{
  "_id": "6a1ef42ab401979e734159be",
  "Package": "glmmTMB",
  "Title": "Generalized Linear Mixed Models using Template Model Builder",
  "Version": "1.1.15",
  "Authors@R": "c(person(\"Mollie\",\"Brooks\",\ncomment=c(ORCID=\"0000-0001-6963-8326\"),\nrole = c(\"aut\", \"cre\"),\nemail = \"mollieebrooks@gmail.com\"),\nperson(\"Ben\",\"Bolker\", role=\"aut\",\ncomment=c(ORCID=\"0000-0002-2127-0443\")),\nperson(\"Kasper\",\"Kristensen\",role=\"aut\"),\nperson(\"Martin\",\"Maechler\", role=\"aut\",\ncomment=c(ORCID=\"0000-0002-8685-9910\")),\nperson(\"Arni\",\"Magnusson\", role=\"aut\",\ncomment=c(ORCID=\"0000-0003-2769-6741\")),\nperson(\"Maeve\",\"McGillycuddy\", role=\"ctb\"),\nperson(\"Hans\",\"Skaug\",role=\"aut\",\ncomment=c(ORCID=\"0000-0003-4235-2592\")),\nperson(\"Anders\",\"Nielsen\", role=\"aut\",\ncomment=c(ORCID=\"0000-0001-9683-9262\")),\nperson(\"Casper\",\"Berg\", role=\"aut\",\ncomment=c(ORCID=\"0000-0002-3812-5269\")),\nperson(\"Koen\",\"van Bentham\", role=\"aut\"),\nperson(\"Nafis\",\"Sadat\",role=\"ctb\",\ncomment=c(ORCID=\"0000-0001-5715-616X\")),\nperson(\"Daniel\",\"Lüdecke\", role=\"ctb\",\ncomment=c(ORCID=\"0000-0002-8895-3206\")),\nperson(\"Russ\",\"Lenth\", role=\"ctb\"),\nperson(\"Joseph\", \"O'Brien\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-9851-5077\")),\nperson(\"Charles J.\",\"Geyer\", role=\"ctb\"),\nperson(\"Mikael\",\"Jagan\", role=\"ctb\",\ncomment = c(ORCID = \"0000-0002-3542-2938\")),\nperson(\"Brenton\", \"Wiernik\", role=\"ctb\",\ncomment = c(ORCID = \"0000-0001-9560-6336\")),\nperson(\"Daniel B.\", \"Stouffer\", role=\"ctb\",\ncomment = c(ORCID = \"0000-0001-9436-9674\")),\nperson(\"Michael\", \"Agronah\", role = \"ctb\",\ncomment = c(ORCID = \"0009-0007-2655-4094\")),\nperson(\"Hatice Tül Kübra\", \"Akdur\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-2144-0518\")),\nperson(\"Daniel\", \"Sabanés Bové\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-0176-9239\")),\nperson(\"Nikolas\", \"Krieger\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4581-3545\")),\nperson(\"Coralie\", \"Williams\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-1312-4953\"))\n)",
  "Description": "Fit linear and generalized linear mixed models with\nvarious extensions, including zero-inflation. The models are\nfitted using maximum likelihood estimation via 'TMB' (Template\nModel Builder). Random effects are assumed to be Gaussian on\nthe scale of the linear predictor and are integrated out using\nthe Laplace approximation. Gradients are calculated using\nautomatic differentiation.",
  "License": "AGPL-3",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr, rmarkdown",
  "URL": "https://github.com/glmmTMB/glmmTMB",
  "LazyData": "TRUE",
  "BugReports": "https://github.com/glmmTMB/glmmTMB/issues",
  "NeedsCompilation": "yes",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://glmmtmb.r-universe.dev",
  "Date/Publication": "2026-06-02 11:59:04 UTC",
  "RemoteUrl": "https://github.com/glmmtmb/glmmtmb",
  "RemoteRef": "HEAD",
  "RemoteSha": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
  "RemoteSubdir": "glmmTMB",
  "Packaged": {
    "Date": "2026-06-02 15:03:59 UTC",
    "User": "root"
  },
  "Author": "Mollie Brooks [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6963-8326>),\nBen Bolker [aut] (ORCID: <https://orcid.org/0000-0002-2127-0443>),\nKasper Kristensen [aut],\nMartin Maechler [aut] (ORCID: <https://orcid.org/0000-0002-8685-9910>),\nArni Magnusson [aut] (ORCID: <https://orcid.org/0000-0003-2769-6741>),\nMaeve McGillycuddy [ctb],\nHans Skaug [aut] (ORCID: <https://orcid.org/0000-0003-4235-2592>),\nAnders Nielsen [aut] (ORCID: <https://orcid.org/0000-0001-9683-9262>),\nCasper Berg [aut] (ORCID: <https://orcid.org/0000-0002-3812-5269>),\nKoen van Bentham [aut],\nNafis Sadat [ctb] (ORCID: <https://orcid.org/0000-0001-5715-616X>),\nDaniel Lüdecke [ctb] (ORCID: <https://orcid.org/0000-0002-8895-3206>),\nRuss Lenth [ctb],\nJoseph O'Brien [ctb] (ORCID: <https://orcid.org/0000-0001-9851-5077>),\nCharles J. Geyer [ctb],\nMikael Jagan [ctb] (ORCID: <https://orcid.org/0000-0002-3542-2938>),\nBrenton Wiernik [ctb] (ORCID: <https://orcid.org/0000-0001-9560-6336>),\nDaniel B. Stouffer [ctb] (ORCID:\n<https://orcid.org/0000-0001-9436-9674>),\nMichael Agronah [ctb] (ORCID: <https://orcid.org/0009-0007-2655-4094>),\nHatice Tül Kübra Akdur [ctb] (ORCID:\n<https://orcid.org/0000-0003-2144-0518>),\nDaniel Sabanés Bové [ctb] (ORCID:\n<https://orcid.org/0000-0002-0176-9239>),\nNikolas Krieger [ctb] (ORCID: <https://orcid.org/0000-0002-4581-3545>),\nCoralie Williams [ctb] (ORCID: <https://orcid.org/0000-0003-1312-4953>)",
