{
  "_id": "6a3a2e266265ec60d62038b2",
  "Package": "ips",
  "Version": "0.1.0",
  "Title": "Interfaces to Phylogenetic Software in R",
  "Authors@R": "c(\nperson(\"Christoph\", \"Heibl\", email = \"christoph.heibl@gmx.net\",\nrole = c(\"aut\")),\nperson(\"Natalie\", \"Cusimano\", role = c(\"aut\")),\nperson(\"Franz-Sebastian\", \"Krah\", role = c(\"aut\")),\nperson(\"Martin R.\", 'Smith', role = c(\"ctb\", \"cre\"),\nemail = \"martin.smith@durham.ac.uk\",\ncomment = c(ORCID = \"0000-0001-5660-1727\"))\n)",
  "URL": "https://github.com/heibl/ips",
  "Description": "Functions that wrap popular phylogenetic software for\nsequence alignment, masking of sequence alignments, and\nestimation of phylogenies and ancestral character states.",
  "License": "GPL-3",
  "Language": "en-US",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://ms609.r-universe.dev",
  "Date/Publication": "2026-06-23 06:29:20 UTC",
  "RemoteUrl": "https://github.com/ms609/ips",
  "RemoteRef": "HEAD",
  "RemoteSha": "b7ad987d3f306244e9316be1f3cf31b864627100",
  "Packaged": {
    "Date": "2026-06-23 06:53:27 UTC",
    "User": "root"
  },
  "Author": "Christoph Heibl [aut],\nNatalie Cusimano [aut],\nFranz-Sebastian Krah [aut],\nMartin R. Smith [ctb, cre] (ORCID:\n<https://orcid.org/0000-0001-5660-1727>)",
  "Maintainer": "Martin R. Smith <martin.smith@durham.ac.uk>",
  "MD5sum": "bdb84c627fa0153e5c539b2b33a89f55",
  "_user": "ms609",
  "_type": "src",
  "_file": "ips_0.1.0.tar.gz",
  "_fileid": "28cb9372900a6d0349dd81bd030275b728fa4ea972ce65e6931ffb67344e9493",
  "_filesize": 365147,
  "_sha256": "28cb9372900a6d0349dd81bd030275b728fa4ea972ce65e6931ffb67344e9493",
  "_created": "2026-06-23T06:53:27.000Z",
  "_published": "2026-06-23T06:56:38.607Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 82894497770,
      "time": 155,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7813569327"
    },
    {
      "job": 82894497749,
      "time": 135,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813563440"
    },
    {
      "job": 82894497760,
      "time": 100,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7813560767"
    },
    {
      "job": 82894497761,
      "time": 85,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813552362"
    },
    {
      "job": 82894088502,
      "time": 163,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813519960"
    },
    {
      "job": 82894497740,
      "time": 89,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813549194"
    },
    {
      "job": 82894497799,
      "time": 114,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7813556773"
    },
    {
      "job": 82894497830,
      "time": 119,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7813558444"
    },
    {
      "job": 82894497764,
      "time": 96,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7813551432"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ms609/ips",
  "_commit": {
    "id": "b7ad987d3f306244e9316be1f3cf31b864627100",
    "author": "R script <martin.smith@durham.ac.uk>",
    "committer": "R script <martin.smith@durham.ac.uk>",
    "message": "roxygen 8.0\n",
    "time": 1782196160
  },
  "_maintainer": {
    "name": "Martin R. Smith",
    "email": "martin.smith@durham.ac.uk",
    "login": "ms609",
    "bluesky": "@palaeosmith.bsky.social",
    "orcid": "0000-0001-5660-1727",
    "description": "Professor in palaeontology, interested in phylogenetic methods ",
    "uuid": 1695515
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    }
  ],
  "_owner": "ms609",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2026-08",
      "n": 6
    },
    {
      "week": "2026-09",
      "n": 4
    },
    {
      "week": "2026-10",
      "n": 10
    },
    {
      "week": "2026-26",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.0.13",
      "date": "2026-02-23"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ms609",
      "count": 21,
      "uuid": 1695515
    }
  ],
  "_userbio": {
    "uuid": 1695515,
    "type": "user",
    "name": "Martin R. Smith",
    "followers": 62,
    "description": "Professor in palaeontology, interested in phylogenetic methods "
  },
  "_downloads": {
    "count": 651,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ips"
  },
