaindens_df", "chaindens_jags", "chaindens_line", "check_neff", "check_Rhat", "comparecat", "comparedens", "comparepriors", "cor_jags", "crossplot", "envelope", "expit", "jags_df", "jags_plist", "kfold", "logit", "nbyname", "nparam", "overlayenvelope", "pairstrace_jags", "plot_postpred", "plotcor_jags", "plotdens", "plotRhats", "pull_post", "qq_postpred", "rcolors", "skeleton", "trace_df", "trace_jags", "trace_line", "tracedens_jags", "traceworstRhat", "ts_postpred" ], "_datasets": [ { "name": "asdf_jags_out", "title": "Example data: asdf jags out", "object": "asdf_jags_out", "class": [ "jagsUI" ], "fields": [], "table": false, "tojson": false }, { "name": "asdf_prior_jags_out", "title": "Example data: asdf prior jags out", "object": "asdf_prior_jags_out", "class": [ "jagsUI" ], "fields": [], "table": false, "tojson": false }, { "name": "SS_data", "title": "Example data: Time series associated with SS JAGS out", "object": "SS_data", "class": [ "data.frame" ], "fields": [ "x", "y" ], "rows": 41, "table": true, "tojson": true }, { "name": "SS_out", "title": "Example data: SS JAGS out", "object": "SS_out", "class": [ "jagsUI" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "jagshelper-package", "title": "Functions for Extracting and Visualizing Output from 'jagsUI'", "topics": [ "jagshelper-package", "jagshelper" ] }, { "page": "asdf_jags_out", "title": "Example data: asdf jags out", "topics": [ "asdf_jags_out" ] }, { "page": "asdf_prior_jags_out", "title": "Example data: asdf prior jags out", "topics": [ "asdf_prior_jags_out" ] }, { "page": "caterpillar", "title": "Caterpillar plot", "topics": [ "caterpillar" ] }, { "page": "chaindens_df", "title": "By-chain kernel density of each column of a 'data.frame'.", "topics": [ "chaindens_df" ] }, { "page": "chaindens_jags", "title": "By-chain kernel densities of 'jagsUI' object", "topics": [ "chaindens_jags" ] }, { "page": "chaindens_line", "title": "Simple by-chain kernel density plot", "topics": [ "chaindens_line" ] }, { "page": "check_neff", "title": "Quick summary of n.eff values by parameter name", "topics": [ "check_neff" ] }, { "page": "check_Rhat", "title": "Quick summary of Rhat values by parameter name", "topics": [ "check_Rhat" ] }, { "page": "comparecat", "title": "Compare Caterpillar Plots", "topics": [ "comparecat" ] }, { "page": "comparedens", "title": "Compare Density", "topics": [ "comparedens" ] }, { "page": "comparepriors", "title": "Compare Priors", "topics": [ "comparepriors" ] }, { "page": "cor_jags", "title": "Correlation matrix from a JAGS object", "topics": [ "cor_jags" ] }, { "page": "crossplot", "title": "Bivariate Plot of Posterior Densities", "topics": [ "crossplot" ] }, { "page": "envelope", "title": "Envelope plot", "topics": [ "envelope" ] }, { "page": "expit", "title": "Expit, or inverse logit", "topics": [ "expit" ] }, { "page": "jags_df", "title": "Extract data.frame", "topics": [ "jags_df" ] }, { "page": "jags_plist", "title": "Plist", "topics": [ "jags_plist" ] }, { "page": "kfold", "title": "Automated K-fold or Leave One Out Cross Validation", "topics": [ "kfold" ] }, { "page": "logit", "title": "Logit", "topics": [ "logit" ] }, { "page": "nbyname", "title": "Number of parameter nodes by parameter name", "topics": [ "nbyname" ] }, { "page": "nparam", "title": "Number of parameters", "topics": [ "nparam" ] }, { "page": "overlayenvelope", "title": "Overlay envelope plots", "topics": [ "overlayenvelope" ] }, { "page": "pairstrace_jags", "title": "Pairs trace plot", "topics": [ "pairstrace_jags" ] }, { "page": "plot_postpred", "title": "Diagnostic plots from posterior predictive distribution", "topics": [ "plot_postpred" ] }, { "page": "plotcor_jags", "title": "Plot a correlation matrix from a JAGS object", "topics": [ "plotcor_jags" ] }, { "page": "plotdens", "title": "Plot kernel densities of single parameter nodes", "topics": [ "plotdens" ] }, { "page": "plotRhats", "title": "Plotting all Rhat values", "topics": [ "plotRhats" ] }, { "page": "pull_post", "title": "Subset from posterior data.frame", "topics": [ "pull_post" ] }, { "page": "qq_postpred", "title": "Quantile-quantile plot from posterior predictive distribution", "topics": [ "qq_postpred" ] }, { "page": "rcolors", "title": "Random Colors", "topics": [ "rcolors" ] }, { "page": "skeleton", "title": "Skeleton", "topics": [ "skeleton" ] }, { "page": "SS_data", "title": "Example data: Time series associated