{
  "_id": "6a1fe67eb401979e7343c60c",
  "Package": "spider",
  "Type": "Package",
  "Title": "Species Identity and Evolution in R",
  "Version": "1.5.2",
  "Date": "2026-04-04",
  "Authors@R": "c(person(given=\"Samuel\",family=\"Brown\",role=\"aut\"),person(given=\"Stephane\",family=\"Boyer\",role=\"aut\"),person(given=\"Marie-Caroline\",family=\"Lefort\",role=\"aut\"),person(given=\"Jagoba\",family=\"Malumbres-Olarte\",role=\"aut\"),person(given=\"Cor\",family=\"Vink\",role=\"aut\"),person(given=\"Rob\",family=\"Cruickshank\",role=\"aut\"),person(given=c(\"Rupert\",\"A.\"),family=\"Collins\",role=c(\"aut\",\"cre\",\"cph\"),email=\"rupertcollins@gmail.com\",comment=c(ORCID=\"0000-0002-9135-1169\")))",
  "Description": "Analysis of species limits and DNA barcoding data.\nIncluded are functions for generating important summary\nstatistics from DNA barcode data, assessing specimen\nidentification efficacy, testing and optimizing divergence\nthreshold limits, assessment of diagnostic nucleotides, and\ncalculation of the probability of reciprocal monophyly.\nAdditionally, a sliding window function offers opportunities to\nanalyse information across a gene, often used for marker design\nin degraded DNA studies. Further information on the package has\nbeen published in Brown et al (2012)\n<doi:10.1111/j.1755-0998.2011.03108.x>.",
  "License": "MIT + file LICENSE",
  "LazyLoad": "yes",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/boopsboops/spider",
  "BugReports": "https://github.com/boopsboops/spider/issues",
  "Language": "en-GB",
  "Encoding": "UTF-8",
  "Repository": "https://boopsboops.r-universe.dev",
  "Date/Publication": "2026-04-04 13:35:20 UTC",
  "RemoteUrl": "https://github.com/boopsboops/spider",
  "RemoteRef": "HEAD",
  "RemoteSha": "9dfe6e9d76bc390b473801b294b909157c436891",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 08:28:33 UTC",
    "User": "root"
  },
  "Author": "Samuel Brown [aut],\nStephane Boyer [aut],\nMarie-Caroline Lefort [aut],\nJagoba Malumbres-Olarte [aut],\nCor Vink [aut],\nRob Cruickshank [aut],\nRupert A. Collins [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-9135-1169>)",
  "Maintainer": "Rupert A. Collins <rupertcollins@gmail.com>",
  "MD5sum": "fb449e6b2a43ba355706b88118a974de",
  "_user": "boopsboops",
  "_type": "src",
  "_file": "spider_1.5.2.tar.gz",
  "_fileid": "7a493c8e738b30a3ca4474207c9c948425f9b4e94b337c2cb908f2865e4d50b5",
  "_filesize": 355991,
  "_sha256": "7a493c8e738b30a3ca4474207c9c948425f9b4e94b337c2cb908f2865e4d50b5",
  "_created": "2026-06-03T08:28:33.000Z",
  "_published": "2026-06-03T08:31:58.126Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79252994902,
      "time": 116,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7379506408"
    },
    {
      "job": 79252994864,
      "time": 113,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7379505149"
    },
    {
      "job": 79252994917,
      "time": 166,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7379514476"
    },
    {
      "job": 79252994993,
      "time": 154,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7379508791"
    },
    {
      "job": 79252509960,
      "time": 169,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7379464384"
    },
    {
      "job": 79252994893,
      "time": 103,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7379501586"
    },
    {
      "job": 79252994994,
      "time": 81,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7379494668"
    },
    {
      "job": 79252994956,
      "time": 85,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7379495278"
    },
    {
      "job": 79252995029,
      "time": 74,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7379491515"
    }
  ],
  "_buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/boopsboops/spider",
  "_commit": {
    "id": "9dfe6e9d76bc390b473801b294b909157c436891",
    "author": "rupert@sorubim <rupertcollins@gmail.com>",
    "committer": "rupert@sorubim <rupertcollins@gmail.com>",
    "message": "update news\n",
    "time": 1775309720
  },
  "_maintainer": {
    "name": "Rupert A. Collins",
    "email": "rupertcollins@gmail.com",
    "login": "boopsboops",
    "description": "ichthyology - biodiversity - phylogenetics  - eDNA - DNA barcoding - collections",
    "uuid": 5559735,
    "orcid": "0000-0002-9135-1169"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "pegas",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "boopsboops",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-14",