  "_mentions": 10,
  "_devurl": "https://github.com/heibl/ips",
  "_searchresults": 200,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/ips.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ms609/ips",
  "_realowner": "ms609",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.0-7",
      "date": "2014-11-09"
    },
    {
      "version": "0.0.11",
      "date": "2019-07-04"
    },
    {
      "version": "0.0.12",
      "date": "2024-04-23"
    },
    {
      "version": "0.0.13",
      "date": "2026-02-23"
    }
  ],
  "_exports": [
    "aliscore",
    "are.tips.consecutive",
    "assembleDataNode",
    "assembleDistributionNode",
    "assembleInitNode",
    "assembleLoggers",
    "assembleStateNode",
    "assembleTreeNode",
    "beastLog",
    "blastn",
    "code.simple.gaps",
    "collapseUnsupportedEdges",
    "combMyTree",
    "del.miss",
    "deleteEmptyCells",
    "deleteGaps",
    "descendants",
    "DNAbin2index",
    "eoi",
    "fixNodes",
    "forceEqualTipHeights",
    "gblocks",
    "identifyEmptyCells",
    "index2DNAbin",
    "mafft",
    "mafft.merge",
    "mrbayes",
    "mrbayes.lset",
    "mrbayes.mcmc",
    "mrbayes.prset",
    "multistateMCMC",
    "multistateML",
    "neighboringPairs",
    "noi",
    "ntip",
    "operator",
    "parameter",
    "partitionfinder",
    "pathd8",
    "phylo2mafft",
    "phylo2mst",
    "pis",
    "prank",
    "raxml",
    "raxml.partitions",
    "rbeauti",
    "rc",
    "read.beast",
    "read.beast.table",
    "read.fas",
    "read.mrbayes",
    "read.nex",
    "read.phy",
    "read.starbeast",
    "read.xml",
    "setClock",
    "sister",
    "splitIntoClades",
    "terminal.clades",
    "terminalSisters",
    "tipHeights",
    "traitRate",
    "trimEnds",
    "unlistFirstLevel",
    "unresolve.clade",
    "write.fas",
    "write.nex",
    "write.phy"
  ],
  "_datasets": [
    {
      "name": "ips.16S",
      "title": "Bark Beetle 16S Sequences",
      "object": "ips.16S",
      "file": "ips.16S.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 42,
      "table": false,
      "tojson": false
    },
    {
      "name": "ips.28S",
      "title": "Bark Beetle 28S Sequences",
      "object": "ips.28S",
      "file": "ips.28S.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 28,
      "table": false,
      "tojson": false
    },
    {
      "name": "ips.cox1",
      "title": "Bark Beetle COX1 Sequences",
      "object": "ips.cox1",
      "file": "ips.cox1.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 26,
      "table": false,
      "tojson": false
    },
    {
      "name": "ips.tree",
      "title": "Ips Phylogeny",
      "object": "ips.tree",
      "file": "ips.tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "log_list",
      "title": "Internal IPS Functions",
      "object": "log_list",
      "file": "log_list.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "clock",
        "tree",
        "tip.dates"
      ],
      "rows": 65,
      "table": true,
      "tojson": true
    },
    {
      "name": "operator_list",
      "title": "Internal IPS Functions",
      "object": "operator_list",
      "file": "operator_list.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "name",
        "clock",
        "tree",
        "tip.date"
      ],
      "rows": 149,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ips-package",
      "title": "Interfaces to Phylogenetic Software",
      "topics": [
        "ips-package",
        "ips"
      ]
    },
    {
      "page": "aliscore",
      "title": "Masking of Sequence Alignments with ALISCORE",
      "topics": [
        "aliscore"
      ]
    },
    {
      "page": "blastn",
      "title": "Nucleotide-Nucleotide BLAST",
      "topics": [
        "blastn"
      ]
    },
    {
      "page": "code.simple.gaps",
      "title": "Simple Gap/Indel Coding",
      "topics": [
        "code.simple.gaps"
      ]
    },
    {
      "page": "collapseUnsupportedEdges",
      "title": "Collapse Unsupported Edges/Branches in a Phylogeny",
      "topics": [
        "collapseUnsupportedEdges"
      ]
    },
    {
      "page": "combMyTree",
      "title": "Graft Polytomies on Tips of Phylogeny",
      "topics": [
        "combMyTree"
      ]
    },
    {
      "page": "del.miss",