  "Maintainer": "Mollie Brooks <mollieebrooks@gmail.com>",
  "MD5sum": "3be39c90da7c0bf29e80fd7d559c3bff",
  "_user": "glmmtmb",
  "_type": "src",
  "_file": "glmmTMB_1.1.15.tar.gz",
  "_fileid": "5c46ae418cc2319d27ee9fb8ce93632fcbdd5d7376727c75995b4cd30ae05e93",
  "_filesize": 6185865,
  "_sha256": "5c46ae418cc2319d27ee9fb8ce93632fcbdd5d7376727c75995b4cd30ae05e93",
  "_created": "2026-06-02T15:03:59.000Z",
  "_published": "2026-06-02T15:18:02.688Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79103694588,
      "time": 375,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7361824359"
    },
    {
      "job": 79103694639,
      "time": 342,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7361807546"
    },
    {
      "job": 79103694526,
      "time": 350,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361812116"
    },
    {
      "job": 79103694535,
      "time": 345,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361808411"
    },
    {
      "job": 79103694771,
      "time": 279,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7361884620"
    },
    {
      "job": 79103694566,
      "time": 648,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7361967664"
    },
    {
      "job": 79103694728,
      "time": 324,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361843402"
    },
    {
      "job": 79103694570,
      "time": 583,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361950840"
    },
    {
      "job": 79101761007,
      "time": 507,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361643523"
    },
    {
      "job": 79103694463,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361732851"
    },
    {
      "job": 79103694891,
      "time": 385,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7361826803"
    },
    {
      "job": 79103694484,
      "time": 401,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7361833704"
    },
    {
      "job": 79103694610,
      "time": 395,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7361833426"
    }
  ],
  "_buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/glmmtmb/glmmtmb",
  "_commit": {
    "id": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
    "author": "Mollie Brooks <mebrooks@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #1269 from dke-chan/vcov_2\n\nUpdate vcov() to no longer create unnamed columns for non-estimated parameters. \n\nNote that `expect_all_equal` requires `testthat` >= 3.3.0",
    "time": 1780401544
  },
  "_maintainer": {
    "name": "Mollie Brooks",
    "email": "mollieebrooks@gmail.com",
    "login": "mebrooks",
    "description": "",
    "uuid": 5310845,
    "orcid": "0000-0001-6963-8326"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "TMB",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "TMB",
      "version": ">= 1.9.0",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "version": ">= 1.1-18.9000",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "role": "Imports"
    },
    {
      "package": "numDeriv",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "reformulas",
      "version": ">= 0.4.3.1",
      "role": "Imports"
    },
    {
      "package": "pbkrtest",
      "role": "Imports"
    },
    {
      "package": "sandwich",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "lattice",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.1",
      "role": "Suggests"
    },
    {
      "package": "mlmRev",
      "role": "Suggests"
    },
    {
      "package": "bbmle",
      "version": ">= 1.0.19",
      "role": "Suggests"
    },
    {
      "package": "pscl",
      "role": "Suggests"
    },
    {
      "package": "coda",
      "role": "Suggests"
    },
    {
      "package": "reshape2",
      "role": "Suggests"
    },
    {
      "package": "car",
      "version": ">= 3.0.6",
      "role": "Suggests"
    },
    {
      "package": "emmeans",
      "version": ">= 1.4",
      "role": "Suggests"
    },
    {
      "package": "estimability",
      "role": "Suggests"
    },
    {
      "package": "DHARMa",
      "role": "Suggests"
    },
    {
      "package": "multcomp",
      "role": "Suggests"
    },
    {
      "package": "MuMIn",
      "role": "Suggests"
    },
    {
      "package": "effects",
      "version": ">= 4.0-1",
      "role": "Suggests"
    },
    {
      "package": "dotwhisker",
