{
  "_id": "6a1fdce3b401979e7343840c",
  "Package": "tapnet",
  "Title": "Trait Matching and Abundance for Predicting Bipartite Networks",
  "Version": "0.6",
  "Authors@R": "c(person(\"Carsten\", \"Dormann\", email = \"carsten.dormann@biom.uni-freiburg.de\", role = c(\"aut\", \"cre\")), person(\"Gita\", \"Benadi\", email=\"gita.benadi@biom.uni-freiburg.de\", role=\"aut\"), person(\"Boris\", \"Tinoco\", email=\"btinoco@uazuay.edu.ec\", role=\"dtc\"), person(\"Ruth\", \"Stephan\", role=\"ctb\"), person(\"Jochen\", \"Fruend\", role=\"ctb\"))",
  "Description": "Functions to produce, fit and predict from bipartite\nnetworks with abundance, trait and phylogenetic information.\nIts methods are described in detail in Benadi, G., Dormann,\nC.F., Fruend, J., Stephan, R. & Vazquez, D.P. (2021)\nQuantitative prediction of interactions in bipartite networks\nbased on traits, abundances, and phylogeny. The American\nNaturalist, in press.",
  "License": "GPL",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "ByteCompile": "true",
  "URL": "https://github.com/biometry/tapnet",
  "VignetteBuilder": "knitr, utils",
  "RoxygenNote": "7.3.3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 07:46:57 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://biometry.r-universe.dev",
  "Date/Publication": "2026-01-20 13:58:40 UTC",
  "RemoteUrl": "https://github.com/biometry/tapnet",
  "RemoteRef": "HEAD",
  "RemoteSha": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
  "RemoteSubdir": "tapnet",
  "Author": "Carsten Dormann [aut, cre],\nGita Benadi [aut],\nBoris Tinoco [dtc],\nRuth Stephan [ctb],\nJochen Fruend [ctb]",
  "Maintainer": "Carsten Dormann <carsten.dormann@biom.uni-freiburg.de>",
  "MD5sum": "212776319a97039a71c5a34583265f2c",
  "_user": "biometry",
  "_type": "src",
  "_file": "tapnet_0.6.tar.gz",
  "_fileid": "3bda27939a96bb9f0c39aa7a7c913653dc4e8e85d07b553fd4ef7e25b4da8cce",
  "_filesize": 856270,
  "_sha256": "3bda27939a96bb9f0c39aa7a7c913653dc4e8e85d07b553fd4ef7e25b4da8cce",
  "_created": "2026-06-03T07:46:57.000Z",
  "_published": "2026-06-03T07:50:59.056Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79246314302,
      "time": 157,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7378675890"
    },
    {
      "job": 79246314308,
      "time": 157,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378675692"
    },
    {
      "job": 79246314380,
      "time": 190,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7378677772"
    },
    {
      "job": 79246314324,
      "time": 197,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378677173"
    },
    {
      "job": 79245801957,
      "time": 194,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378620954"
    },
    {
      "job": 79246314404,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7378660127"
    },
    {
      "job": 79246314303,
      "time": 110,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7378659588"
    },
    {
      "job": 79246314316,
      "time": 105,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7378657973"
    },
    {
      "job": 79246314445,
      "time": 114,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7378661324"
    }
  ],
  "_buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/biometry/tapnet",
  "_commit": {
    "id": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
    "author": "Carsten Dormann <carsten.dormann@biom.uni-freiburg.de>",
    "committer": "Carsten Dormann <carsten.dormann@biom.uni-freiburg.de>",
    "message": "removed fit_tapnetDE from package; version 0.6 uploaded to CRAN\n",
    "time": 1768917520
  },
  "_maintainer": {
    "name": "Carsten Dormann",
    "email": "carsten.dormann@biom.uni-freiburg.de",
    "login": "cdormann",
    "description": "",
    "uuid": 7498402
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "bipartite",
      "role": "Imports"
    },
    {
      "package": "MPSEM",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "biometry",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-04",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "cdormann",
      "count": 38,
      "uuid": 7498402
    }
  ],
  "_userbio": {
    "uuid": 7467671,
    "type": "organization",
    "name": "Biometry and Environmental System Analysis, University of Freiburg",
    "description": "Repository of the Department of Biometry and Environmental System Analysis "
  },
  "_downloads": {
    "count": 133,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tapnet"
  },
  "_devurl": "https://github.com/biometry/tapnet",
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/tapnet.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/biometry/tapnet",
  "_realowner": "biometry",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.3",
      "date": "2021-01-28"
    },
    {
      "version": "0.6",
      "date": "2026-01-20"
    }
  ],
  "_exports": [
    "fit_tapnet",
    "gof_tapnet",
    "make_tapnet",
    "predict_tapnet",
    "simnetfromtap",
    "simulate_tapnet",
    "tapnet2df"
  ],
  "_datasets": [
    {
      "name": "humm_abun",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "humm_traits",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Bill_length_mean_mm"
      ],
      "rows": 14,
      "table": true,
      "tojson": true
    },
    {
