{
  "_id": "6a1f225fb401979e73420889",
  "Package": "surface",
  "Type": "Package",
  "Title": "Fitting Hansen Models to Investigate Convergent Evolution",
  "Version": "0.6",
  "Date": "2024-08-19",
  "Authors@R": "person(given = \"Travis\",\nfamily = \"Ingram\",\nrole = c(\"aut\", \"cre\"),\nemail = \"travis.ingram@otago.ac.nz\")",
  "Description": "This data-driven phylogenetic comparative method fits\nstabilizing selection models to continuous trait data, building\non the 'ouch' methodology of Butler and King (2004)\n<doi:10.1086/426002>. The main functions fit a series of Hansen\nmodels using stepwise AIC, then identify cases of convergent\nevolution where multiple lineages have shifted to the same\nadaptive peak. For more information see Ingram and Mahler\n(2013) <doi:10.1111/2041-210X.12034>.",
  "License": "GPL (>= 2)",
  "URL": "https://www.otago.ac.nz/ecoevotago/research/code/index.html",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 07:15:30 UTC",
    "User": "root"
  },
  "Author": "Travis Ingram [aut, cre]",
  "Maintainer": "Travis Ingram <travis.ingram@otago.ac.nz>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://tingram.r-universe.dev",
  "Date/Publication": "2024-08-20 02:55:10 UTC",
  "RemoteUrl": "https://github.com/cran/surface",
  "RemoteRef": "HEAD",
  "RemoteSha": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
  "MD5sum": "e56ec7ddb2681aec4dfa1fcffdde8670",
  "_user": "tingram",
  "_type": "src",
  "_file": "surface_0.6.tar.gz",
  "_fileid": "f8f316c44ba9c9cfc4dba0d16295b674e7317abde66c6d25f5949a609b2121d3",
  "_filesize": 278281,
  "_sha256": "f8f316c44ba9c9cfc4dba0d16295b674e7317abde66c6d25f5949a609b2121d3",
  "_created": "2026-05-16T07:15:30.000Z",
  "_published": "2026-06-02T18:35:11.290Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79144626936,
      "time": 150,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7031517170"
    },
    {
      "job": 79144626589,
      "time": 143,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031516461"
    },
    {
      "job": 79144626859,
      "time": 207,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7031519726"
    },
    {
      "job": 79144626786,
      "time": 187,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031517660"
    },
    {
      "job": 79144625675,
      "time": 234,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031501507"
    },
    {
      "job": 79144625639,
      "time": 112,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7366602740"
    },
    {
      "job": 79144626851,
      "time": 110,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7031512929"
    },
    {
      "job": 79144626764,
      "time": 99,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7031511901"
    },
    {
      "job": 79144626780,
      "time": 97,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7031511670"
    }
  ],
  "_buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/surface",
  "_commit": {
    "id": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
    "author": "Travis Ingram <travis.ingram@otago.ac.nz>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.6\n",
    "time": 1724122510
  },
  "_maintainer": {
    "name": "Travis Ingram",
    "email": "travis.ingram@otago.ac.nz",
    "login": "tingram",
    "uuid": 6834511
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.6",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Depends"
    },
    {
      "package": "ouch",
      "role": "Depends"
    },
    {
      "package": "MASS",
      "role": "Depends"
    },
    {
      "package": "geiger",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "tingram",
      "count": 4,
      "uuid": 6834511
    }
  ],
  "_userbio": {
    "uuid": 6834511,
    "type": "user",
    "name": "Travis Ingram"
  },
  "_downloads": {
    "count": 272,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/surface"
  },
  "_mentions": 7,
  "_searchresults": 23,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/surface.html",
    "manual.pdf"
  ],
  "_realowner": "tingram",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.2",
      "date": "2013-01-04"
    },
    {
      "version": "0.3",
      "date": "2013-02-21"
    },
    {
      "version": "0.4",
      "date": "2013-11-01"
    },
    {
      "version": "0.4-1",
      "date": "2014-02-14"
    },
    {
      "version": "0.5",
      "date": "2020-12-18"
    },
    {
      "version": "0.6",
      "date": "2024-08-19"
    }
  ],
  "_exports": [
    "addRegime",
    "collapseRegimes",
    "convertBack",
    "convertTreeData",
    "getAIC",
    "getBranchTimes",
    "nameNodes",
    "npSurface",
    "ouchDescendants",
    "propRegMatch",
    "repaint",
    "runSurface",
    "startingModel",
    "surfaceAICMultiPlot",
    "surfaceAICPlot",
    "surfaceBackward",
    "surfaceForward",
    "surfaceSimulate",
    "surfaceSummary",
    "surfaceTraitPlot",
    "surfaceTreePlot"
  ],
  "_datasets": [
    {
      "name": "surfaceDemo",
      "title": "Tree and Data for Demonstrating SURFACE",
      "object": "surfaceDemo",
      "file": "surfaceDemo.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "surface-package",
      "title": "Fitting Hansen Models to Investigate Convergent Evolution",