      "role": "Suggests"
    },
    {
      "package": "broom",
      "role": "Suggests"
    },
    {
      "package": "broom.mixed",
      "role": "Suggests"
    },
    {
      "package": "plyr",
      "role": "Suggests"
    },
    {
      "package": "png",
      "role": "Suggests"
    },
    {
      "package": "boot",
      "role": "Suggests"
    },
    {
      "package": "texreg",
      "role": "Suggests"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    },
    {
      "package": "huxtable",
      "role": "Suggests"
    },
    {
      "package": "parallel",
      "role": "Suggests"
    },
    {
      "package": "blme",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    },
    {
      "package": "ade4",
      "role": "Suggests"
    },
    {
      "package": "ape",
      "role": "Suggests"
    },
    {
      "package": "gsl",
      "role": "Suggests"
    },
    {
      "package": "lmerTest",
      "role": "Suggests"
    },
    {
      "package": "metafor",
      "role": "Suggests"
    }
  ],
  "_owner": "glmmtmb",
  "_selfowned": true,
  "_usedby": 38,
  "_updates": [
    {
      "week": "2025-26",
      "n": 2
    },
    {
      "week": "2025-28",
      "n": 2
    },
    {
      "week": "2025-29",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-33",
      "n": 2
    },
    {
      "week": "2025-34",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-42",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-51",
      "n": 1
    },
    {
      "week": "2025-52",
      "n": 5
    },
    {
      "week": "2026-02",
      "n": 7
    },
    {
      "week": "2026-03",
      "n": 2
    },
    {
      "week": "2026-10",
      "n": 1
    },
    {
      "week": "2026-13",
      "n": 1
    },
    {
      "week": "2026-21",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 6
    }
  ],
  "_tags": [],
  "_stars": 366,
  "_contributors": [
    {
      "user": "bbolker",
      "count": 2088,
      "uuid": 78918
    },
    {
      "user": "mebrooks",
      "count": 561,
      "uuid": 5310845
    },
    {
      "user": "kaskr",
      "count": 266,
      "uuid": 5426937
    },
    {
      "user": "mmaechler",
      "count": 57,
      "uuid": 995722
    },
    {
      "user": "mmcgillycuddy",
      "count": 56,
      "uuid": 45033271
    },
    {
      "user": "danielinteractive",
      "count": 41,
      "uuid": 1071227
    },
    {
      "user": "stouffer",
      "count": 36,
      "uuid": 1916363
    },
    {
      "user": "koenvanbenthem",
      "count": 28,
      "uuid": 6603436
    },
    {
      "user": "bwiernik",
      "count": 17,
      "uuid": 4773225
    },
    {
      "user": "fishfollower",
      "count": 13,
      "uuid": 5370999
    },
    {
      "user": "coraliewilliams",
      "count": 10,
      "uuid": 19731465
    },
    {
      "user": "strengejacke",
      "count": 9,
      "uuid": 26301769
    },
    {
      "user": "psmorris15",
      "count": 5,
      "uuid": 42654456
    },
    {
      "user": "rvlenth",
      "count": 4,
      "uuid": 26777519
    },
    {
      "user": "skaug",
      "count": 4,
      "uuid": 5491904
    },
    {
      "user": "dke-chan",
      "count": 3,
      "uuid": 24399605
    },
    {
      "user": "magronah",
      "count": 3,
      "uuid": 70163204
    },
    {
      "user": "copilot",
      "count": 3,
      "uuid": 198982749
    },
    {
      "user": "d-morrison",
      "count": 3,
      "uuid": 2474437
    },
    {
      "user": "seananderson",
      "count": 2,
      "uuid": 19349
    },
    {
      "user": "annahuynhly",
      "count": 2,
      "uuid": 97189987
    },
    {
      "user": "arni-magnusson",
      "count": 1,
      "uuid": 3720910
    },
    {
      "user": "bertvanderveen",
      "count": 1,
      "uuid": 19729157
    },
    {
      "user": "amoeba",
      "count": 1,
      "uuid": 563
    },
    {
      "user": "casperwberg",
      "count": 1,
      "uuid": 5446499
    },
    {
      "user": "gavinsimpson",
      "count": 1,
      "uuid": 514696
    },
    {
      "user": "henrikbengtsson",
      "count": 1,
      "uuid": 1616850
    },
    {
      "user": "raffaelemancuso",
      "count": 1,
      "uuid": 54762742
    }
  ],
  "_userbio": {
    "uuid": 13640228,
    "type": "organization",
    "name": "glmmTMB"
  },
  "_downloads": {
    "count": 55611,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/glmmTMB"
  },
  "_mentions": 373,
  "_devurl": "https://github.com/glmmtmb/glmmtmb",
  "_searchresults": 7504,
  "_topics": [