      "n": 6
    }
  ],
  "_tags": [
    {
      "name": "v1.5.2",
      "date": "2026-04-04"
    }
  ],
  "_topics": [
    "dna-barcode",
    "edna",
    "evolution",
    "species-delimitation",
    "species-identity"
  ],
  "_stars": 5,
  "_contributors": [
    {
      "user": "boopsboops",
      "count": 91,
      "uuid": 5559735
    },
    {
      "user": "killidude",
      "count": 1,
      "uuid": 4395998
    }
  ],
  "_userbio": {
    "uuid": 5559735,
    "type": "user",
    "name": "Rupert A. Collins",
    "description": "ichthyology - biodiversity - phylogenetics  - eDNA - DNA barcoding - collections"
  },
  "_downloads": {
    "count": 656,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/spider"
  },
  "_mentions": 8,
  "_devurl": "https://github.com/boopsboops/spider",
  "_searchresults": 69,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/spider.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/boopsboops/spider",
  "_realowner": "boopsboops",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.1-0",
      "date": "2011-11-12"
    },
    {
      "version": "1.1-1",
      "date": "2011-12-27"
    },
    {
      "version": "1.1-2",
      "date": "2012-03-14"
    },
    {
      "version": "1.1-3",
      "date": "2012-04-23"
    },
    {
      "version": "1.1-5",
      "date": "2012-11-15"
    },
    {
      "version": "1.2-0",
      "date": "2012-12-25"
    },
    {
      "version": "1.3-0",
      "date": "2013-12-27"
    },
    {
      "version": "1.5.0",
      "date": "2018-02-16"
    },
    {
      "version": "1.5.1",
      "date": "2025-05-09"
    },
    {
      "version": "1.5.2",
      "date": "2026-04-04"
    }
  ],
  "_exports": [
    "bestCloseMatch",
    "blockAlignment",
    "cgraph",
    "chaoHaplo",
    "checkDNA",
    "dataStat",
    "haploAccum",
    "heatmapSpp",
    "is.ambig",
    "localMinima",
    "maxInDist",
    "minInDist",
    "monophyly",
    "monophylyBoot",
    "nearNeighbour",
    "nonConDist",
    "nucDiag",
    "ordinDNA",
    "paa",
    "polyBalance",
    "rankSlidWin",
    "read.BOLD",
    "read.GB",
    "rmSingletons",
    "rnucDiag",
    "rosenberg",
    "search.BOLD",
    "seeBarcode",
    "seqStat",
    "slideAnalyses",
    "slideBoxplots",
    "slideNucDiag",
    "slidingWindow",
    "sppDist",
    "sppDistMatrix",
    "stats.BOLD",
    "tajima.K",
    "tclust",
    "threshID",
    "threshOpt",
    "tiporder",
    "titv",
    "tree.comp"
  ],
  "_datasets": [
    {
      "name": "anoteropsis",
      "title": "Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species",
      "object": "anoteropsis",
      "file": "anoteropsis.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 33,
      "table": false,
      "tojson": false
    },
    {
      "name": "dolomedes",
      "title": "Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species",
      "object": "dolomedes",
      "file": "dolomedes.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 37,
      "table": false,
      "tojson": false
    },
    {
      "name": "salticidae",
      "title": "Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae",
      "object": "salticidae",
      "file": "salticidae.rda",
      "class": [
        "DNAbin"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sarkar",
      "title": "Dummy sequences illustrating the categories of diagnostic nucleotides",
      "object": "sarkar",
      "file": "sarkar.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 8,
      "table": false,
      "tojson": false
    },
    {
      "name": "woodmouse",
      "title": "Cytochrome b Gene Sequences of Woodmice",
      "object": "woodmouse",
      "file": "woodmouse.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 15,
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "spider-package",
      "title": "Species Identity and Evolution in R",
      "topics": [
        "spider-package",
        "spider"
      ]
    },
    {
      "page": "anoteropsis",
      "title": "Cytochrome oxidase I (COI) sequences of New Zealand _Anoteropsis_ species",
      "topics": [
        "anoteropsis"
      ]
    },
    {
      "page": "bestCloseMatch",
      "title": "Measures of identification accuracy",
      "topics": [
        "bestCloseMatch"
      ]
    },
    {
      "page": "blockAlignment",
      "title": "Make all sequences the same length",
      "topics": [
        "blockAlignment"
      ]
    },
    {
      "page": "cgraph",
      "title": "Complete graph",
      "topics": [
        "cgraph"
      ]
    },
    {
