{ "_id": "6a1e9e711d7bb097a0a6fe77", "Package": "adnuts", "Title": "No-U-Turn MCMC Sampling for 'ADMB' Models", "Version": "1.1.3", "Authors@R": "person(\"Cole\", \"Monnahan\", email = \"monnahc@uw.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0871-6700\"))", "Description": "Bayesian inference using the no-U-turn (NUTS) algorithm by\nHoffman and Gelman (2014)\n. Designed for\n'AD Model Builder' ('ADMB') models, or when R functions for\nlog-density and log-density gradient are available, such as\n'Template Model Builder' models and other special cases.\nFunctionality is similar to 'Stan', and the 'rstan' and\n'shinystan' packages are used for diagnostics and inference.", "URL": "https://github.com/Cole-Monnahan-NOAA/adnuts,\nhttps://cole-monnahan-noaa.github.io/adnuts/", "BugReports": "https://github.com/Cole-Monnahan-NOAA/adnuts/issues", "License": "GPL-3 | file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "ByteCompile": "true", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "make", "Repository": "https://cole-monnahan-noaa.r-universe.dev", "Date/Publication": "2026-04-03 16:32:13 UTC", "RemoteUrl": "https://github.com/cole-monnahan-noaa/adnuts", "RemoteRef": "HEAD", "RemoteSha": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 09:07:17 UTC", "User": "root" }, "Author": "Cole Monnahan [aut, cre] (ORCID:\n)", "Maintainer": "Cole Monnahan ", "MD5sum": "227fc5f4a067bf113dcbb1259b3d409c", "_user": "cole-monnahan-noaa", "_type": "src", "_file": "adnuts_1.1.3.tar.gz", "_fileid": "e2a817faecf0826123135ae6d6c5a7d7d079ea43e23ab5d98e5e307f3231b7d4", "_filesize": 3300969, "_sha256": "e2a817faecf0826123135ae6d6c5a7d7d079ea43e23ab5d98e5e307f3231b7d4", "_created": "2026-06-02T09:07:17.000Z", "_published": "2026-06-02T09:12:17.875Z", "_distro": "noble", "_jobs": [ { "job": 79036991121, "time": 232, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7353601153" }, { "job": 79036991071, "time": 232, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7353600934" }, { "job": 79036991096, "time": 230, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7353589725" }, { "job": 79036991081, "time": 255, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7353595456" }, { "job": 79036167263, "time": 285, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7353518151" }, { "job": 79036991118, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7353571069" }, { "job": 79036991182, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7353578217" }, { "job": 79036991097, "time": 165, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7353577495" }, { "job": 79036991396, "time": 197, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7353588407" } ], "_buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cole-monnahan-noaa/adnuts", "_commit": { "id": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "author": "Cole-Monnahan-NOAA ", "committer": "Cole-Monnahan-NOAA ", "message": "Remove check badges and bump version for release\n", "time": 1775233933 }, "_maintainer": { "name": "Cole Monnahan", "email": "monnahc@uw.edu", "login": "colemonnahan", "description": "Personal account. See @Cole-Monnahan-NOAA for professional account.", "uuid": 4804974, "orcid": "0000-0003-0871-6700" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "snowfall", "version": ">= 1.84.6.1", "role": "Depends" }, { "package": "ellipse", "role": "Imports" }, { "package": "rstan", "role": "Imports" }, { "package": "R2admb", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "shinystan", "version": ">= 2.5.0", "role": "Suggests" }, { "package": "matrixcalc", "version": ">= 1.0.3", "role": "Suggests" }, { "package": "stats", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "TMB", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "cole-monnahan-noaa", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 8 } ], "_tags": [ { "name": "v1.1.3", "date": "2026-04-03" } ], "_stars": 25, "_contributors": [ { "user": "colemonnahan", "count": 305, "uuid": 4804974 }, { "user": "cole-monnahan-noaa", "count": 169, "uuid": 58868176 }, { "user": "iagomosqueira", "count": 1, "uuid": 1029847 }, { "user": "kaskr", "count": 1, "uuid": 5426937 } ], "_userbio": { "uuid": 58868176, "type": "user", "name": "Cole Monnahan", "description": "Quantitative ecologist at NOAA's AFSC" }, "_downloads": { "count": 283, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/adnuts" }, "_mentions": 1, "_devurl": "https://github.com/cole-monnahan-noaa/adnuts", "_pkgdown": "https://cole-monnahan-noaa.github.io/adnuts/", "_searchresults": 72, "_rbuild": "4.6.0", "_assets": [ "extra/adnuts.