{
  "_id": "6abb8eb199f7aa8c6aa46017",
  "Package": "bGMYC4",
  "Type": "Package",
  "Title": "Bayesian General Mixed Yule-Coalescent Model for Species\nDelimitation",
  "Version": "4.1.6",
  "Authors@R": "c(\nperson(\"Noah\", \"Reid\", email = \"noah.reid@gmail.com\",\nrole = c(\"aut\", \"cph\"), comment = \"Original author of bGMYC\"),\nperson(\"Dmitry\", \"Karabanov\", email = \"dk@ibiw.ru\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6008-7441\"))\n)",
  "Description": "Implements a Bayesian version of the general mixed\nYule-coalescent model for species delimitation. It uses Markov\nChain Monte Carlo simulation to evaluate the posterior\ndistribution of the model and supports flexible prior\nspecification on model parameters.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr, rmarkdown",
  "URL": "https://github.com/DmitryKarabanov/bGMYC4",
  "BugReports": "https://github.com/DmitryKarabanov/bGMYC4/issues",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "8.0.0",
  "Repository": "https://dmitrykarabanov.r-universe.dev",
  "Date/Publication": "2026-09-29 04:59:28 UTC",
  "RemoteUrl": "https://github.com/dmitrykarabanov/bgmyc4",
  "RemoteRef": "HEAD",
  "RemoteSha": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-29 09:17:03 UTC",
    "User": "root"
  },
  "Author": "Noah Reid [aut, cph] (Original author of bGMYC),\nDmitry Karabanov [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6008-7441>)",
  "Maintainer": "Dmitry Karabanov <dk@ibiw.ru>",
  "_user": "dmitrykarabanov",
  "_type": "src",
  "_file": "bGMYC4_4.1.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/08d5533bddbabdd58c23e0f886a49667ac4ea5eed1e2d7cd97504428e52dd27b",
  "_filesize": 306471,
  "_sha256": "08d5533bddbabdd58c23e0f886a49667ac4ea5eed1e2d7cd97504428e52dd27b",
  "_expires": "2027-01-07T10:10:55.000Z",
  "_created": "2026-09-29T09:17:03.000Z",
  "_published": "2026-09-29T10:10:57.475Z",
  "_jobs": [
    {
      "job": 109339566915,
      "time": 160,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11023900762"
    },
    {
      "job": 109339566924,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11023601885"
    },
    {
      "job": 109339566891,
      "time": 231,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11025956304"
    },
    {
      "job": 109339566850,
      "time": 166,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11024574533"
    },
    {
      "job": 109338294556,
      "time": 212,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11023436703"
    },
    {
      "job": 109339566877,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11023721498"
    },
    {
      "job": 109339567181,
      "time": 96,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11023750703"
    },
    {
      "job": 109339567041,
      "time": 95,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11022939666"
    },
    {
      "job": 109339567058,
      "time": 77,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11023222840"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106",
  "_status": "success",
  "_upstream": "https://github.com/dmitrykarabanov/bgmyc4",
  "_commit": {
    "id": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
    "author": "Dmitry Karabanov <dkarabanow@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update LICENSE",
    "time": 1790657968
  },
  "_maintainer": {
    "name": "Dmitry Karabanov",
    "email": "dk@ibiw.ru",
    "orcid": "0000-0001-6008-7441"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.0",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "mcmcse",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "base64enc",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "htmltools",
      "role": "Suggests"
    },
    {
      "package": "htmlwidgets",
      "role": "Suggests"
    },
    {
      "package": "treeio",
      "role": "Suggests"
    },
    {
      "package": "ggtree",
      "role": "Suggests"
    },
    {
      "package": "dplyr",
      "role": "Suggests"
    }
  ],
  "_owner": "dmitrykarabanov",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-19",
      "n": 34
    },
    {
      "week": "2026-20",
      "n": 6
    },
    {
      "week": "2026-22",
      "n": 8
    },
    {
      "week": "2026-23",
      "n": 17
    },
    {
      "week": "2026-30",
      "n": 10
    },
    {
      "week": "2026-31",
      "n": 6
    },
    {
      "week": "2026-32",
      "n": 3
    },
    {
      "week": "2026-35",
      "n": 2
    },
    {
      "week": "2026-37",
      "n": 3
    },
    {
      "week": "2026-38",
      "n": 1
    },
    {
      "week": "2026-40",
      "n": 4
    }
  ],
  "_tags": [
    {
      "name": "bGMYC",
      "date": "2026-05-06"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "dmitrykarabanov",
      "count": 94,
      "uuid": 233921671
    }
  ],
  "_userbio": {
    "uuid": 233921671,
    "type": "user",
    "name": "Dmitry Karabanov",
    "followers": 0,
    "description": "Biologist."