with SS JAGS out", "topics": [ "SS_data" ] }, { "page": "SS_out", "title": "Example data: SS JAGS out", "topics": [ "SS_out" ] }, { "page": "trace_df", "title": "Trace plot of each column of a 'data.frame'.", "topics": [ "trace_df" ] }, { "page": "trace_jags", "title": "Trace plot of jagsUI object", "topics": [ "trace_jags" ] }, { "page": "trace_line", "title": "Simple trace plot", "topics": [ "trace_line" ] }, { "page": "tracedens_jags", "title": "Combination of trace plots and by-chain kernel densities of 'jagsUI' object", "topics": [ "tracedens_jags" ] }, { "page": "traceworstRhat", "title": "Trace plots corresponding to the worst values of Rhat", "topics": [ "traceworstRhat" ] }, { "page": "ts_postpred", "title": "Time series plot of centered posterior predictive distribution", "topics": [ "ts_postpred" ] } ], "_readme": "https://github.com/mbtyers/jagshelper/raw/HEAD/README.md", "_rundeps": [ "coda", "jagsUI", "lattice", "MASS", "rjags" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2404.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary\nJAGS is Just Another Gibbs Sampler. It is a program for analysis of\nBayesian hierarchical models using Markov Chain Monte Carlo (MCMC)\nsimulation not wholly unlike BUGS.\n\nJAGS was written with three aims in mind:\n* To have an engine for the BUGS language that runs on Unix\n* To be extensible, allowing users to write their own functions,\ndistributions and samplers.\n* To be a plaftorm for experimentation with ideas in Bayesian modelling\n\nThis package contains the 'jags' binary as well as the associated\nshared library modules loaded by the binary." }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "jagshelper-vignette.Rmd", "filename": "jagshelper-vignette.html", "title": "jagshelper-vignette", "engine": "knitr::rmarkdown", "headings": [ "jagshelper", "Model template", "Output summary & Assessing convergence", "A simple model", "A more complex model", "Additional functionality", "Extracting output as data.frame", "Plotting a matrix associated with a vector of parameter nodes", "A single matrix", "Multiple matrices or multiple models", "Comparison between priors and posteriors" ], "created": "2022-10-07 12:16:43", "modified": "2024-10-23 19:40:18", "commits": 13 } ], "_score": 4.7160033436347994, "_indexed": true, "_nocasepkg": "jagshelper", "_universes": [ "mbtyers" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.1", "date": "2026-06-04T18:03:26.000Z", "distro": "noble", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "64bce5620b71adce42fc0c3f7ab7862515f7649fb20551515093d6ea702eb0ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.6.0", "os": "linux", "version": "0.4.1", "date": "2026-06-04T18:03:08.000Z", "distro": "noble", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "6fc55fc3ff19bb09ae97915d8c90daf570d50d2211a0ba1e71de33fe022ac50d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.5.3", "os": "mac", "version": "0.4.1", "date": "2026-06-04T18:02:21.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "6670aa521786aa59faf33fae0a83c0f2596017f5ee6c1c5f64d81059cd12e6e3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.6.0", "os": "mac", "version": "0.4.1", "date": "2026-06-04T18:01:59.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "716fde2c56ae8be337b25a29a66d877da5238aee664c994c052ec38e74bd9272", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.1", "date": "2026-06-04T18:02:39.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "df5fc70d4e6f04d976f7e9b2121488ee8b2c22c4522f27d6a172ba0df5b9c2c2", "status": "success", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.7.0", "os": "win", "version": "0.4.1", "date": "2026-06-04T18:01:51.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "51a0703bf7dea90e74010323c8b88a13d337e3f204e990e487f5d25f14285d10", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.5.3", "os": "win", "version": "0.4.1", "date": "2026-06-04T18:01:38.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "ba62b574e7ac8d8688a3efd0e73ccc27490f5b191486b4bc6b3a0aa821a02611", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" }, { "r": "4.6.0", "os": "win", "version": "0.4.1", "date": "2026-06-04T18:01:56.000Z", "commit": "cad36332f87781172e9b3596d57f2a7983cbb9e1", "fileid": "24166fcd4dbb7269f825c12e1838359989f0267252190af30fa854dd0ec5f074", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mbtyers/actions/runs/26969830310" } ] }