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/cole-monnahan-noaa/adnuts", "_realowner": "cole-monnahan-noaa", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2018-02-08" }, { "version": "1.0.1", "date": "2019-04-04" }, { "version": "1.1.2", "date": "2021-03-02" } ], "_exports": [ "adfit", "check_identifiable", "extract_sampler_params", "extract_samples", "is.adfit", "launch_shinyadmb", "pairs_admb", "plot_marginals", "plot_sampler_params", "plot_uncertainties", "sample_admb", "sample_inits", "sample_nuts", "sample_rwm", "sample_tmb" ], "_help": [ { "page": "dot-check_ADMB_version", "title": "Check that the model is compiled with the right version of ADMB which is 12.0 or later", "topics": [ ".check_ADMB_version" ] }, { "page": "dot-check_console_printing", "title": "Check if the session is interactive or Rstudio which has implications for parallel output", "topics": [ ".check_console_printing" ] }, { "page": "dot-check_model_path", "title": "Check that the file can be found", "topics": [ ".check_model_path" ] }, { "page": "dot-getADMBHessian", "title": "Read in admodel.hes file", "topics": [ ".getADMBHessian" ] }, { "page": "dot-sample_admb", "title": "Hidden wrapper function for sampling from ADMB models", "topics": [ ".sample_admb" ] }, { "page": "dot-update_model", "title": "Convert model name depending on system", "topics": [ ".update_model" ] }, { "page": "adfit", "title": "Constructor for the \"adfit\" (A-D fit) class", "topics": [ "adfit" ] }, { "page": "adnuts", "title": "adnuts: No-U-turn sampling for AD Model Builder (ADMB)", "topics": [ "adnuts" ] }, { "page": "as.data.frame.adfit", "title": "Convert object of class adfit to data.frame. Calls 'extract_samples'", "topics": [ "as.data.frame.adfit" ] }, { "page": "check_identifiable", "title": "Check identifiability from model Hessian", "topics": [ "check_identifiable" ] }, { "page": "extract_sampler_params", "title": "Extract sampler parameters from a fit.", "topics": [ "extract_sampler_params" ] }, { "page": "extract_samples", "title": "Extract posterior samples from a model fit.", "topics": [ "extract_samples" ] }, { "page": "is.adfit", "title": "Check object of class adfit", "topics": [ "is.adfit" ] }, { "page": "launch_shinyadmb", "title": "Launch shinystan for an ADMB fit.", "topics": [ "launch_shinyadmb" ] }, { "page": "launch_shinytmb", "title": "Launch shinystan for a TMB fit.", "topics": [ "launch_shinytmb" ] }, { "page": "pairs_admb", "title": "Plot pairwise parameter posteriors and optionally the MLE points and confidence ellipses.", "topics": [ "pairs_admb" ] }, { "page": "plot_marginals", "title": "Plot marginal distributions for a fitted model", "topics": [ "plot_marginals" ] }, { "page": "plot_sampler_params", "title": "Plot adaptation metrics for a fitted model.", "topics": [ "plot_sampler_params" ] }, { "page": "plot_uncertainties", "title": "Plot MLE vs MCMC marginal standard deviations for each parameter", "topics": [ "plot_uncertainties" ] }, { "page": "plot.adfit", "title": "Plot object of class adfit", "topics": [ "plot.adfit" ] }, { "page": "print.adfit", "title": "Print summary of adfit object", "topics": [ "print.adfit" ] }, { "page": "sample_admb", "title": "Deprecated version of wrapper function. Use sample_nuts or sample_rwm instead.", "topics": [ "sample_admb" ] }, { "page": "sample_inits", "title": "Function to generate random initial values from a previous fit using adnuts", "topics": [ "sample_inits" ] }, { "page": "wrappers", "title": "Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS) or random walk Metropolis (RWM) algorithms.", "topics": [ "sample_nuts", "sample_rwm", "wrappers" ] }, { "page": "sample_tmb", "title": "Bayesian