{
  "_id": "6a1d69921d7bb097a0a4ed93",
  "Package": "sidier",
  "Type": "Package",
  "Title": "Substitution and Indel Distances to Infer Evolutionary\nRelationships",
  "Version": "4.1.1",
  "Date": "2025-06-06",
  "Authors@R": "c(person(given = \"A.J.\",\nfamily = \"Muñoz-Pajares\",\nrole = c(\"cre\",\"aut\"),\nemail = \"ajesusmp@ugr.es\"))",
  "Encoding": "UTF-8",
  "Description": "Evolutionary reconstruction based on substitutions and\ninsertion-deletion (indels) analyses in a distance-based\nframework as described in Muñoz-Pajares (2013)\n<doi:10.1111/2041-210X.12118>.",
  "License": "GPL-2",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-01 11:11:29 UTC",
    "User": "root"
  },
  "Author": "A.J. Muñoz-Pajares [cre, aut]",
  "Maintainer": "A.J. Muñoz-Pajares <ajesusmp@ugr.es>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-06-06 13:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/sidier",
  "RemoteRef": "HEAD",
  "RemoteSha": "a2bb46e2b439e7cb13f8db81d3b9222393c11440",
  "MD5sum": "5dbfa6d37beb4b1e0eedb8f0e5fd6c9f",
  "_user": "cran",
  "_type": "src",
  "_file": "sidier_4.1.1.tar.gz",
  "_fileid": "1274880d69890ff40a1316a25c49f77a7eb97c0a1e1efb70bd4ef63652c04373",
  "_filesize": 441372,
  "_sha256": "1274880d69890ff40a1316a25c49f77a7eb97c0a1e1efb70bd4ef63652c04373",
  "_created": "2026-06-01T11:11:29.000Z",
  "_published": "2026-06-01T11:14:26.214Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78839899969,
      "time": 135,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7329985172"
    },
    {
      "job": 78839899726,
      "time": 126,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7329981961"
    },
    {
      "job": 78839395215,
      "time": 194,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7329942900"
    },
    {
      "job": 78839899699,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7329978287"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26751194557",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/sidier",
  "_commit": {
    "id": "a2bb46e2b439e7cb13f8db81d3b9222393c11440",
    "author": "A.J. Muñoz-Pajares <ajesusmp@ugr.es>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 4.1.1\n",
    "time": 1749217202
  },
  "_maintainer": {
    "name": "A.J. Muñoz-Pajares",
    "email": "ajesusmp@ugr.es"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "network",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "gridBase",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "ggmap",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-23",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "4.1.1",
      "date": "2025-06-06"
    }
  ],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 171,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sidier"
  },
  "_mentions": 1,
  "_searchresults": 36,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/sidier.html",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2013-02-19"
    },
    {
      "version": "2.0",
      "date": "2013-03-29"
    },
    {
      "version": "2.2",
      "date": "2013-07-01"
    },
    {
      "version": "2.3",
      "date": "2013-08-09"
    },
    {
      "version": "3.0",
      "date": "2014-11-18"
    },
    {
      "version": "3.0.1",
      "date": "2015-02-27"
    },
    {
      "version": "4.0.1",
      "date": "2017-06-06"
    },
    {
      "version": "4.0.2",
      "date": "2017-06-08"
    },
    {
      "version": "4.0.3",
      "date": "2018-07-09"
    },
    {
      "version": "4.1.0",
      "date": "2021-06-25"
    },
    {
      "version": "4.1.1",
      "date": "2025-06-06"
    }
  ],
  "_exports": [
    "assign.whole.taxo",
    "barcode.gap",
    "barcode.quality",
    "barcode.summary",
    "BARRIEL",
    "colour.scheme",
    "compare.dist",
    "distance.comb",
    "double.plot",
    "FIFTH",
    "filter.whole.taxo",
    "FilterHaplo",
    "FindHaplo",
    "genbank.sp.names",
    "get.majority.taxo",
