{ "_id": "6a1042a4acfb0bcc41c9dc0c", "Package": "dreamer", "Title": "Dose Response Models for Bayesian Model Averaging", "Version": "3.2.0.9000", "Authors@R": "c(\nperson(given = c(\"Richard\", \"Daniel\"),\nfamily = \"Payne\",\nrole = c(\"aut\", \"cre\"),\nemail = \"paynestatistics@gmail.com\"),\nperson(given = \"William Michael\",\nfamily = \"Landau\",\nrole = c(\"rev\"),\nemail = \"will.landau@gmail.com\"),\nperson(\"Mitch\", \"Thomann\",\nrole = c(\"rev\"),\nemail = \"mitchell.thomann@lilly.com\"),\nperson(family = \"Eli Lilly and Company\",\nrole = \"cph\"))", "Description": "Fits dose-response models utilizing a Bayesian model\naveraging approach as outlined in Gould (2019)\n for both continuous and binary\nresponses. Longitudinal dose-response modeling is also\nsupported in a Bayesian model averaging framework as outlined\nin Payne, Ray, and Thomann (2024)\n. Functions for plotting and\ncalculating various posterior quantities (e.g. posterior mean,\nquantiles, probability of minimum efficacious dose, etc.) are\nalso implemented. Copyright Eli Lilly and Company (2019).", "URL": "https://rich-payne.github.io/dreamer/,\nhttps://github.com/rich-payne/dreamer", "BugReports": "https://github.com/rich-payne/dreamer/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "Language": "en-US", "Config/pak/sysreqs": "jags libicu-dev", "Repository": "https://rich-payne.r-universe.dev", "Date/Publication": "2024-12-19 14:40:20 UTC", "RemoteUrl": "https://github.com/rich-payne/dreamer", "RemoteRef": "HEAD", "RemoteSha": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 07:17:06 UTC", "User": "root" }, "Author": "Richard Daniel Payne [aut, cre],\nWilliam Michael Landau [rev],\nMitch Thomann [rev],\nEli Lilly and Company [cph]", "Maintainer": "Richard Daniel Payne ", "MD5sum": "992fc77bc071c6fd53ad7ac6ff789800", "_user": "rich-payne", "_type": "src", "_file": "dreamer_3.2.0.9000.tar.gz", "_fileid": "bf38c0edda8d5c11e09ae4a07d5e5dfa88d28d9463efbd7b3d62a9258db0f655", "_filesize": 1940947, "_sha256": "bf38c0edda8d5c11e09ae4a07d5e5dfa88d28d9463efbd7b3d62a9258db0f655", "_created": "2026-05-11T07:17:06.000Z", "_published": "2026-05-22T11:48:52.145Z", "_distro": "noble", "_jobs": [ { "job": 77373465056, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6912469759" }, { "job": 77373465289, "time": 226, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6912472381" }, { "job": 77373465350, "time": 160, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6912458217" }, { "job": 77373465271, "time": 141, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6912453077" }, { "job": 77373464622, "time": 234, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6912406974" }, { "job": 77373464382, "time": 112, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7159756167" }, { "job": 77373464901, "time": 210, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6912467618" }, { "job": 77373464890, "time": 245, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6912478240" }, { "job": 77373465189, "time": 196, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6912463599" } ], "_buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rich-payne/dreamer", "_commit": { "id": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "author": "Richard Payne ", "committer": "Richard Payne ", "message": "bump to development version\n", "time": 1734619220 }, "_maintainer": { "name": "Richard Daniel Payne", "email": "paynestatistics@gmail.com", "login": "richardbayes", "uuid": 22532423 }, "_registered": true, "_dependencies": [ { "package": "coda", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ellipsis", "version": ">= 0.3", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rootSolve", "role": "Imports" }, { "package": "rjags", "version": ">= 4-8", "role": "Imports" }, { "package": "rlang", "version": ">= 0.4.5", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.0.2", "role": "Imports" }, { "package": "tidyselect", "version": ">= 1.2", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0", "role": "Suggests" }, { "package": "fs", "version": ">= 1.5", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" } ], "_owner": "rich-payne", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "bayesian", "dose-response-modeling", "jags", "cpp" ], "_stars": 10, "_contributors": [ { "user": "rich-payne", "count": 170, "uuid": 39996197 }, { "user": "olivroy", "count": 1, "uuid": 52606734 } ], "_userbio": { "uuid": 39996197, "type": "user", "name": "Richard Payne", "description": "Statistician specializing in Bayesian methods and R-package development." }, "_downloads": { "count": 283, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dreamer" }, "_devurl": "https://github.com/rich-payne/dreamer", "_pkgdown": "https://rich-payne.github.io/dreamer/", "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/dreamer.