{
  "_id": "6a168848acfb0bcc41d75fbb",
  "Package": "DAMOCLES",
  "Type": "Package",
  "Title": "Dynamic Assembly Model of Colonization, Local Extinction and\nSpeciation",
  "Version": "3.1",
  "Date": "2024-11-26",
  "Author": "Rampal S. Etienne & Alex L. Pigot",
  "Maintainer": "Rampal S. Etienne <r.s.etienne@rug.nl>",
  "License": "GPL-2",
  "Description": "Simulates and computes (maximum) likelihood of a dynamical\nmodel of community assembly that takes into account\nphylogenetic history.",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "URL": "https://rsetienne.github.io/DAMOCLES/",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2025-08-29 13:02:49 UTC",
  "RemoteUrl": "https://github.com/rsetienne/DAMOCLES",
  "RemoteRef": "HEAD",
  "RemoteSha": "c709c593b911127682ca506056fdecfe9a62bf43",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-26 07:46:31 UTC",
    "User": "root"
  },
  "MD5sum": "ceb1c7af8b3577c4a9d517b777588b34",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "DAMOCLES_3.1.tar.gz",
  "_fileid": "1e7160cf75323e975d64775c97d161a169eca74875c308c9188179678e6e16f6",
  "_filesize": 169375,
  "_sha256": "1e7160cf75323e975d64775c97d161a169eca74875c308c9188179678e6e16f6",
  "_created": "2026-05-26T07:46:31.000Z",
  "_published": "2026-05-27T05:59:36.118Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78016532949,
      "time": 225,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211620728"
    },
    {
      "job": 78016532985,
      "time": 220,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211619015"
    },
    {
      "job": 78016532955,
      "time": 199,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211613005"
    },
    {
      "job": 78016533036,
      "time": 207,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211615227"
    },
    {
      "job": 78016532995,
      "time": 120,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7211589910"
    },
    {
      "job": 78016533084,
      "time": 272,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7211635148"
    },
    {
      "job": 78016532881,
      "time": 130,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211593200"
    },
    {
      "job": 78016532948,
      "time": 443,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211686573"
    },
    {
      "job": 78016532586,
      "time": 219,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211553890"
    },
    {
      "job": 78016533024,
      "time": 161,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211601535"
    },
    {
      "job": 78016532814,
      "time": 190,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211610418"
    },
    {
      "job": 78016532750,
      "time": 197,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7232998994"
    },
    {
      "job": 78016532946,
      "time": 178,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211607777"
    }
  ],
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/rsetienne/DAMOCLES",
  "_commit": {
    "id": "c709c593b911127682ca506056fdecfe9a62bf43",
    "author": "Rampal S. Etienne <rampaletienne@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #12 from rsetienne/fix/wrong-link\n\nDAISIE -> DAMOCLES",
    "time": 1756472569
  },
  "_maintainer": {
    "name": "Rampal S. Etienne",
    "email": "r.s.etienne@rug.nl",
    "login": "rsetienne",
    "description": "",
    "uuid": 14234521
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.2",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.10",
      "role": "LinkingTo"
    },
    {
      "package": "RcppEigen",
      "role": "LinkingTo"
    },
    {
      "package": "BH",
      "version": ">= 1.81.0-1",
      "role": "LinkingTo"
    },
    {
      "package": "caper",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "deSolve",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "expm",
      "role": "Imports"
    },
    {
      "package": "picante",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "DDD",
      "version": ">= 3.4",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    }
  ],
  "_owner": "rsetienne",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-35",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "rsetienne",
      "count": 37,
      "uuid": 14234521
    },
    {
      "user": "neves-p",
      "count": 12,
      "uuid": 10762799
    },
    {
      "user": "thijsjanzen",
      "count": 1,
      "uuid": 19486664
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic"
  },
  "_downloads": {
    "count": 255,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DAMOCLES"
  },
  "_mentions": 39,
  "_devurl": "https://github.com/rsetienne/damocles",
  "_pkgdown": "https://rsetienne.github.io/DAMOCLES/",
  "_searchresults": 11,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/DAMOCLES.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rsetienne/damocles",
  "_realowner": "rsetienne",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2014-10-29"
    },
    {
      "version": "1.1",
      "date": "2015-03-05"
    },
    {
      "version": "2.2",
      "date": "2020-01-22"
    },
    {
