{ "_id": "6a102a75acfb0bcc41c92001", "Package": "ggmcmc", "Title": "Tools for Analyzing MCMC Simulations from Bayesian Inference", "Description": "Tools for assessing and diagnosing convergence of Markov\nChain Monte Carlo simulations, as well as for graphically\ndisplay results from full MCMC analysis. The package also\nfacilitates the graphical interpretation of models by providing\nflexible functions to plot the results against observed\nvariables, and functions to work with hierarchical/multilevel\nbatches of parameters (Fernández-i-Marín, 2016\n).", "Version": "1.5.1.2", "Authors@R": "person(\"Xavier\", \"Fernández i Marín\", email = \"xavier.fim@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9522-8870\"))", "License": "GPL-2", "URL": "http://xavier-fim.net/packages/ggmcmc/,\nhttps://github.com/xfim/ggmcmc/", "BugReports": "https://github.com/xfim/ggmcmc/issues/", "Encoding": "UTF-8", "Collate": "'data.R' 'functions.R' 'ggmcmc.R' 'ggs.R' 'ggs_Rhat.R'\n'ggs_autocorrelation.R' 'ggs_caterpillar.R'\n'ggs_compare_partial.R' 'ggs_crosscorrelation.R'\n'ggs_density.R' 'ggs_effective.R' 'ggs_geweke.R'\n'ggs_diagnostics.R' 'ggs_grb.R' 'ggs_histogram.R' 'ggs_pairs.R'\n'ggs_pcp.R' 'ggs_ppmean.R' 'ggs_ppsd.R' 'ggs_rocplot.R'\n'ggs_running.R' 'ggs_separation.R' 'ggs_traceplot.R'\n'globals.R' 'help.R'", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libssl-dev", "Repository": "https://xfim.r-universe.dev", "Date/Publication": "2025-10-02 14:28:48 UTC", "RemoteUrl": "https://github.com/xfim/ggmcmc", "RemoteRef": "HEAD", "RemoteSha": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 10:02:25 UTC", "User": "root" }, "Author": "Xavier Fernández i Marín [aut, cre] (ORCID:\n)", "Maintainer": "Xavier Fernández i Marín ", "MD5sum": "40be850a634e11039728d8b8f0240d40", "_user": "xfim", "_type": "src", "_file": "ggmcmc_1.5.1.2.tar.gz", "_fileid": "9c59117bc2a7c5140251ca33d06237b2e4d011b5eca6da49962feb1d770daa1d", "_filesize": 5023132, "_sha256": "9c59117bc2a7c5140251ca33d06237b2e4d011b5eca6da49962feb1d770daa1d", "_created": "2026-05-22T10:02:25.000Z", "_published": "2026-05-22T10:05:41.547Z", "_distro": "noble", "_jobs": [ { "job": 77358263867, "time": 140, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7157934708" }, { "job": 77358264005, "time": 161, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7157941379" }, { "job": 77358263907, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7157932690" }, { "job": 77358264119, "time": 150, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7157930190" }, { "job": 77357694396, "time": 218, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7157891031" }, { "job": 77358263876, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7157927905" }, { "job": 77358264079, "time": 122, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7157929623" }, { "job": 77358263872, "time": 100, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7157922618" }, { "job": 77358263851, "time": 112, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7157927755" } ], "_buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/xfim/ggmcmc", "_commit": { "id": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "author": "Xavier Fernández i Marín ", "committer": "Xavier Fernández i Marín ", "message": "Version bump 1.5.1.2\n", "time": 1759415328 }, "_maintainer": { "name": "Xavier Fernández i Marín", "email": "xavier.fim@gmail.com", "login": "xfim", "description": "", "uuid": 674675, "orcid": "0000-0002-9522-8870" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.0.0", "role": "Depends" }, { "package": "tidyr", "version": ">= 1.1.0", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "GGally", "version": ">= 1.1.0", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "coda", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggthemes", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "Cairo", "role": "Suggests" }, { "package": "extrafont", "role": "Suggests" } ], "_owner": "xfim", "_selfowned": true, "_usedby": 8, "_updates": [ { "week": "2025-40", "n": 6 } ], "_tags": [ { "name": "v1.5.1.2", "date": "2025-10-02" } ], "_topics": [ "bayesian-data-analysis", "ggplot2", "graphical", "jags", "mcmc", "stan" ], "_stars": 113, "_contributors": [ { "user": "xfim", "count": 333, "uuid": 674675 }, { "user": "jucor", "count": 11, "uuid": 660037 }, { "user": "jonathan-g", "count": 9, "uuid": 5304060 }, { "user": "schloerke", "count": 4, "uuid": 93231 }, { "user": "zmjones", "count": 3, "uuid": 1114501 }, { "user": "mbjoseph", "count": 2, "uuid": 2664564 }, { "user": "alvinwmtan", "count": 1, "uuid": 66404649 }, { "user": "brianstock", "count": 1, "uuid": 5124211 }, { "user": "juste", "count": 1, "uuid": 316322 }, { "user": "stragu", "count": 1, "uuid": 1747497 }, { "user": "akrawitz", "count": 1, "uuid": 266509 }, { "user": "johnaponte", "count": 1, "uuid": 3891174 }, { "user": "knokknok", "count": 1, "uuid": 1275796 } ], "_userbio": { "uuid": 674675, "type": "user", "name": "Xavier Fernández i Marín" }, "_downloads": { "count": 2738, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ggmcmc" }, "_mentions": 7, "_devurl": "https://github.com/xfim/ggmcmc", "_searchresults": 1460, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ggmcmc.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/xfim/ggmcmc", "_realowner": "xfim", "_cranurl": true, "_releases": [ { "version": "0.2", "date": "2012-09-05" }, { "version": "0.3", "date": "2012-12-09" }, { "version": "0.4", "date": "2013-07-05" }, { "version": "0.4.1", "date": "2013-07-30" }, { "version": "0.4.2", "date": "2013-08-12" }, { "version": "0.5", "date": "2013-09-14" }, { "version": "0.5.1", "date": "2013-10-03" }, { "version": "0.6", "date": "2014-12-30" }, { "version": "0.7.1", "date": "2015-07-29" }, { "version": "0.7.2", "date": "2015-09-03" }, { "version": "0.7.3", "date": "2016-01-04" }, { "version": "0.8", "date": "2016-03-14" }, { "version": "1.0", "date": "2016-05-12" }, { "version": "1.1", "date": "2016-06-28" }, { "version": "1.1.1", "date": "2019-01-23" }, { "version": "1.2", "date": "2019-02-15" }, { "version": "1.3", "date": "2019-07-03" }, { "version": "1.4.1", "date": "2020-04-02" }, { "version": "1.5.0", "date": "2020-08-29" }, { "version": "1.5.1.1", "date": "2021-02-10" }, { "version": "1.5.1.2", "date": "2025-10-03" } ], "_exports": [ "ac", "calc_bin", "ci", "ggmcmc", "ggs", "ggs_autocorrelation", "ggs_caterpillar", "ggs_compare_partial", "ggs_crosscorrelation", "ggs_density", "ggs_diagnostics", "ggs_effective", "ggs_geweke", "ggs_grb", "ggs_histogram", "ggs_pairs", "ggs_pcp", "ggs_ppmean", "ggs_ppsd", "ggs_Rhat", "ggs_rocplot", "ggs_running", "ggs_separation", "ggs_traceplot", "gl_unq", "plab", "roc_calc", "sde0f" ], "_datasets": [ { "name": "radon", "title": "Simulations of the parameters of a hierarchical model", "object": "radon", "file": "radon.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "s", "title": "Simulations of the parameters of a simple linear regression with fake data.", "object": "linear", "file": "linear.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "s", "title": "Simulations of the parameters of a simple linear regression with fake data.", "object": "s", "file": "s.binary.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "s.binary", "title": "Simulations of the parameters of a simple linear regression with fake data.", "object": "binary", "file": "binary.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "s.binary", "title": "Simulations of the parameters of a simple linear regression with fake data.", "object": "s.binary", "file": "s.binary.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "s.y.rep", "title": "Simulations of the posterior predictive distribution of a simple linear regression with fake data.", "object": "linear", "file": "linear.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "s.y.rep", "title": "Simulations of the posterior predictive distribution of a simple linear regression with fake data.", "object": "s.y.rep", "file": "s.y.rep.rda", "class": [ "mcmc.list" ], "fields": [], "table": true, "tojson": false }, { "name": "y", "title": "Values for the observed outcome of a simple linear regression with fake data.", "object": "linear", "file": "linear.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "y", "title": "Values for the observed outcome of a simple linear regression with fake data.", "object": "y", "file": "y.binary.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "y.binary", "title": "Values for the observed outcome of a binary logistic regression with fake data.", "object": "binary", "file": "binary.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "y.binary", "title": "Values for the observed outcome of a binary logistic regression with fake data.", "object": "y.binary", "file": "y.binary.