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/glmmTMB.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/glmmtmb/glmmtmb",
  "_realowner": "glmmtmb",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.1",
      "date": "2017-02-20"
    },
    {
      "version": "0.1.4",
      "date": "2017-10-26"
    },
    {
      "version": "0.2.0",
      "date": "2017-12-11"
    },
    {
      "version": "0.2.1.0",
      "date": "2018-05-10"
    },
    {
      "version": "0.2.2.0",
      "date": "2018-07-03"
    },
    {
      "version": "0.2.3",
      "date": "2019-01-11"
    },
    {
      "version": "1.0.0",
      "date": "2020-02-03"
    },
    {
      "version": "1.0.1",
      "date": "2020-03-15"
    },
    {
      "version": "1.0.2.1",
      "date": "2020-07-02"
    },
    {
      "version": "1.1.1",
      "date": "2021-06-24"
    },
    {
      "version": "1.1.2",
      "date": "2021-07-20"
    },
    {
      "version": "1.1.2.2",
      "date": "2021-09-02"
    },
    {
      "version": "1.1.2.3",
      "date": "2021-09-20"
    },
    {
      "version": "1.1.3",
      "date": "2022-03-14"
    },
    {
      "version": "1.1.4",
      "date": "2022-07-12"
    },
    {
      "version": "1.1.5",
      "date": "2022-11-16"
    },
    {
      "version": "1.1.6",
      "date": "2023-03-19"
    },
    {
      "version": "1.1.7",
      "date": "2023-04-05"
    },
    {
      "version": "1.1.8",
      "date": "2023-10-07"
    },
    {
      "version": "1.1.9",
      "date": "2024-03-20"
    },
    {
      "version": "1.1.10",
      "date": "2024-09-26"
    },
    {
      "version": "1.1.11",
      "date": "2025-04-02"
    },
    {
      "version": "1.1.12",
      "date": "2025-08-18"
    },
    {
      "version": "1.1.13",
      "date": "2025-10-09"
    },
    {
      "version": "1.1.14",
      "date": "2026-01-15"
    }
  ],
  "_exports": [
    "bell",
    "beta_family",
    "betabinomial",
    "bread",
    "compois",
    "dbell",
    "dgenpois",
    "diagnose",
    "dof_KR",
    "dof_satt",
    "dtruncated_nbinom1",
    "dtruncated_nbinom2",
    "dtruncated_poisson",
    "estfun",
    "family_params",
    "finalizeTMB",
    "fitTMB",
    "fixef",
    "genpois",
    "get_cor",
    "getCapabilities",
    "getGroups",
    "getGrpVar",
    "getME",
    "getReStruc",
    "glmmTMB",
    "glmmTMBControl",
    "gt_load",
    "lognormal",
    "meatHC",
    "nbinom1",
    "nbinom12",
    "nbinom2",
    "numFactor",
    "omp_check",
    "ordbeta",
    "parseNumLevels",
    "pbell",
    "pgenpois",
    "put_cor",
    "ranef",
    "refit",
    "rgenpois",
    "sandwich",
    "set_simcodes",
    "sigma",
    "simulate_new",
    "skewnormal",
    "t_family",
    "truncated_compois",
    "truncated_genpois",
    "truncated_nbinom1",
    "truncated_nbinom2",
    "truncated_poisson",
    "tweedie",
    "up2date",
    "VarCorr",
    "vcovHC",
    "ziGamma"
  ],
  "_datasets": [
    {
      "name": "epil2",
      "title": "Seizure Counts for Epileptics - Extended",
      "object": "epil2",
      "class": [
        "data.frame"
      ],
      "fields": [
        "y",
        "trt",
        "base",
        "age",
        "V4",
        "subject",
        "period",
        "lbase",
        "lage",
        "Visit",
        "Base",
        "Age"
      ],
      "rows": 236,
      "table": true,
      "tojson": true
    },
    {
      "name": "Owls",
      "title": "Begging by Owl Nestlings",
      "object": "Owls",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Nest",
        "FoodTreatment",
        "SexParent",
        "ArrivalTime",
        "SiblingNegotiation",
        "BroodSize",
        "NegPerChick",
        "logBroodSize"
      ],
      "rows": 599,
      "table": true,
      "tojson": true
    },
    {
      "name": "Salamanders",
      "title": "Repeated counts of salamanders in streams",
      "object": "Salamanders",
      "class": [
        "data.frame"
      ],
      "fields": [
        "site",
        "mined",
        "cover",
        "sample",
        "DOP",
        "Wtemp",
        "DOY",
        "spp",
        "count"
      ],
      "rows": 644,
      "table": true,
      "tojson": true
    },
    {
      "name": "spider_long",
      "title": "Spider data from CANOCO, long format",
      "object": "spider_long",
      "class": [
        "data.frame"
      ],
      "fields": [
        "soil.dry",
        "bare.sand",
        "fallen.leaves",
        "moss",
        "herb.layer",
        "reflection",
        "id",