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rich-payne/dreamer", "_realowner": "rich-payne", "_cranurl": true, "_releases": [ { "version": "3.0.0", "date": "2021-08-20" }, { "version": "3.1.0", "date": "2022-09-01" }, { "version": "3.2.0", "date": "2024-12-19" } ], "_exports": [ "diagnostics", "dreamer_data_beta", "dreamer_data_beta_binary", "dreamer_data_emax", "dreamer_data_emax_binary", "dreamer_data_exp", "dreamer_data_exp_binary", "dreamer_data_independent", "dreamer_data_independent_binary", "dreamer_data_linear", "dreamer_data_linear_binary", "dreamer_data_loglinear", "dreamer_data_loglinear_binary", "dreamer_data_logquad", "dreamer_data_logquad_binary", "dreamer_data_quad", "dreamer_data_quad_binary", "dreamer_mcmc", "dreamer_plot_prior", "model_beta", "model_beta_binary", "model_emax", "model_emax_binary", "model_exp", "model_exp_binary", "model_independent", "model_independent_binary", "model_linear", "model_linear_binary", "model_loglinear", "model_loglinear_binary", "model_logquad", "model_logquad_binary", "model_longitudinal_idp", "model_longitudinal_itp", "model_longitudinal_linear", "model_quad", "model_quad_binary", "plot_comparison", "plot_trace", "post_medx", "post_perc_effect", "posterior", "pr_eoi", "pr_med", "pr_medx" ], "_help": [ { "page": "diagnostics", "title": "Calculate MCMC Diagnostics for Parameters", "topics": [ "diagnostics" ] }, { "page": "dreamer_data", "title": "Generate Data from Dose Response Models", "topics": [ "dreamer_data", "dreamer_data_beta", "dreamer_data_beta_binary", "dreamer_data_emax", "dreamer_data_emax_binary", "dreamer_data_exp", "dreamer_data_exp_binary", "dreamer_data_independent", "dreamer_data_independent_binary", "dreamer_data_linear", "dreamer_data_linear_binary", "dreamer_data_loglinear", "dreamer_data_loglinear_binary", "dreamer_data_logquad", "dreamer_data_logquad_binary", "dreamer_data_quad", "dreamer_data_quad_binary" ] }, { "page": "dreamer_mcmc", "title": "Bayesian Model Averaging of Dose Response Models", "topics": [ "dreamer_mcmc" ] }, { "page": "dreamer_plot_prior", "title": "Plot Prior", "topics": [ "dreamer_plot_prior" ] }, { "page": "dreamerplot", "title": "Posterior Plot of Bayesian Model Averaging", "topics": [ "dreamerplot", "plot.dreamer_mcmc" ] }, { "page": "model", "title": "Model Creation", "topics": [ "model", "model_beta", "model_beta_binary", "model_emax", "model_emax_binary", "model_exp", "model_exp_binary", "model_independent", "model_independent_binary", "model_linear", "model_linear_binary", "model_loglinear", "model_loglinear_binary", "model_logquad", "model_logquad_binary", "model_quad", "model_quad_binary" ] }, { "page": "model_longitudinal", "title": "Model Creation: Longitudinal Models", "topics": [ "model_longitudinal", "model_longitudinal_idp", "model_longitudinal_itp", "model_longitudinal_linear" ] }, { "page": "plot_comparison", "title": "Compare Posterior Fits", "topics": [ "plot_comparison", "plot_comparison.default", "plot_comparison.dreamer_bma" ] }, { "page": "plot_trace", "title": "Traceplots", "topics": [ "plot_trace" ] }, { "page": "post_medx", "title": "Posterior Distribution of Minimum X% Effective Dose", "topics": [ "post_medx", "post_medx.dreamer_bma", "post_medx.dreamer_mcmc" ] }, { "page": "post_perc_effect", "title": "Calculate Posterior of a Dose's Percentage Effect", "topics": [ "post_perc_effect", "post_perc_effect.dreamer_bma", "post_perc_effect.dreamer_mcmc" ] }, { "page": "posterior", "title": "Posterior Quantities from Bayesian Model Averaging", "topics": [ "posterior", "posterior.dreamer_bma", "posterior.dreamer_mcmc", "posterior.dreamer_mcmc_independent" ] }, { "page": "pr_eoi", "title": "Calculate Probability of Meeting Effect of Interest (EOI)", "topics": [ "pr_eoi" ] }, { "page": "pr_med", "title": "Pr(minimum efficacious dose)", "topics": [ "pr_med" ] }, { "page": "pr_medx", "title": "Probability of minimum X% effective dose", "topics": [ "pr_medx" ] }, { "page": "summary.dreamer_bma", "title": "Summarize Bayesian Model Averaging MCMC Output", "topics": [ "summary.dreamer_bma" ] }, { "page": "summary.dreamer_mcmc", "title": "Summarize Model Output", "topics": [ "summary.dreamer_mcmc" ] } ], "_readme": "https://github.com/rich-payne/dreamer/raw/HEAD/README.md", "_rundeps": [ "cli", "coda", "cpp11", "dplyr", "ellipsis", "farver", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "pillar", "pkgconfig", "purrr", "R6", "RColorBrewer", "rjags", "rlang", "rootSolve", "S7", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_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": "dreamer.Rmd", "filename": "dreamer.html", "title": "Dose REsponse models for bAyesian Model avERaging (dreamer)", "author": "Richard Payne", "engine": "knitr::rmarkdown", "headings": [ "dreamer", "Generate data", "Fit Model", "Model Output", "Posterior Credible Intervals", "Posterior Plots", "Posterior Quantities", "Probability of Meeting Effect of Interest (EOI)", "Probability of Minimum Efficacious Dose (MED)", "Probability of Minimum Dose with at Least X% Efficacy", "Posterior Probability of MEDX", "Posterior Distribution of Percentage Effect", "MCMC Diagnostics", "Visualizing Priors", "Independent Model", "Longitudinal Modeling", "Reference" ], "created": "2021-08-16 14:51:24", "modified": "2022-08-30 18:01:33", "commits": 5 }, { "source": "dreamer_method.Rmd", "filename": "dreamer_method.html", "title": "dreamer Methods", "engine": "knitr::rmarkdown", "headings": [ "Bayesian Model Averaging in dreamer", "Reference" ], "created": "2021-08-20 14:10:52", "modified": "2022-07-12 14:08:23", "commits": 2 } ], "_score": 5, "_indexed": true, "_nocasepkg": "dreamer", "_universes": [ "rich-payne", "richardbayes" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.2.0.9000", "date": "2026-05-11T07:19:24.000Z", "distro": "noble", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "33360dec4ade26fbe7b90b66e1dfe471bbd8d9995de25625f766a6a8e85f165a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.6.0", "os": "linux", "version": "3.2.0.9000", "date": "2026-05-11T07:19:30.000Z", "distro": "noble", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "c146fd33f4e98ad55b245f23e07e4a625cde15053dff1b2f38c373bd16d2f0a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.5.3", "os": "mac", "version": "3.2.0.9000", "date": "2026-05-11T07:19:19.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "3f03b2532e3bcca2443e293219d59ffef6d88ba8b6409a2f90641b7a9c66bacb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.6.0", "os": "mac", "version": "3.2.0.9000", "date": "2026-05-11T07:19:06.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "2a02dfa0e7b041e08860981e316e5595766998441f92d24008a22351b32cb521", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.7.0", "os": "win", "version": "3.2.0.9000", "date": "2026-05-11T07:18:29.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "e8789cde390eb88958ae7508e17707890e2f1d80fc3fce792f8dc2cb342c4ca5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.5.3", "os": "win", "version": "3.2.0.9000", "date": "2026-05-11T07:19:01.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "9480514faf724821e31d12513aba9e626fd0a963e8e5a4fee919d722d4927906", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.6.0", "os": "win", "version": "3.2.0.9000", "date": "2026-05-11T07:18:44.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "45f2c9fdc3493caa62cf1b6df35cd82fef0ea7df2cfbe8814c454c488d2f8fb5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" }, { "r": "4.6.0", "os": "wasm", "version": "3.2.0.9000", "date": "2026-05-22T11:48:36.000Z", "commit": "a16fbb0f17421cbf41d8f2b680a65c8502d10d3b", "fileid": "706f135b321e745ae9281643466430a4e38ddf6389e9f72628cfb2b777c2c770", "status": "success", "buildurl": "https://github.com/r-universe/rich-payne/actions/runs/25655779769" } ] }