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "ac", "title": "Calculate the autocorrelation of a single chain, for a specified amount of lags", "topics": [ "ac" ] }, { "page": "binary", "title": "Simulated data for a binary logistic regression and its MCMC samples", "topics": [ "binary" ] }, { "page": "calc_bin", "title": "Calculate binwidths by parameter, based on the total number of bins.", "topics": [ "calc_bin" ] }, { "page": "ci", "title": "Calculate Credible Intervals (wide and narrow).", "topics": [ "ci" ] }, { "page": "custom.sort", "title": "Auxiliary function that sorts Parameter names taking into account numeric values", "topics": [ "custom.sort" ] }, { "page": "get_family", "title": "Subset a ggs object to get only the parameters with a given regular expression.", "topics": [ "get_family" ] }, { "page": "ggmcmc", "title": "Wrapper function that creates a single pdf file with all plots that ggmcmc can produce.", "topics": [ "ggmcmc-package", "ggmcmc" ] }, { "page": "ggs", "title": "Import MCMC samples into a ggs object than can be used by all ggs_* graphical functions.", "topics": [ "ggs" ] }, { "page": "ggs_autocorrelation", "title": "Plot an autocorrelation matrix", "topics": [ "ggs_autocorrelation" ] }, { "page": "ggs_caterpillar", "title": "Caterpillar plot with thick and thin CI", "topics": [ "ggs_caterpillar" ] }, { "page": "ggs_chain", "title": "Auxiliary function that extracts information from a single chain.", "topics": [ "ggs_chain" ] }, { "page": "ggs_compare_partial", "title": "Density plots comparing the distribution of the whole chain with only its last part.", "topics": [ "ggs_compare_partial" ] }, { "page": "ggs_crosscorrelation", "title": "Plot the Cross-correlation between-chains", "topics": [ "ggs_crosscorrelation" ] }, { "page": "ggs_density", "title": "Density plots of the chains", "topics": [ "ggs_density" ] }, { "page": "ggs_diagnostics", "title": "Formal diagnostics of convergence and sampling quality", "topics": [ "ggs_diagnostics" ] }, { "page": "ggs_effective", "title": "Dotplot of the effective number of independent draws", "topics": [ "ggs_effective" ] }, { "page": "ggs_geweke", "title": "Dotplot of the Geweke diagnostic, the standard Z-score", "topics": [ "ggs_geweke" ] }, { "page": "ggs_grb", "title": "Gelman-Rubin-Brooks plot (Rhat shrinkage)", "topics": [ "ggs_grb" ] }, { "page": "ggs_histogram", "title": "Histograms of the paramters.", "topics": [ "ggs_histogram" ] }, { "page": "ggs_pairs", "title": "Create a plot matrix of posterior simulations", "topics": [ "ggs_pairs" ] }, { "page": "ggs_pcp", "title": "Plot for model fit of binary response variables: percent correctly predicted", "topics": [ "ggs_pcp" ] }, { "page": "ggs_ppmean", "title": "Posterior predictive plot comparing the outcome mean vs the distribution of the predicted posterior means.", "topics": [ "ggs_ppmean" ] }, { "page": "ggs_ppsd", "title": "Posterior predictive plot comparing the outcome standard deviation vs the distribution of the predicted posterior standard deviations.", "topics": [ "ggs_ppsd" ] }, { "page": "ggs_Rhat", "title": "Dotplot of Potential Scale Reduction Factor (Rhat)", "topics": [ "ggs_Rhat" ] }, { "page": "ggs_rocplot", "title": "Receiver-Operator Characteristic (ROC) plot for models with binary outcomes", "topics": [ "ggs_rocplot" ] }, { "page": "ggs_running", "title": "Running means of the chains", "topics": [ "ggs_running" ] }, { "page": "ggs_separation", "title": "Separation plot for models with binary response variables", "topics": [ "ggs_separation" ] }, { "page": "ggs_traceplot", "title": "Traceplot of the chains", "topics": [ "ggs_traceplot" ] }, { "page": "gl_unq", "title": "Generate a factor with unequal number of repetitions.", "topics": [ "gl_unq" ] }, { "page": "linear", "title": "Simulated data for a continuous linear regression and its MCMC samples", "topics": [ "linear" ] }, { "page": "plab", "title": "Generate a data frame suitable for matching parameter names with their labels", "topics": [ "plab" ] }, { "page": "radon", "title": "Simulations of the parameters of a hierarchical model", "topics": [ "radon" ] }, { "page": "roc_calc", "title": "Calculate the ROC curve for a set of observed outcomes and predicted probabilities", "topics": [ "roc_calc" ] }, { "page": "s", "title": "Simulations of the parameters of a simple linear regression with fake data.", "topics": [ "s" ] }, { "page": "s.binary", "title": "Simulations of the parameters of a simple linear regression with fake data.", "topics": [ "s.binary" ] }, { "page": "s.y.rep", "title": "Simulations of the posterior predictive distribution of a simple linear regression with fake data.", "topics": [ "s.y.rep" ] }, { "page": "sde0f", "title": "Spectral Density Estimate at Zero Frequency.", "topics": [ "sde0f" ] }, { "page": "y", "title": "Values for the observed outcome of a simple linear regression with fake data.", "topics": [ "y" ] }, { "page": "y.binary", "title": "Values for the observed outcome of a binary logistic regression with fake data.", "topics": [ "y.binary" ] } ], "_readme": "https://github.com/xfim/ggmcmc/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "crayon", "dplyr", "farver", "forcats", "generics", "GGally", "ggplot2", "ggstats", "glue", "gtable", "hms", "isoband", "labeling", "lifecycle", "magrittr", "MASS", "patchwork", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "rlang", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "v70i09.Rnw", "filename": "v70i09.pdf", "title": "ggmcmc: Analysis of MCMC Samples and Bayesian Inference", "engine": "knitr::knitr", "headings": [], "created": "2016-05-11 10:39:26", "modified": "2021-02-10 15:40:34", "commits": 4 }, { "source": "using_ggmcmc.Rmd", "filename": "using_ggmcmc.html", "title": "Using the ggmcmc package", "author": "Xavier Fernández-i-Marín", "engine": "knitr::rmarkdown", "headings": [ "Why ggmcmc?", "Importing MCMC samples into ggmcmc using ggs()", "Using ggmcmc()", "Using individual functions", "Histograms", "Density plots", "Traceplots", "Running means", "Comparison of the whole chain with the latest part", "Autocorrelation plots", "Crosscorrelation plot", "Potential Scale Reduction Factor", "Geweke Diagnostics", "Select a family of parametrs", "Change parameter labels", "Caterpillar plots", "Posterior predictive checks and model fit", "Continuous outcomes", "Binary outcomes", "Percent of correctly predicted", "Paired plots", "Greek letters", "Aesthetic variations", "Combination with the power of ggplot2", "Development", "Acknowledgements", "References" ], "created": "2016-03-14 12:14:37", "modified": "2025-10-02 14:25:10", "commits": 15 } ], "_score": 11.959355270839316, "_indexed": true, "_nocasepkg": "ggmcmc", "_universes": [ "xfim" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.1.2", "date": "2026-05-22T10:04:32.000Z", "distro": "noble", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "1ed1061ea839c174a668d63f9ecd87e3a763aad45992e41d6802e818ebba1425", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.6.0", "os": "linux", "version": "1.5.1.2", "date": "2026-05-22T10:04:45.000Z", "distro": "noble", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "a0aca55c1da7ce30d7a47e3e38132b1e1b2cb75f081b03975a8937df2536942c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.5.3", "os": "mac", "version": "1.5.1.2", "date": "2026-05-22T10:04:34.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "2a78b2586f244b6d083a7acc6ec0a3c0e193a871b1e181e4bbea45dc11e735ca", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.6.0", "os": "mac", "version": "1.5.1.2", "date": "2026-05-22T10:04:25.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "2320b1fb3e632099b4307cbe1ad4e7b22cbc6c3009e47f289c842a15922595cf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.1.2", "date": "2026-05-22T10:04:40.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "fdc08ac92d7b9877ad62a9f61a1d17aa67c5f9b70ac3dd21abb476e5b28255af", "status": "success", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.7.0", "os": "win", "version": "1.5.1.2", "date": "2026-05-22T10:03:55.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "62c33445d058c153af89a0df9194d5395bf40057048c98a586d6d6d32fee5e83", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.5.3", "os": "win", "version": "1.5.1.2", "date": "2026-05-22T10:03:37.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "3711ac3e6ae6b326de2bf9efbdbfc59dee69dd4fcd295b7aa4028995ffafed4d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" }, { "r": "4.6.0", "os": "win", "version": "1.5.1.2", "date": "2026-05-22T10:03:55.000Z", "commit": "84333cb3dd58be78f84d69e0b1a2f25ba7a9e96a", "fileid": "166e4ee1c163029eec5c1bebde156cb2d3360b26ea8650499edcc244a2267987", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/xfim/actions/runs/26281235250" } ] }