    "GetHaplo",
    "HapPerPop",
    "inter.intra.plot",
    "MCIC",
    "mergeNodes",
    "mutation.network",
    "mutationSummary",
    "NINA.thr",
    "nt.gap.comb",
    "perc.thr",
    "pie.network",
    "pop.dist",
    "rule",
    "SIC",
    "simplify.network",
    "simuEvolution",
    "single.network",
    "single.network.module",
    "spatial.plot",
    "zero.thr"
  ],
  "_datasets": [
    {
      "name": "alignExample",
      "title": "example alignment #1 ('DNAbin' class)",
      "object": "ex_alignment1",
      "file": "ex_alignment1.rda",
      "class": [
        "DNAbin"
      ],
      "fields": {},
      "rows": 16,
      "table": false,
      "tojson": false
    },
    {
      "name": "ex_BLAST",
      "title": "example BLAST output",
      "object": "ex_BLAST",
      "file": "ex_BLAST.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "stitle",
        "qseqid",
        "evalue",
        "pident",
        "qcovs"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "ex_Coords",
      "title": "example coordinates",
      "object": "ex_Coords",
      "file": "ex_Coords.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "POP",
        "X",
        "Y"
      ],
      "rows": 8,
      "table": true,
      "tojson": true
    },
    {
      "name": "Example_Spatial.plot_Alignment",
      "title": "example alignment #1 (fasta format)",
      "object": "Example_Spatial.plot_Alignment",
      "file": "Example_Spatial.plot_Alignment.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X.Pop01_H40"
      ],
      "rows": 226,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "sidier-package",
      "title": "SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships",
      "topics": [
        "sidier-package",
        "sidier"
      ]
    },
    {
      "page": "alignExample",
      "title": "example alignment #1 ('DNAbin' class)",
      "topics": [
        "alignExample"
      ]
    },
    {
      "page": "assign.whole.taxo",
      "title": "Get taxonomy described in sequence names",
      "topics": [
        "assign.whole.taxo"
      ]
    },
    {
      "page": "barcode.gap",
      "title": "Barcode gap identification",
      "topics": [
        "barcode.gap"
      ]
    },
    {
      "page": "barcode.quality",
      "title": "Estimates of barcode quality",
      "topics": [
        "barcode.quality"
      ]
    },
    {
      "page": "barcode.summary",
      "title": "Summary of the inter- and intraspecific distances",
      "topics": [
        "barcode.summary"
      ]
    },
    {
      "page": "BARRIEL",
      "title": "Indel distances following Barriel method",
      "topics": [
        "BARRIEL"
      ]
    },
    {
      "page": "colour.scheme",
      "title": "internal function for node colour scheme",
      "topics": [
        "colour.scheme"
      ]
    },
    {
      "page": "compare.dist",
      "title": "Threshold to discriminate species comparing intra- and interspecific distance distributions",
      "topics": [
        "compare.dist"
      ]
    },
    {
      "page": "distance.comb",
      "title": "Distance matrices combination",
      "topics": [
        "distance.comb"
      ]
    },
    {
      "page": "double.plot",
      "title": "Haplotype and population networks including mutations and haplotype frequencies.",
      "topics": [
        "double.plot"
      ]
    },
    {
      "page": "ex_alignment1",
      "title": "example alignment #1",
      "topics": [
        "ex_alignment1"
      ]
    },
    {
      "page": "ex_BLAST",
      "title": "example BLAST output",
      "topics": [
        "ex_BLAST"
      ]
    },
    {
      "page": "ex_Coords",
      "title": "example coordinates",
      "topics": [
        "ex_Coords"
      ]
    },
    {
      "page": "Example_Spatial.plot_Alignment",
      "title": "example alignment #1 (fasta format)",
      "topics": [
        "Example_Spatial.plot_Alignment"