      "title": "Delete Missing Data from DNA Sequences",
      "topics": [
        "del.miss"
      ]
    },
    {
      "page": "deleteEmptyCells",
      "title": "Delete Spurious Rows and Columns from DNA Alignments",
      "topics": [
        "deleteEmptyCells"
      ]
    },
    {
      "page": "deleteGaps",
      "title": "Remove Gap Positions From DNA Sequences",
      "topics": [
        "deleteGaps"
      ]
    },
    {
      "page": "descendants",
      "title": "Descendants of an Internal Node in a Phylogeny",
      "topics": [
        "descendants"
      ]
    },
    {
      "page": "DNAbin2index",
      "title": "Conversion of DNAbin to Index",
      "topics": [
        "DNAbin2index"
      ]
    },
    {
      "page": "EmptyCells",
      "title": "Identify/Delete Spurious Rows and Columns from DNA Alignments",
      "topics": [
        "EmptyCells",
        "identifyEmptyCells"
      ]
    },
    {
      "page": "oi",
      "title": "Identification of Stem-Lineage-Edges and MRCAs",
      "topics": [
        "eoi",
        "noi",
        "oi"
      ]
    },
    {
      "page": "fixNodes",
      "title": "Standard Node Numbering in Phylo Objects",
      "topics": [
        "fixNodes"
      ]
    },
    {
      "page": "forceEqualTipHeights",
      "title": "Equal Tip Heights",
      "topics": [
        "forceEqualTipHeights"
      ]
    },
    {
      "page": "gblocks",
      "title": "Masking of Sequence Alignments with GBLOCKS",
      "topics": [
        "gblocks"
      ]
    },
    {
      "page": "index2DNAbin",
      "title": "Conversion of Index to DNAbin",
      "topics": [
        "index2DNAbin"
      ]
    },
    {
      "page": "ips.16S",
      "title": "Bark Beetle 16S Sequences",
      "topics": [
        "ips.16S"
      ]
    },
    {
      "page": "ips.28S",
      "title": "Bark Beetle 28S Sequences",
      "topics": [
        "ips.28S"
      ]
    },
    {
      "page": "ips.cox1",
      "title": "Bark Beetle COX1 Sequences",
      "topics": [
        "ips.cox1"
      ]
    },
    {
      "page": "ips.tree",
      "title": "Ips Phylogeny",
      "topics": [
        "ips.tree"
      ]
    },
    {
      "page": "mafft",
      "title": "Sequence Alignment with MAFFT",
      "topics": [
        "mafft"
      ]
    },
    {
      "page": "mafft.merge",
      "title": "Profile Alignment with MAFFT",
      "topics": [
        "mafft.merge"
      ]
    },
    {
      "page": "mrbayes",
      "title": "Bayesian MCMC Tree Search with MrBayes",
      "topics": [
        "mrbayes"
      ]
    },
    {
      "page": "mrbayes.lset",
      "title": "MrBayes model settings",
      "topics": [
        "mrbayes.lset"
      ]
    },
    {
      "page": "mrbayes.mcmc",
      "title": "MrBayes MCMC settings",
      "topics": [
        "mrbayes.mcmc"
      ]
    },
    {
      "page": "mrbayes.prset",
      "title": "MrBayes prior settings",
      "topics": [
        "mrbayes.prset"
      ]
    },
    {
      "page": "multistate",
      "title": "MULTISTATE",
      "topics": [
        "multistate",
        "multistateMCMC",
        "multistateML"
      ]
    },
    {
      "page": "neighboringPairs",
      "title": "Neighboring Nodes in a Minimum Spanning Tree",
      "topics": [
        "neighboringPairs"
      ]
    },
    {
      "page": "ntip",
      "title": "Numbers of Tips of (Sub)trees",
      "topics": [
        "ntip"
      ]
    },
    {
      "page": "partitionfinder",
      "title": "PartitionFinder",
      "topics": [
        "partitionfinder"
      ]
    },
    {
      "page": "pathd8",
      "title": "PATHd8",
      "topics": [
        "pathd8"
      ]
    },
    {
      "page": "phylo2mafft",
      "title": "Convert Trees for MAFFT",
      "topics": [
        "phylo2mafft"
      ]
    },
    {
      "page": "phylo2mst",
      "title": "Conversion from PHYLO to MST Object",
      "topics": [
        "phylo2mst"
      ]
    },
    {
      "page": "pis",
      "title": "Number of Potentially-Informative Sites",
      "topics": [
        "pis"
      ]
    },
    {
      "page": "prank",
      "title": "PRANK",
      "topics": [
        "prank"
      ]
    },
    {
      "page": "raxml",
      "title": "Maximum Likelihood Tree Estimation with RAxML",
      "topics": [