      "version": "2.3",
      "date": "2020-08-12"
    }
  ],
  "_exports": [
    "DAMOCLES_bootstrap",
    "DAMOCLES_loglik",
    "DAMOCLES_ML",
    "DAMOCLES_sim",
    "HERACLES_ImportanceSampling"
  ],
  "_datasets": [
    {
      "name": "NWPrimates_data",
      "title": "Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu",
      "object": "NWPrimates_data",
      "file": "NWPrimates_data.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "DAMOCLES_bootstrap",
      "title": "Phylogenetic community structure hypothesis test",
      "topics": [
        "DAMOCLES_bootstrap"
      ]
    },
    {
      "page": "DAMOCLES_loglik",
      "title": "Likelihood for DAMOCLES model",
      "topics": [
        "DAMOCLES_loglik"
      ]
    },
    {
      "page": "DAMOCLES_ML",
      "title": "Maximization of the loglikelihood under the DAMOCLES model",
      "topics": [
        "DAMOCLES_ML"
      ]
    },
    {
      "page": "DAMOCLES_sim",
      "title": "Simulating DAMOCLES",
      "topics": [
        "DAMOCLES_sim"
      ]
    },
    {
      "page": "HERACLES_ImportanceSampling",
      "title": "Importance Sampling from the HERACLES model",
      "topics": [
        "HERACLES_ImportanceSampling"
      ]
    },
    {
      "page": "NWPrimates_data",
      "title": "Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu",
      "topics": [
        "NWPrimates_data"
      ]
    }
  ],
  "_readme": "https://github.com/rsetienne/DAMOCLES/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "backports",
    "base64enc",
    "BH",
    "bslib",
    "cachem",
    "caper",
    "checkmate",
    "cli",
    "cluster",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "data.table",
    "DDD",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "evaluate",
    "expm",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "mvtnorm",
    "nlme",
    "nnet",
    "numDeriv",
    "optimParallel",
    "osqp",
    "parallelly",
    "permute",
    "phangorn",
    "phytools",
    "picante",
    "pkgconfig",
    "progressr",
    "pso",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "rlang",
    "rmarkdown",
    "rpart",
    "rstudioapi",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "SparseM",
    "stringi",
    "stringr",
    "subplex",
    "tinytex",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_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"
    }
  ],
  "_score": 4.041392685158225,
  "_indexed": false,
  "_nocasepkg": "damocles",
  "_universes": [
    "phylotastic"
  ],
  "_indexurl": "https://rsetienne.r-universe.dev/DAMOCLES",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-05-26T07:49:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "c8609a8d5fe1ed31956834bf01b3abfb994100889dca000d3beee5ef46dc403f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-05-26T07:49:16.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "303e6dd9436e6f0b3befda973c62dceff3f8cafea1c27c56e36f19fc471163ef",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-05-26T07:49:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "464dbcf628dd4155cc9d7d84e089e454c6c8b8b027a9d6c4774955d31281c5e4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-05-26T07:49:15.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "c02702c0bdaba6608b47c237d7cc12b9bc2408e0ff4f0209f3f2a35048738323",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1",
      "date": "2026-05-26T07:48:07.000Z",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "3c20fc0487e03e07fbdf2998b96f6d2ffa41f526d5154228d1c9c4925b35f225",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1",
      "date": "2026-05-26T07:49:44.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "c5dc283ab1ca5a78df41f2d7e6c201947c097c07d47854748a3139803208ec9f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.1",
      "date": "2026-05-26T07:48:21.000Z",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "56b66908d17d6260eda55f40051d1896e75153c8dee880b3992fa98c063f47fc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "3.1",
      "date": "2026-05-26T07:51:22.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "04bbdb7cf5cfbbdb213745abe2b954851660cc36c427e6a49c7fb4d7bb60d90f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.1",
      "date": "2026-05-26T07:49:27.000Z",
      "arch": "emscripten",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "d1717ef7dbce27c3f4957f981a00733c8db2d197f3a3eb10a6917193ac4598be",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.1",
      "date": "2026-05-26T07:48:17.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "b8e3e3dda071ab04d1d2e91d5a3ce758b89e0975814555ae5f6920c5a46ec033",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.1",
      "date": "2026-05-27T05:57:44.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "d43d39d1a5e6b6383b9057cf61e998eeac3bef577dd50b55eb9f881d06c6b9bb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "3.1",
      "date": "2026-05-26T07:48:21.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "7cf5aa6637f9cbe0570ef5ffdc68edd41932cbf4ff4eb36547c424adfccc8b71",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/26439237540"
    }
  ]
}