      "page": "chaoHaplo",
      "title": "Chao estimator of haplotype number",
      "topics": [
        "chaoHaplo"
      ]
    },
    {
      "page": "checkDNA",
      "title": "Check a DNA alignment for missing data",
      "topics": [
        "checkDNA"
      ]
    },
    {
      "page": "dataStat",
      "title": "Taxa statistics",
      "topics": [
        "dataStat"
      ]
    },
    {
      "page": "dolomedes",
      "title": "Cytochrome oxidase I (COI) sequences of New Zealand _Dolomedes_ species",
      "topics": [
        "dolomedes"
      ]
    },
    {
      "page": "haploAccum",
      "title": "Haplotype accumulation curves",
      "topics": [
        "haploAccum"
      ]
    },
    {
      "page": "heatmapSpp",
      "title": "Visualise a distance matrix using a heatmap",
      "topics": [
        "heatmapSpp"
      ]
    },
    {
      "page": "is.ambig",
      "title": "Missing bases in alignments",
      "topics": [
        "is.ambig"
      ]
    },
    {
      "page": "localMinima",
      "title": "Determine thresholds from a density plot",
      "topics": [
        "localMinima"
      ]
    },
    {
      "page": "maxInDist",
      "title": "Nearest non-conspecific and maximum intra-specific distances",
      "topics": [
        "maxInDist"
      ]
    },
    {
      "page": "minInDist",
      "title": "Nearest non-conspecific and maximum intra-specific distances",
      "topics": [
        "minInDist"
      ]
    },
    {
      "page": "monophyly",
      "title": "Species monophyly over a tree",
      "topics": [
        "monophyly"
      ]
    },
    {
      "page": "monophylyBoot",
      "title": "Species monophyly over a tree",
      "topics": [
        "monophylyBoot"
      ]
    },
    {
      "page": "nearNeighbour",
      "title": "Measures of identification accuracy",
      "topics": [
        "nearNeighbour"
      ]
    },
    {
      "page": "nonConDist",
      "title": "Nearest non-conspecific and maximum intra-specific distances",
      "topics": [
        "nonConDist"
      ]
    },
    {
      "page": "nucDiag",
      "title": "Nucleotide diagnostics for species alignments",
      "topics": [
        "nucDiag"
      ]
    },
    {
      "page": "ordinDNA",
      "title": "Calculates a Principal Components Ordination of genetic distances",
      "topics": [
        "ordinDNA"
      ]
    },
    {
      "page": "paa",
      "title": "Population Aggregate Analysis",
      "topics": [
        "paa"
      ]
    },
    {
      "page": "plot.haploAccum",
      "title": "Plotting haplotype accumulation curves",
      "topics": [
        "plot.haploAccum"
      ]
    },
    {
      "page": "plot.ordinDNA",
      "title": "Plot an 'ordinDNA' object",
      "topics": [
        "plot.ordinDNA"
      ]
    },
    {
      "page": "plot.slidWin",
      "title": "Plot a 'slidWin' object",
      "topics": [
        "plot.slidWin"
      ]
    },
    {
      "page": "polyBalance",
      "title": "Balance of a phylogenetic tree with polytomies",
      "topics": [
        "polyBalance"
      ]
    },
    {
      "page": "rankSlidWin",
      "title": "Rank a 'slidWin' object.",
      "topics": [
        "rankSlidWin"
      ]
    },
    {
      "page": "read.BOLD",
      "title": "Downloads DNA sequences from the Barcode of Life Database (BOLD)",
      "topics": [
        "read.BOLD"
      ]
    },
    {
      "page": "read.GB",
      "title": "Download sequences from GenBank with metadata.",
      "topics": [
        "read.GB"
      ]
    },
    {
      "page": "rmSingletons",
      "title": "Detect and remove singletons",
      "topics": [
        "rmSingletons"
      ]
    },
    {
      "page": "rnucDiag",
      "title": "Nucleotide diagnostics for species alignments",
      "topics": [
        "rnucDiag"
      ]
    },
    {
      "page": "rosenberg",
      "title": "Rosenberg's probability of reciprocal monophyly",
      "topics": [
        "rosenberg"
      ]
    },
    {
      "page": "salticidae",
      "title": "Cytochrome oxidase I (COI) sequences of world-wide species of Salticidae",
      "topics": [
        "salticidae"
      ]
    },
    {
      "page": "sarkar",
      "title": "Dummy sequences illustrating the categories of diagnostic nucleotides",
      "topics": [
        "sarkar"
      ]
    },
    {
      "page": "search.BOLD",
      "title": "Downloads DNA sequences from the Barcode of Life Database (BOLD)",
      "topics": [
        "search.BOLD"
      ]
    },
    {
      "page": "seeBarcode",
      "title": "Create illustrative barcodes",