        "raxml"
      ]
    },
    {
      "page": "raxml.partitions",
      "title": "Partition scheme for RAxML",
      "topics": [
        "raxml.partitions"
      ]
    },
    {
      "page": "rbeauti",
      "title": "XML Input Files for BEAST",
      "topics": [
        "rbeauti"
      ]
    },
    {
      "page": "rc",
      "title": "Reverse-Complement of DNA sequences",
      "topics": [
        "rc"
      ]
    },
    {
      "page": "read",
      "title": "Reading Sequence Files",
      "topics": [
        "read",
        "read.fas",
        "read.nex",
        "read.phy"
      ]
    },
    {
      "page": "read.beast",
      "title": "Read Bayesian Trees",
      "topics": [
        "read.beast",
        "read.mrbayes",
        "read.starbeast"
      ]
    },
    {
      "page": "read.beast.table",
      "title": "Extract node data from BEAST chronogram",
      "topics": [
        "read.beast.table"
      ]
    },
    {
      "page": "sister",
      "title": "Identification of Sister Nodes and Clades",
      "topics": [
        "sister"
      ]
    },
    {
      "page": "splitIntoClades",
      "title": "Find Monophyletic Subsets in Species Lists",
      "topics": [
        "splitIntoClades"
      ]
    },
    {
      "page": "terminalSisters",
      "title": "Find Pairs of Sister Species",
      "topics": [
        "terminalSisters"
      ]
    },
    {
      "page": "tipHeights",
      "title": "Tip Heights in a Phylogenetic Tree",
      "topics": [
        "tipHeights"
      ]
    },
    {
      "page": "traitRate",
      "title": "Trait-Dependent Shifts in Molecular Rate",
      "topics": [
        "traitRate"
      ]
    },
    {
      "page": "trimEnds",
      "title": "Trim Alignment Ends",
      "topics": [
        "trimEnds"
      ]
    },
    {
      "page": "unlistFirstLevel",
      "title": "Unlist To First Level Only",
      "topics": [
        "unlistFirstLevel"
      ]
    },
    {
      "page": "write.fas",
      "title": "Write DNA Sequences to File",
      "topics": [
        "write.fas",
        "write.nex",
        "write.phy"
      ]
    }
  ],
  "_readme": "https://github.com/ms609/ips/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "cpp11",
    "data.table",
    "digest",
    "fastmatch",
    "generics",
    "glue",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "nlme",
    "phangorn",
    "pkgconfig",
    "plyr",
    "quadprog",
    "Rcpp",
    "rlang",
    "vctrs",
    "XML"
  ],
  "_score": 6.380211241711606,
  "_indexed": true,
  "_nocasepkg": "ips",
  "_universes": [
    "ms609",
    "heibl"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-23T06:55:40.000Z",
      "distro": "noble",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "c3483ca50f7119c70cb7d47bc881f8d1efaa31945079e81f44f1d1d84e4585fb",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-23T06:55:37.000Z",
      "distro": "noble",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "da27ba532ef5f8d3060b1b2688ff09d0c85d9b4637d8a01baf34be3648bc26c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-23T06:55:28.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "e02f84b655b8cd428f76929a9c07e6cb011794f2e46120fda4e08af02ccf5e66",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-23T06:55:04.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "7451a15d2ca645b50aab02100f789bd00b5febc94516bd2dd4fb2a063565f07b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-06-23T06:55:17.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "f377cab7d3170e53acdc6af0ac277a36da018ea8bb7d576d1a0427f227d9c67a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-23T06:54:42.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "253043c270bb0e3c3ff4e2cfbd08a24c9fd3eb07066272edb47bd2513861e78e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-23T06:54:57.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "6416b1cc701be8b0662ad72e0c0b4975e508c1333aaa715cc0d3a8f69fc62343",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-23T06:54:35.000Z",
      "commit": "b7ad987d3f306244e9316be1f3cf31b864627100",
      "fileid": "27ce0c8b1264c25bfe1fa27b1ba83e7a1d0d6572f0e3e9589267df8a831ba13e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/ms609/actions/runs/28007918064"
    }
  ]
}