  },
  "_downloads": {
    "count": 377,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bGMYC4"
  },
  "_devurl": "https://github.com/dmitrykarabanov/bgmyc4",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/bGMYC4.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/dmitrykarabanov/bgmyc4",
  "_realowner": "dmitrykarabanov",
  "_cranurl": true,
  "_releases": [
    {
      "version": "4.1.6",
      "date": "2026-09-08"
    }
  ],
  "_exports": [
    "bgmyc.dataprep",
    "bgmyc.gibbs",
    "bgmyc.lik",
    "bgmyc.multiphylo",
    "bgmyc.point",
    "bgmyc.prior",
    "bgmyc.singlephy",
    "bgmyc.spec",
    "checkrates",
    "plot.bgmycprobmat",
    "plot.bgmycrates",
    "plot.interactive.probmat",
    "plot.multibgmyc",
    "plot.singlebgmyc",
    "spec.probmat"
  ],
  "_datasets": [
    {
      "name": "east10",
      "title": "10 trees sampled from a posterior distribution. based on simulated data.",
      "object": "east10",
      "class": [
        "multiPhylo"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "bGMYC-package",
      "title": "A Bayesian MCMC implementation of the general mixed Yule-coalescent model for species delimitation.",
      "topics": [
        "bGMYC"
      ]
    },
    {
      "page": "bgmyc.dataprep",
      "title": "Prepares a tree for analysis.",
      "topics": [
        "bgmyc.dataprep"
      ]
    },
    {
      "page": "bgmyc.gibbs",
      "title": "MCMC sampler",
      "topics": [
        "bgmyc.gibbs"
      ]
    },
    {
      "page": "bgmyc.lik",
      "title": "GMYC likelihood function",
      "topics": [
        "bgmyc.lik"
      ]
    },
    {
      "page": "bgmyc.multiphylo",
      "title": "Multi-tree GMYC analysis",
      "topics": [
        "bgmyc.multiphylo"
      ]
    },
    {
      "page": "bgmyc.point",
      "title": "Returns a point estimate of species limits based on a posterior probability threshold input by the user.",
      "topics": [
        "bgmyc.point"
      ]
    },
    {
      "page": "bgmyc.prior",
      "title": "a function to return the prior probability of a model.",
      "topics": [
        "bgmyc.prior"
      ]
    },
    {
      "page": "bgmyc.singlephy",
      "title": "Single tree GMYC analysis.",
      "topics": [
        "bgmyc.singlephy"
      ]
    },
    {
      "page": "bgmyc.spec",
      "title": "bGMYC output processing.",
      "topics": [
        "bgmyc.spec"
      ]
    },
    {
      "page": "checkrates",
      "title": "bGMYC output processing.",
      "topics": [
        "checkrates"
      ]
    },
    {
      "page": "east10",
      "title": "10 trees sampled from a posterior distribution. based on simulated data.",
      "topics": [
        "east10"
      ]
    },
    {
      "page": "gmyc.5parameter.lik",
      "title": "5 parameter likelihood function.",
      "topics": [
        "gmyc.5parameter.lik"
      ]
    },
    {
      "page": "plot.bgmycprobmat",
      "title": "Plots the matrix of probability of conspecificity.",
      "topics": [
        "plot.bgmycprobmat"
      ]
    },
    {
      "page": "plot.bgmycrates",
      "title": "Plots relative coalescent and Yule rates for model fit evaluation.",
      "topics": [
        "plot.bgmycrates"
      ]
    },
    {
      "page": "plot.interactive.probmat",
      "title": "Interactive Probability Matrix Plot for bGMYC Results",
      "topics": [
        "plot.interactive.probmat"
      ]
    },
    {
      "page": "plot.multibgmyc",
      "title": "Plot MCMC output.",
      "topics": [
        "plot.multibgmyc"
      ]
    },
    {
      "page": "plot.singlebgmyc",
      "title": "Plot MCMC output.",
      "topics": [
        "plot.singlebgmyc"
      ]
    },
    {
      "page": "spec.probmat",
      "title": "Return matrix of probability of conspecificity.",
      "topics": [
        "spec.probmat"
      ]
    }
  ],
  "_pkglogo": "https://github.com/dmitrykarabanov/bgmyc4/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/dmitrykarabanov/bgmyc4/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "codetools",
    "digest",
    "future",
    "future.apply",
    "globals",
    "lattice",
    "listenv",
    "nlme",
    "parallelly",
    "Rcpp"
  ],
  "_vignettes": [
    {
      "source": "bGMYC4-interactive.Rmd",
      "filename": "bGMYC4-interactive.html",
      "title": "bGMYC4 Interactive Workflow",
      "author": "Dmitry Karabanov & Qwen",
      "engine": "knitr::rmarkdown",