      "topics": [
        "seeBarcode"
      ]
    },
    {
      "page": "seqStat",
      "title": "Sequence statistics",
      "topics": [
        "seqStat"
      ]
    },
    {
      "page": "slideAnalyses",
      "title": "Sliding window analyses",
      "topics": [
        "slideAnalyses"
      ]
    },
    {
      "page": "slideBoxplots",
      "title": "Boxplots across windows",
      "topics": [
        "slideBoxplots"
      ]
    },
    {
      "page": "slideNucDiag",
      "title": "Sliding nucleotide diagnostics",
      "topics": [
        "slideNucDiag"
      ]
    },
    {
      "page": "slidingWindow",
      "title": "Create windows along an alignment",
      "topics": [
        "slidingWindow"
      ]
    },
    {
      "page": "sppDist",
      "title": "Intra and inter-specific distances",
      "topics": [
        "sppDist"
      ]
    },
    {
      "page": "sppDistMatrix",
      "title": "Mean intra- and inter-specific distance matrix",
      "topics": [
        "sppDistMatrix"
      ]
    },
    {
      "page": "sppVector",
      "title": "Species Vectors",
      "topics": [
        "sppVector"
      ]
    },
    {
      "page": "stats.BOLD",
      "title": "Downloads DNA sequences from the Barcode of Life Database (BOLD)",
      "topics": [
        "stats.BOLD"
      ]
    },
    {
      "page": "tajima.K",
      "title": "Calculate Tajima's K index of divergence",
      "topics": [
        "tajima.K"
      ]
    },
    {
      "page": "tclust",
      "title": "Clustering by a threshold",
      "topics": [
        "tclust"
      ]
    },
    {
      "page": "threshID",
      "title": "Measures of identification accuracy",
      "topics": [
        "threshID"
      ]
    },
    {
      "page": "threshOpt",
      "title": "Threshold optimisation",
      "topics": [
        "threshOpt"
      ]
    },
    {
      "page": "tiporder",
      "title": "Orders tip labels by their position on the tree.",
      "topics": [
        "tiporder"
      ]
    },
    {
      "page": "titv",
      "title": "Number of pairwise transitions and transversions in an alignment.",
      "topics": [
        "titv"
      ]
    },
    {
      "page": "tree.comp",
      "title": "Tree comparisons",
      "topics": [
        "tree.comp"
      ]
    },
    {
      "page": "woodmouse",
      "title": "Cytochrome b Gene Sequences of Woodmice",
      "topics": [
        "woodmouse"
      ]
    }
  ],
  "_readme": "https://github.com/boopsboops/spider/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "digest",
    "lattice",
    "nlme",
    "pegas",
    "Rcpp"
  ],
  "_score": 5.6170003411208995,
  "_indexed": true,
  "_nocasepkg": "spider",
  "_universes": [
    "boopsboops"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-03T08:30:29.000Z",
      "distro": "noble",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "087ff5f9f7507a4beba1bb215181184a7c8378eec72f909e13f0a8e1dae2df21",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.2",
      "date": "2026-06-03T08:30:27.000Z",
      "distro": "noble",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "ede72df25c3a46ff648ee9bc395e37e0594f13859260c80e80ff63bd618b17ac",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-03T08:30:57.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "75384cdac889c4a5f248c995c03ac39ea9aeb4e636caa74f9496f908e58cf99c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.2",
      "date": "2026-06-03T08:30:40.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "86c941c532450dc9935feceb6feb89dbf45a2b443ce7047d1aae86375acc375f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.2",
      "date": "2026-06-03T08:30:35.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "133134973b1cde3ba752529b6be915cf2210457fbd64a93d4d13764fd4b2ff98",
      "status": "success",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-03T08:29:48.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "1d02175e36a5076c0b8c35653eceac26f95a6e8c56ae4844dc768503cc931eed",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-03T08:29:48.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "3d0e17fa51a53337b2633c378c401fe7bbe1c49e6ad7bf7da68b15b502e2e64a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.5.2",
      "date": "2026-06-03T08:29:39.000Z",
      "commit": "9dfe6e9d76bc390b473801b294b909157c436891",
      "fileid": "53d36e4e6de293a53ac01acaafdb1e2aa67c39fa60724202ae6e25ef430a4554",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/boopsboops/actions/runs/26872885078"
    }
  ]
}