      "name": "humm_tree",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "networks",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "plant_abun",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "plant_traits",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Corolla_length_mm"
      ],
      "rows": 32,
      "table": true,
      "tojson": true
    },
    {
      "name": "plant_tree",
      "title": "Hummingbird-flower networks",
      "object": "Tinoco",
      "class": [
        "phylo",
        "phylomatic"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "fit_tapnet",
      "title": "Fit the tapnet model to a network",
      "topics": [
        "fit_tapnet"
      ]
    },
    {
      "page": "fit_tapnetDE",
      "title": "Fit the tapnet model to a network",
      "topics": [
        "fit_tapnetDE"
      ]
    },
    {
      "page": "gof_tapnet",
      "title": "Goodness-of-fit of a tapnet fit",
      "topics": [
        "gof_tapnet"
      ]
    },
    {
      "page": "internalFunctions",
      "title": "Helper functions for tapnet",
      "topics": [
        "bjornloglik",
        "fit_abund",
        "functions",
        "helper",
        "internalFunctions",
        "latent_cor",
        "loglik_tapnet",
        "param_vec2list",
        "pems_from_tree",
        "refit_params",
        "select_relevant_pems",
        "tmatch",
        "web_indices"
      ]
    },
    {
      "page": "make_tapnet",
      "title": "Constructs an object of type \"tapnet\"",
      "topics": [
        "make_tapnet"
      ]
    },
    {
      "page": "predict_tapnet",
      "title": "Predict from fitted tapnet to new data",
      "topics": [
        "predict_tapnet"
      ]
    },
    {
      "page": "simnetfromtap",
      "title": "Simulates a network from parameters, abundances, traits and phylogeny provided",
      "topics": [
        "simnetfromtap"
      ]
    },
    {
      "page": "simulate_tapnet",
      "title": "Creates a simulated along with all parameters, abundances, traits and phylogeny used",
      "topics": [
        "simulate_tapnet"
      ]
    },
    {
      "page": "tapnet2df",
      "title": "Convert tapnet object into data.frame",
      "topics": [
        "tapnet2df"
      ]
    },
    {
      "page": "Tinoco",
      "title": "Hummingbird-flower networks",
      "topics": [
        "humm_abun",
        "humm_traits",
        "humm_tree",
        "networks",
        "plant_abun",
        "plant_traits",
        "plant_tree",
        "Tinoco"
      ]
    }
  ],
  "_readme": "https://github.com/biometry/tapnet/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "bipartite",
    "cli",
    "cluster",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "corpcor",
    "cpp11",
    "DEoptim",
    "digest",
    "doParallel",
    "dotCall64",
    "expm",
    "fastmatch",
    "fields",
    "foreach",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mgcv",
    "mnormt",
    "MPSEM",
    "network",
    "nlme",
    "numDeriv",
    "optimParallel",
    "permute",
    "phangorn",
    "phytools",
    "pillar",
    "pkgconfig",
    "quadprog",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "scatterplot3d",
    "sna",
    "spam",
    "statnet.common",
    "tibble",
    "utf8",
    "vctrs",
    "vegan",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "CaseStudy.Rnw",
      "filename": "CaseStudy.pdf",
      "title": "Case Study",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2021-01-18 15:43:35",
      "modified": "2021-01-19 17:49:54",
      "commits": 2
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "tapnet",
  "_universes": [
    "biometry",
    "cdormann"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.6",
      "date": "2026-06-03T07:49:12.000Z",
      "distro": "noble",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "1de761b47992f56f558175b70c5ac0c5fabcb62d600562617eb5f883faa48894",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.6",
      "date": "2026-06-03T07:49:12.000Z",
      "distro": "noble",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "2f9bbce1e2acc397de1162a269237118cb7e2f3f99e488addaa3067fdfbb175c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.6",
      "date": "2026-06-03T07:49:26.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "da0329974107f11cdd7e94076d175ea1d236e7dc65b7eed2b83daaf36b6d44ce",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.6",
      "date": "2026-06-03T07:49:18.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "c17299b8d6752a98eabcc1b43e4cd26d44092c6b671d9945f6b82cbef61b36e2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.6",
      "date": "2026-06-03T07:49:14.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "15395af481c0221ed2d8d3f9f09ec065060e5acb485af9c4274b76a76a52dfef",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.6",
      "date": "2026-06-03T07:48:20.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "8f6a047f8bd0e2ab539d1e74628732caeb4a23ac4e1b1e5f46fdf75ae1aadfe9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.6",
      "date": "2026-06-03T07:48:16.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "94dcfd6a1d454b522fcc52da0914f40f70b35b616e5f01b734deba0e55af7550",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.6",
      "date": "2026-06-03T07:48:24.000Z",
      "commit": "22f4c5df97041b93bb320501ba7a72fa8dcd75c6",
      "fileid": "94612caaf2eda5e7c79f4e08d1b74b2e96ff1026b5ea7448429235939c8ed8cd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biometry/actions/runs/26870916515"
    }
  ]
}