inference of a TMB model using the no-U-turn sampler.", "topics": [ "sample_tmb" ] }, { "page": "sample_tmb_hmc", "title": "Draw MCMC samples from a model posterior using a static HMC sampler.", "topics": [ "sample_tmb_hmc" ] }, { "page": "sample_tmb_nuts", "title": "Draw MCMC samples from a model posterior using the No-U-Turn (NUTS) sampler with dual averaging.", "topics": [ "sample_tmb_nuts" ] }, { "page": "sample_tmb_rwm", "title": "[Deprecated] Draw MCMC samples from a model posterior using a Random Walk Metropolis (RWM) sampler.", "topics": [ "sample_tmb_rwm" ] }, { "page": "summary.adfit", "title": "Print summary of object of class adfit", "topics": [ "summary.adfit" ] } ], "_readme": "https://github.com/cole-monnahan-noaa/adnuts/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "coda", "cpp11", "desc", "distributional", "ellipse", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "matrixStats", "numDeriv", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "QuickJSR", "R2admb", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "S7", "scales", "snow", "snowfall", "StanHeaders", "tensorA", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "adnuts.Rmd", "filename": "adnuts.html", "title": "No-U-turn sampling for ADMB models", "author": "Cole C. Monnahan", "engine": "knitr::rmarkdown", "headings": [ "Summary", "Sampling for ADMB models", "Setting up the model", "Sampling with sample_nuts and sample_rwm", "mceval phase and posterior outputs", "Bounds & Priors", "Initializing chains", "Parallel sampling", "Diagnostics and plotting results", "Diagnosing MCMC chains", "Plotting output", "Mass matrix adaptation", "Sampling for TMB models", "The no-U-turn sampler implementation", "Brief review of Hamiltonian Monte Carlo", "Algorithm implementation details", "User intervention", "Algorithm validity", "References" ], "created": "2017-12-03 23:48:54", "modified": "2026-04-03 15:45:54", "commits": 19 } ], "_score": 6.431363764158988, "_indexed": true, "_nocasepkg": "adnuts", "_universes": [ "cole-monnahan-noaa", "colemonnahan" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.3", "date": "2026-06-02T09:10:10.000Z", "distro": "noble", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "5ffe7f3750b52e22f5799653a40f473af2dff7895260d7138b3c7beb5086d46c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.6.0", "os": "linux", "version": "1.1.3", "date": "2026-06-02T09:10:10.000Z", "distro": "noble", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "1bcfc69e6f42872a93ad78dd7fa7aeb4631ae32eaa565fa0528fcff993f9485e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.5.3", "os": "mac", "version": "1.1.3", "date": "2026-06-02T09:10:02.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "26e570657176183fa1b0eac4f30daf965d53edcccdb6a336b2a1f746c2b5d5eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.6.0", "os": "mac", "version": "1.1.3", "date": "2026-06-02T09:10:05.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "ffd5be11da204be263bc65af5b9d739bf873c803072feddfc0ea490bd650f85a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.3", "date": "2026-06-02T09:10:05.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "80f78000cce6388a0125fa28ed41ce9b5163ef09a18896b5e1eb2f5105298c93", "status": "success", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.7.0", "os": "win", "version": "1.1.3", "date": "2026-06-02T09:08:59.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "04fc63a7559d763a82df20eeea6974e2d52d1005ba1c14c7ce050982d3b7c4c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.5.3", "os": "win", "version": "1.1.3", "date": "2026-06-02T09:08:56.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "f1c2f8f62953b2e54fbdd61a9ab9fc7bc20e4ae2c72f81844dc7da34f59b176d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" }, { "r": "4.6.0", "os": "win", "version": "1.1.3", "date": "2026-06-02T09:09:10.000Z", "commit": "c401649b84924e873bcb96b9ad6ff6b48c401ada", "fileid": "949c1e2f98ceeae6a4d00e100504fefc33c8ed153ed7f3039311c32333c03dea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cole-monnahan-noaa/actions/runs/26809693674" } ] }