        "Species",
        "abund"
      ],
      "rows": 336,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "downstream_methods",
      "title": "Downstream methods",
      "topics": [
        "Anova.glmmTMB",
        "downstream_methods",
        "Effect.glmmTMB",
        "emmeans.glmmTMB"
      ]
    },
    {
      "page": "as.theta.vcov",
      "title": "Get theta parameterisation of a covariance structure",
      "topics": [
        "as.theta.vcov"
      ]
    },
    {
      "page": "bread.glmmTMB",
      "title": "Bread Matrix for Sandwich Estimator",
      "topics": [
        "bread",
        "bread.glmmTMB"
      ]
    },
    {
      "page": "confint.glmmTMB",
      "title": "Calculate confidence intervals",
      "topics": [
        "confint.glmmTMB"
      ]
    },
    {
      "page": "dbell",
      "title": "The Bell Distribution",
      "topics": [
        "dbell",
        "pbell"
      ]
    },
    {
      "page": "dgenpois",
      "title": "The Generalized Poisson Distribution",
      "topics": [
        "dgenpois",
        "pgenpois",
        "rgenpois"
      ]
    },
    {
      "page": "diagnose",
      "title": "diagnose model problems",
      "topics": [
        "diagnose"
      ]
    },
    {
      "page": "dof_KR",
      "title": "compute denominator degrees-of-freedom approximations",
      "topics": [
        "dof_KR",
        "dof_satt"
      ]
    },
    {
      "page": "dtruncated_nbinom2",
      "title": "truncated distributions",
      "topics": [
        "dtruncated_nbinom1",
        "dtruncated_nbinom2",
        "dtruncated_poisson"
      ]
    },
    {
      "page": "epil2",
      "title": "Seizure Counts for Epileptics - Extended",
      "topics": [
        "epil2"
      ]
    },
    {
      "page": "estfun.glmmTMB",
      "title": "Extract Empirical Estimating Functions",
      "topics": [
        "estfun",
        "estfun.glmmTMB"
      ]
    },
    {
      "page": "family_params",
      "title": "Retrieve family-specific parameters",
      "topics": [
        "family_params"
      ]
    },
    {
      "page": "fitTMB",
      "title": "Optimize TMB models and package results, modularly",
      "topics": [
        "finalizeTMB",
        "fitTMB"
      ]
    },
    {
      "page": "fixef",
      "title": "Extract fixed-effects estimates",
      "topics": [
        "fixef",
        "fixef.glmmTMB"
      ]
    },
    {
      "page": "formula.glmmTMB",
      "title": "Extract the formula of a glmmTMB object",
      "topics": [
        "formula.glmmTMB"
      ]
    },
    {
      "page": "get_autopar",
      "title": "retrieve current value of TMB autopar setting",
      "topics": [
        "get_autopar"
      ]
    },
    {
      "page": "get_cor",
      "title": "transform correlation parameters to and from glmmTMB parameterization",
      "topics": [
        "get_cor",
        "put_cor"
      ]
    },
    {
      "page": "getCapabilities",
      "title": "List model options that glmmTMB knows about",
      "topics": [
        "getCapabilities"
      ]
    },
    {
      "page": "getGroups.glmmTMB",
      "title": "Extract Grouping Factors from an Object",
      "topics": [
        "getGroups",
        "getGroups.glmmTMB"
      ]
    },
    {
      "page": "getME.glmmTMB",
      "title": "Extract or Get Generalize Components from a Fitted Mixed Effects Model",
      "topics": [
        "getME",
        "getME.glmmTMB"
      ]
    },
    {
      "page": "getReStruc",
      "title": "Calculate random effect structure Calculates number of random effects, number of parameters, block size and number of blocks.  Mostly for internal use.",
      "topics": [
        "getReStruc"
      ]
    },
    {
      "page": "getXReTrms",
      "title": "Create X and random effect terms from formula",
      "topics": [
        "getXReTrms"
      ]
    },
    {
      "page": "glmmTMB",
      "title": "Fit Models with TMB",
      "topics": [
        "glmmTMB"
      ]
    },
    {
      "page": "glmmTMBControl",
      "title": "Control parameters for glmmTMB optimization",
      "topics": [
        "glmmTMBControl"
      ]
    },
    {
      "page": "bootmer_methods",
      "title": "support methods for parametric bootstrapping",
      "topics": [
        "isLMM.glmmTMB",
        "refit.glmmTMB"
      ]
    },
    {
      "page": "map.theta.propto",
      "title": "Set map values for theta to be fixed (NA) for propto",
      "topics": [
        "map.theta.propto"
      ]
    },
    {
      "page": "meatHC",
