{
  "_id": "6a47959d2f27a93436c0e43b",
  "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://rsetienne.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": "2026-07-03 05:34:12 UTC",
    "User": "root"
  },
  "_user": "rsetienne",
  "_type": "src",
  "_file": "DAMOCLES_3.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/ed775f94756872608736387a6f1652b78bfca4133a70b291849ae4ba018609c9",
  "_filesize": 170891,
  "_sha256": "ed775f94756872608736387a6f1652b78bfca4133a70b291849ae4ba018609c9",
  "_expires": "2026-10-11T10:57:32.000Z",
  "_created": "2026-07-03T05:34:12.000Z",
  "_published": "2026-07-03T10:57:33.332Z",
  "_jobs": [
    {
      "job": 84985341425,
      "time": 208,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058608351"
    },
    {
      "job": 84985341640,
      "time": 271,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058621203"
    },
    {
      "job": 84985341711,
      "time": 212,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058609028"
    },
    {
      "job": 84985341700,
      "time": 233,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058612853"
    },
    {
      "job": 84985341666,
      "time": 151,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058595631"
    },
    {
      "job": 84985341632,
      "time": 257,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058618336"
    },
    {
      "job": 84985341487,
      "time": 125,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058590246"
    },
    {
      "job": 84985341473,
      "time": 379,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058645174"
    },
    {
      "job": 84985341218,
      "time": 201,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058563887"
    },
    {
      "job": 84985341727,
      "time": 186,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8058603077"
    },
    {
      "job": 84985341648,
      "time": 181,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8058602079"
    },
    {
      "job": 84985341524,
      "time": 182,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8058602254"
    },
    {
      "job": 84985341547,
      "time": 185,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8058602697"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660",
  "_status": "success",
  "_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
  },
  "_distro": "resolute",
  "_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": true,
  "_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": 14234521,
    "type": "user",
    "name": "Rampal S. Etienne",
    "followers": 25
  },
  "_downloads": {
    "count": 335,
    "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": "4.6.1",
  "_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",
    "fastmatch",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "mvtnorm",
    "nlme",
    "nnet",
    "numDeriv",
    "optimParallel",
    "permute",
    "phangorn",
    "phytools",
    "picante",
    "pkgconfig",
    "pso",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "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": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 4.041392685158225,
  "_indexed": true,
  "_nocasepkg": "damocles",
  "_universes": [
    "rsetienne"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-07-03T05:37:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/c778646d960cc0b3a6cce00fcaa25cb5bd6c16c31f34b58dbb4140bd609813d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.1",
      "date": "2026-07-03T05:37:49.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/1b87978be9821b333000463e94ad0fafdc16753d54438bf4da26a989437abc6c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.1",
      "date": "2026-07-03T05:37:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/1a5e8c1c77bce07fee3dbfe95f07ce35a18e05eef04f25f7eb10dcdcfbbd1bb3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.1",
      "date": "2026-07-03T05:37:03.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/934a22799007018359a4738b1f1387feefbc581a3681ea303a8ee10b36624f27",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1",
      "date": "2026-07-03T05:36:01.000Z",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/154bcbf4cd63605724f08432659d3c07f013c1e6db4aa6bcf3430e34072dd97f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.1",
      "date": "2026-07-03T05:37:10.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/21d1dc601cd3f2a24cdfed1e19be1bb398e73e50cafbda1a1fb8d4c8d847803d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.1",
      "date": "2026-07-03T05:35:48.000Z",
      "arch": "aarch64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/fe8ce732160ab9d5f7ade5d053a5839b7e9caf9fdcecbaaa4e6aea311a4dcbd9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.1",
      "date": "2026-07-03T05:37:57.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/8587dab4d11a67efb9328be429283c0c61bf19522199f5327829ecfb2709a12d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.1",
      "date": "2026-07-03T05:37:31.000Z",
      "arch": "emscripten",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/41bb46c8abebcfc3005f3fd84bf47a99e886e2473d37036883b6f7a8b66087db",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.1",
      "date": "2026-07-03T05:35:46.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/96064a402845d21fa7fd08826e93a42a0cf42197546cd490888a7d6d5821ce20",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.1",
      "date": "2026-07-03T05:35:49.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/c9c80a882357eca9f4e52e94ab46a314ea2dd955ca8bc72ec3946e2b53ba551d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.1",
      "date": "2026-07-03T05:35:49.000Z",
      "arch": "x86_64",
      "commit": "c709c593b911127682ca506056fdecfe9a62bf43",
      "fileid": "https://r2.ropensci.org/f6c06b1cd05b5198497dcafd70b9f52d5115925779724825daa774a4bfd9a545",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rsetienne/actions/runs/28640595660"
    }
  ]
}