      "topics": [
        "surface-package",
        "surface"
      ]
    },
    {
      "page": "convertTreeData",
      "title": "Utilities for Formatting Objects for SURFACE Analysis",
      "topics": [
        "convertBack",
        "convertTreeData",
        "nameNodes"
      ]
    },
    {
      "page": "getAIC",
      "title": "Akaike's Information Criterion for SURFACE Models",
      "topics": [
        "getAIC",
        "npSurface"
      ]
    },
    {
      "page": "getBranchTimes",
      "title": "Extract Branching Times from an 'ouch' Tree",
      "topics": [
        "getBranchTimes"
      ]
    },
    {
      "page": "ouchDescendants",
      "title": "Obtain Descendants from an 'ouch' Tree",
      "topics": [
        "ouchDescendants"
      ]
    },
    {
      "page": "propRegMatch",
      "title": "Similarity of Two Hansen Models",
      "topics": [
        "propRegMatch"
      ]
    },
    {
      "page": "repaint",
      "title": "Paint the Branches of a Tree",
      "topics": [
        "repaint"
      ]
    },
    {
      "page": "runSurface",
      "title": "Run All Steps of a SURFACE Analysis",
      "topics": [
        "runSurface"
      ]
    },
    {
      "page": "startingModel",
      "title": "Create an Initial Model for a SURFACE Analysis",
      "topics": [
        "startingModel"
      ]
    },
    {
      "page": "surfaceAICPlot",
      "title": "Plot the AIC Throughout a SURFACE Analysis",
      "topics": [
        "surfaceAICMultiPlot",
        "surfaceAICPlot"
      ]
    },
    {
      "page": "surfaceBackward",
      "title": "Collapsing Convergent Regimes in a Hansen Model",
      "topics": [
        "collapseRegimes",
        "surfaceBackward"
      ]
    },
    {
      "page": "surfaceDemo",
      "title": "Tree and Data for Demonstrating SURFACE",
      "topics": [
        "surfaceDemo"
      ]
    },
    {
      "page": "surfaceForward",
      "title": "Adding Regimes to a Hansen Model",
      "topics": [
        "addRegime",
        "surfaceForward"
      ]
    },
    {
      "page": "surfaceSimulate",
      "title": "Simulate Data for SURFACE",
      "topics": [
        "surfaceSimulate"
      ]
    },
    {
      "page": "surfaceSummary",
      "title": "Summarize SURFACE Output",
      "topics": [
        "surfaceSummary"
      ]
    },
    {
      "page": "surfaceTreePlot",
      "title": "Visualize Results of a SURFACE Analysis",
      "topics": [
        "surfaceTraitPlot",
        "surfaceTreePlot"
      ]
    }
  ],
  "_rundeps": [
    "ape",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "expm",
    "fastmatch",
    "foreach",
    "geiger",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "mvtnorm",
    "ncbit",
    "nlme",
    "numDeriv",
    "optimParallel",
    "ouch",
    "phangorn",
    "phytools",
    "pkgconfig",
    "quadprog",
    "Rcpp",
    "rlang",
    "scatterplot3d",
    "subplex",
    "vctrs"
  ],
  "_vignettes": [
    {
      "source": "surface_tutorial.Rnw",
      "filename": "surface_tutorial.pdf",
      "title": "Introduction to surface",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2012-12-23",
      "modified": "2020-12-18 12:20:02",
      "commits": 4
    }
  ],
  "_score": 3.20682587603185,
  "_indexed": true,
  "_nocasepkg": "surface",
  "_universes": [
    "tingram"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.6",
      "date": "2026-05-16T07:17:40.000Z",
      "distro": "noble",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "ef6c44ffe28cc02a0225734bc232f0540ddf43a479c9ea55bcd66188509074df",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.6",
      "date": "2026-05-16T07:17:37.000Z",
      "distro": "noble",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "add46dc8183c1e8c2667a18b9527f45401a66d0b16f13fbc044f47bde51de0bc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.6",
      "date": "2026-05-16T07:18:18.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "39a25174d02df22df0ca0459980d9d38a5bdc314fc81c68e9984b0bf6fccba05",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.6",
      "date": "2026-05-16T07:17:54.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "38d38da3fb2a1078695a13f7f73b2f44003f134b16d33cbf1a089b1980fca322",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.6",
      "date": "2026-05-16T07:16:53.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "7d31243d713a462c6aa7b6193d190e1fc2e90eafa3f7959c9e0c5afb7f5d4207",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.6",
      "date": "2026-05-16T07:16:48.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "976e64cfe8c8d41d29e35016d932fa514bd9da7326ad70910ccbeca33ead7c17",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.6",
      "date": "2026-05-16T07:16:44.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "52d1d7abadafd72fd43083578007c0c352bcc9776da0eb29bb8755b3686fc7ba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.6",
      "date": "2026-06-02T18:34:46.000Z",
      "commit": "8308983b8c3cbe7acb1d8996231a6748a1995f1b",
      "fileid": "d47c0e1814c361cd62660190830600b23f60acbed6a3bbbea9de0332ee43076f",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tingram/actions/runs/25955836367"
    }
  ]
}