      "title": "Simple Cluster Based Meat Matrix Estimator",
      "topics": [
        "meatHC",
        "meatHC.default",
        "meatHC.glmmTMB"
      ]
    },
    {
      "page": "nbinom2",
      "title": "Family functions for glmmTMB",
      "topics": [
        "bell",
        "betabinomial",
        "beta_family",
        "compois",
        "family_glmmTMB",
        "genpois",
        "lognormal",
        "nbinom1",
        "nbinom12",
        "nbinom2",
        "ordbeta",
        "skewnormal",
        "truncated_compois",
        "truncated_genpois",
        "truncated_nbinom1",
        "truncated_nbinom2",
        "truncated_poisson",
        "tweedie",
        "t_family",
        "ziGamma"
      ]
    },
    {
      "page": "numFactor",
      "title": "Factor with numeric interpretable levels.",
      "topics": [
        "numFactor",
        "parseNumLevels"
      ]
    },
    {
      "page": "omp_check",
      "title": "Check OpenMP status",
      "topics": [
        "omp_check",
        "openmp"
      ]
    },
    {
      "page": "Owls",
      "title": "Begging by Owl Nestlings",
      "topics": [
        "OwlModel",
        "OwlModel_nb1_bs",
        "OwlModel_nb1_bs_mcmc",
        "Owls"
      ]
    },
    {
      "page": "predict.glmmTMB",
      "title": "prediction",
      "topics": [
        "predict.glmmTMB"
      ]
    },
    {
      "page": "print.VarCorr.glmmTMB",
      "title": "Printing The Variance and Correlation Parameters of a 'glmmTMB'",
      "topics": [
        "print.VarCorr.glmmTMB"
      ]
    },
    {
      "page": "priors",
      "title": "use of priors in glmmTMB",
      "topics": [
        "priors"
      ]
    },
    {
      "page": "profile.glmmTMB",
      "title": "Compute likelihood profiles for a fitted model",
      "topics": [
        "confint.profile.glmmTMB",
        "profile.glmmTMB"
      ]
    },
    {
      "page": "ranef.glmmTMB",
      "title": "Extract Random Effects",
      "topics": [
        "as.data.frame.ranef.glmmTMB",
        "coef.glmmTMB",
        "ranef",
        "ranef.glmmTMB"
      ]
    },
    {
      "page": "reinstalling",
      "title": "Reinstalling binary dependencies",
      "topics": [
        "reinstalling"
      ]
    },
    {
      "page": "residuals.glmmTMB",
      "title": "Compute residuals for a glmmTMB object",
      "topics": [
        "deviance.glmmTMB",
        "residuals.glmmTMB"
      ]
    },
    {
      "page": "Salamanders",
      "title": "Repeated counts of salamanders in streams",
      "topics": [
        "Salamanders"
      ]
    },
    {
      "page": "sandwich",
      "title": "Sandwich Estimator based on Bread and Meat Matrices",
      "topics": [
        "sandwich",
        "sandwich.default",
        "sandwich.glmmTMB"
      ]
    },
    {
      "page": "set_simcodes",
      "title": "helper function to modify simulation settings for random effects",
      "topics": [
        "set_simcodes"
      ]
    },
    {
      "page": "sigma.glmmTMB",
      "title": "Extract residual standard deviation or dispersion parameter",
      "topics": [
        "sigma",
        "sigma.glmmTMB"
      ]
    },
    {
      "page": "simulate_new",
      "title": "Simulate from covariate/metadata in the absence of a real data set (EXPERIMENTAL)",
      "topics": [
        "simulate_new"
      ]
    },
    {
      "page": "simulate.glmmTMB",
      "title": "Simulate from a glmmTMB fitted model",
      "topics": [
        "simulate.glmmTMB"
      ]
    },
    {
      "page": "spider_long",
      "title": "Spider data from CANOCO, long format",
      "topics": [
        "spider_long"
      ]
    },
    {
      "page": "summary.glmmTMB",
      "title": "summary for glmmTMB fits",
      "topics": [
        "summary.glmmTMB"
      ]
    },
    {
      "page": "glmmTMB_methods",
      "title": "Methods for extracting developer-level information from 'glmmTMB' models",
      "topics": [
        "model.matrix.glmmTMB",
        "terms.glmmTMB"
      ]
    },
    {
      "page": "gt_load",
      "title": "conditionally update glmmTMB object fitted with an old TMB version",
      "topics": [
        "gt_load",
        "up2date"
      ]
    },
    {
      "page": "vcov.glmmTMB",
      "title": "Calculate Variance-Covariance Matrix for a Fitted glmmTMB model",
      "topics": [
        "vcov.glmmTMB"
      ]
    },
    {
      "page": "vcovHC.glmmTMB",
      "title": "Cluster Robust Variance-Covariance Matrix Estimator",
      "topics": [
        "vcovHC",