      "headings": [
        "🌍 Introduction / Введение",
        "EN: This vignette documents the complete interactive workflow for Bayesian species delimitation using bGMYC4. It guides you through data selection, tree preprocessing (BEAST2 annotations), interactive MCMC diagnostics with parameter auto-tuning, multi-tree uncertainty pooling via parallel computing, and custom interactive visualization.RU: Эта виньетка описывает полный интерактивный рабочий процесс байесовской делимитации видов с помощью bGMYC4. Она проведёт вас через выбор данных, предобработку деревьев (аннотации BEAST2), интерактивную диагностику MCMC с автонастройкой параметров, усреднение филогенетической неопределённости через параллельные вычисления и кастомную интерактивную визуализацию.",
        "1. Setup & Helper Functions / Настройка окружения и вспомогательные функции",
        "2. Data Selection & Tree Preprocessing / Выбор данных и предобработка деревьев",
        "3. Interactive Diagnostics & Parameter Tuning / Интерактивная диагностика и настройка",
        "4. Multi-Tree Analysis / Многодеревный анализ",
        "5. Custom Interactive Visualization / Кастомная визуализация (Plotly)",
        "6. Delimitation & Export / Делимитация и экспорт",
        "⚡ Performance & Export / Производительность и экспорт",
        "EN: bgmyc.multiphylo() automatically parallelizes across physical CPU cores. To limit cores (e.g., to 6), run before analysis: options(mc.cores = 6).RU: bgmyc.multiphylo() автоматически использует все физические ядра. Чтобы ограничить число ядер (например, до 6), выполните перед запуском: options(mc.cores = 6).",
        "📊 Parameter Reference Guide / Справочник по параметрам",
        "🔍 Convergence Diagnostics Guide / Руководство по диагностике сходимости",
        "📎 Notes for CRAN & Local Use / Примечания для CRAN и локального запуска"
      ],
      "created": "2026-05-06 07:25:55",
      "modified": "2026-07-27 13:36:56",
      "commits": 9
    },
    {
      "source": "index.Rmd",
      "filename": "index.html",
      "title": "bGMYC4: Package Overview",
      "author": "Dmitry Karabanov",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Main functions",
        "Vignettes",
        "References"
      ],
      "created": "2026-07-27 07:55:46",
      "modified": "2026-07-27 08:16:50",
      "commits": 3
    }
  ],
  "_score": 5.041392685158225,
  "_indexed": true,
  "_nocasepkg": "bgmyc4",
  "_universes": [
    "dmitrykarabanov"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.1.6",
      "date": "2026-09-29T09:19:35.000Z",
      "distro": "resolute",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/6a5177aeb112ddf12576261673707480a27da322b9808b2a5bb7ccfd54d04765",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "4.1.6",
      "date": "2026-09-29T09:19:24.000Z",
      "distro": "resolute",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/b50f8e23e995967de5c2a014e6bdbf9b43eb5c349843c84f649450f7bc3bc047",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "4.1.6",
      "date": "2026-09-29T10:09:34.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/fcbd133a07eb682c6fc409c392e65014e4d05297658c8cfe787d82d0f6cba0c7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "4.1.6",
      "date": "2026-09-29T10:06:09.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/213d92521fbb971e4cc27e713b4185d7c0d797aeffd9bd889de25e5c8ff64764",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.1.6",
      "date": "2026-09-29T09:19:37.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/d76a314acd7ea07bd8044868ee61d6103643163dbb2fdd7d62ba058f536661fd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "4.1.6",
      "date": "2026-09-29T09:18:23.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/21300c4c35f592f0d0eea017e8b2ecc7aac451e048735d49c613fa69b0d770fc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "4.1.6",
      "date": "2026-09-29T09:18:28.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/0b28c0d45484898720746f64673d8abc82e22057a6b2d12e031e34e396b23a84",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "4.1.6",
      "date": "2026-09-29T09:18:08.000Z",
      "commit": "cc6a240a1af4d527611c49fc157a40e02e1b3d06",
      "fileid": "https://r2.ropensci.org/4608dc6b8caa686d0f146e77e36dfba6c6534f04a629c89948ec6eb20adc72d4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/dmitrykarabanov/actions/runs/36547751106"
    }
  ]
}