        "vcovHC.glmmTMB"
      ]
    },
    {
      "page": "weights.glmmTMB",
      "title": "Extract weights from a glmmTMB object",
      "topics": [
        "weights.glmmTMB"
      ]
    }
  ],
  "_readme": "https://github.com/glmmtmb/glmmtmb/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "boot",
    "broom",
    "cli",
    "colorspace",
    "cowplot",
    "cpp11",
    "Deriv",
    "doBy",
    "dplyr",
    "farver",
    "forecast",
    "fracdiff",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "S7",
    "sandwich",
    "scales",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "TMB",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_sysdeps": [
    {
      "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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "glmmTMB.Rnw",
      "filename": "glmmTMB.pdf",
      "title": "basic examples of glmmTMB usage",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2015-12-01 10:55:42",
      "modified": "2026-01-14 11:58:00",
      "commits": 19
    },
    {
      "source": "covstruct.rmd",
      "filename": "covstruct.html",
      "title": "Covariance structures with glmmTMB",
      "author": "Kasper Kristensen, Maeve McGillycuddy, and Coralie Williams",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "The AR(1) covariance structure",
        "Demonstration on simulated data",
        "Increasing the sample size",
        "The unstructured covariance",
        "The Toeplitz structure",
        "Compound symmetry",
        "Anova tables",
        "Adding coordinate information",
        "Ornstein–Uhlenbeck",
        "Spatial correlations",
        "Matérn",
        "Gaussian",
        "Exponential",
        "A spatial covariance example",
        "Mappings",
        "Unstructured",
        "Generalized latent variable model",
        "Reduced-rank",
        "Proportional",
        "Equal",
        "Construction of structured covariance matrices",
        "References"
      ],
      "created": "2016-12-02 14:38:58",
      "modified": "2026-01-08 14:34:57",
      "commits": 47
    },
    {
      "source": "hacking.rmd",
      "filename": "hacking.html",
      "title": "Hacking glmmTMB",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Adding a family",
        "C++",
        "modify glmmTMB.cpp",
        "R code",
        "modifying family.R",
        "modifying glmmTMB.R",
        "updating NAMESPACE",
        "updating enum.R",
        "Finishing up",
        "Reinstall",
        "Test",
        "Additional distributional parameters",
        "Adding a covariance structure",
        "C++ code",
        "Structure of a glmmTMB object"
      ],
      "created": "2022-10-24 12:40:05",
      "modified": "2023-07-19 16:42:14",
      "commits": 6
    },
    {
      "source": "miscEx.rmd",
      "filename": "miscEx.html",
      "title": "Miscellaneous examples",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Beta dispersion model"
      ],
      "created": "2017-05-03 11:23:26",
      "modified": "2021-01-03 14:48:01",
      "commits": 4
    },
    {
      "source": "model_evaluation.Rnw",
      "filename": "model_evaluation.pdf",
      "title": "Model evaluation",
      "engine": "knitr::knitr",
      "headings": [],
      "created": "2019-06-18 13:14:17",
      "modified": "2025-08-14 13:42:32",
      "commits": 20
    },
    {
      "source": "parallel.rmd",
      "filename": "parallel.html",
      "title": "Parallel optimization using glmmTMB",
      "author": "Nafis Sadat",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Notes on OpenMP support",
        "System information"
      ],
      "created": "2019-06-18 13:14:17",
      "modified": "2022-10-24 12:40:05",
      "commits": 3
    },
    {
      "source": "mcmc.rmd",
      "filename": "mcmc.html",
      "title": "Post-hoc MCMC with glmmTMB",
      "author": "Ben Bolker and Mollie Brooks",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup",
        "Salamander example",
        "Metropolis-Hastings (DIY)",
        "tmbstan",
        "Sleep study example"
      ],
      "created": "2016-10-19 22:30:48",
      "modified": "2025-04-02 13:05:01",
      "commits": 16
    },
    {
      "source": "priors.rmd",
      "filename": "priors.html",
      "title": "Priors in glmmTMB",
      "author": "Ben Bolker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Motivation",
        "Load packages",
        "Culcita example: near-complete separation",
        "Gopher tortoise example: mitigate singular fit",
        "Zero-inflation",
        "TO DO/FIX ME",
        "Development issues",
        "References"
      ],
      "created": "2024-03-17 14:57:04",
      "modified": "2026-06-01 16:24:46",
      "commits": 4
    },
    {
      "source": "sim.rmd",
      "filename": "sim.html",
      "title": "Simulate from a fitted glmmTMB model or a formula",
      "author": "Mollie Brooks and Ben Bolker",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulating from a fitted model",
        "Simulating from scratch (de novo)",
        "example 1: linear regression",
        "example 2: random effects (including correlations)",
        "example 3: AR1 model",
        "FIXME/TO DO"
      ],
      "created": "2016-11-22 20:37:48",
      "modified": "2024-06-20 12:02:37",
      "commits": 7
    },
    {
      "source": "troubleshooting.rmd",
      "filename": "troubleshooting.html",
      "title": "Troubleshooting with glmmTMB",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Warnings",
        "Model convergence problem; non-positive-definite Hessian matrix; NA values for likelihood/AIC/etc.",
        "Example 1.",
        "Example 2.",
        "Example 3.",
        "Model convergence problem:  eigenvalue problems",
        "NA/NaN function evaluation",
        "false convergence",
        "Errors",
        "NA/NaN gradient evaluation",
        "gradient length"
      ],
      "created": "2017-02-16 13:34:36",
      "modified": "2025-07-07 11:28:42",
      "commits": 15
    }
  ],
  "_score": 17.64992683620363,
  "_indexed": true,
  "_nocasepkg": "glmmtmb",
  "_universes": [
    "glmmtmb",
    "mebrooks"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.15",
      "date": "2026-06-02T15:09:31.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "cb4683570285a7328c73ba9e31bd3b735c277f88a2af3424f8e67a377bd7312a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.15",
      "date": "2026-06-02T15:08:48.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "e81475f08a2fd8c5239fe5efcf26ace25388398f75819fa220f782a0fa8ff3b2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.15",
      "date": "2026-06-02T15:09:06.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "ee86fe39be98237f2a0163d6cf53d0829f55bc4a801c4b1e80e36f18bed27636",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.15",
      "date": "2026-06-02T15:08:47.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "8ea31dad1ebf06189579c7f77c304203bce862169b4a350534ba47c7a700ab3b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.15",
      "date": "2026-06-02T15:11:37.000Z",
      "arch": "aarch64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "a7c3bb0bcf14556a06411c56a9a9066c55160ce0469286cb0afa59c9a9284313",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.15",
      "date": "2026-06-02T15:13:42.000Z",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "8e7666a9439b2065b2c3828ea0570345a3b08edcd5d3f41a977494742cbcf187",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.15",
      "date": "2026-06-02T15:09:37.000Z",
      "arch": "aarch64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "f3e39d655cc58da12ff86ae976bc0c90a799ec686a5b9dd3b820730df9400d4b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.15",
      "date": "2026-06-02T15:11:13.000Z",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "6517b661b0d741a076a1f9b62eb7228f41ce1017de525f9344368824ed7a23e2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.15",
      "date": "2026-06-02T15:08:33.000Z",
      "arch": "emscripten",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "8b64c037a27fb19fd5abc20f51734ad5b334c0cb96b8a706c206a938885f7ffc",
      "status": "success",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.15",
      "date": "2026-06-02T15:08:09.000Z",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "27a57416a301c4b0d7fa61a790022e2b54dd130642a9246f9222eba22f4941e6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.15",
      "date": "2026-06-02T15:07:41.000Z",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "59b2db870010290def910b7831cda54a1ee21eb1a4c95dcb8ae6c22afdcacd3c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.15",
      "date": "2026-06-02T15:07:32.000Z",
      "arch": "x86_64",
      "commit": "a43566b9e03e90b9350a5181ea97b20f7aa28ea2",
      "fileid": "b3d4dfca114c85ac3c1d30658edf4eb12bee1aaa9981ed7ec82cb2f599101633",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/glmmtmb/actions/runs/26828207963"
    }
  ]
}