      ]
    },
    {
      "page": "FIFTH",
      "title": "Indel distances following the fifth state rationale",
      "topics": [
        "FIFTH"
      ]
    },
    {
      "page": "filter.whole.taxo",
      "title": "Get consensus taxonomy",
      "topics": [
        "filter.whole.taxo"
      ]
    },
    {
      "page": "FilterHaplo",
      "title": "Filter haplotypes by occurrence",
      "topics": [
        "FilterHaplo"
      ]
    },
    {
      "page": "FindHaplo",
      "title": "Find equal haplotypes",
      "topics": [
        "FindHaplo"
      ]
    },
    {
      "page": "genbank.sp.names",
      "title": "Species names from genbank accessions",
      "topics": [
        "genbank.sp.names"
      ]
    },
    {
      "page": "get.majority.taxo",
      "title": "Get majority taxonomy for a sequence",
      "topics": [
        "get.majority.taxo"
      ]
    },
    {
      "page": "GetHaplo",
      "title": "Get sequences of unique haplotypes",
      "topics": [
        "GetHaplo"
      ]
    },
    {
      "page": "HapPerPop",
      "title": "Returns the number of haplotypes per population.",
      "topics": [
        "HapPerPop"
      ]
    },
    {
      "page": "inter.intra.plot",
      "title": "Histogram of the intra- and interspecific distances",
      "topics": [
        "inter.intra.plot"
      ]
    },
    {
      "page": "MCIC",
      "title": "Modified Complex Indel Coding as distance matrix",
      "topics": [
        "MCIC"
      ]
    },
    {
      "page": "mergeNodes",
      "title": "Merges nodes showing distance values equal to zero",
      "topics": [
        "mergeNodes"
      ]
    },
    {
      "page": "mutation.network",
      "title": "Haplotype network depiction including mutations",
      "topics": [
        "mutation.network"
      ]
    },
    {
      "page": "mutationSummary",
      "title": "Summary of observed mutations",
      "topics": [
        "mutationSummary"
      ]
    },
    {
      "page": "NINA.thr",
      "title": "No Isolated Nodes Allowed network",
      "topics": [
        "NINA.thr"
      ]
    },
    {
      "page": "nt.gap.comb",
      "title": "substitution and indel distance combinations",
      "topics": [
        "nt.gap.comb"
      ]
    },
    {
      "page": "perc.thr",
      "title": "Percolation threshold network",
      "topics": [
        "perc.thr"
      ]
    },
    {
      "page": "pie.network",
      "title": "Population network depiction including haplotype frequencies",
      "topics": [
        "pie.network"
      ]
    },
    {
      "page": "pop.dist",
      "title": "Distances among populations",
      "topics": [
        "pop.dist"
      ]
    },
    {
      "page": "rule",
      "title": "Threshold to discriminate species.",
      "topics": [
        "rule"
      ]
    },
    {
      "page": "SIC",
      "title": "Indel distances following the Simple Index Coding method",
      "topics": [
        "SIC"
      ]
    },
    {
      "page": "simplify.network",
      "title": "Network showing modules as nodes",
      "topics": [
        "simplify.network"
      ]
    },
    {
      "page": "simuEvolution",
      "title": "Simulate sequences evolution",
      "topics": [
        "simuEvolution"
      ]
    },
    {
      "page": "single.network",
      "title": "Plot a network given a threshold",
      "topics": [
        "single.network"
      ]
    },
    {
      "page": "single.network.module",
      "title": "Get modules and network given a threshold",
      "topics": [
        "single.network.module"
      ]
    },
    {
      "page": "spatial.plot",
      "title": "spatial plot of populations",
      "topics": [
        "spatial.plot"
      ]
    },
    {
      "page": "zero.thr",
      "title": "Zero distance networks",
      "topics": [
        "zero.thr"
      ]
    }
  ],
  "_rundeps": [
    "ape",
    "askpass",
    "bitops",
    "cli",
    "coda",
    "cpp11",
    "curl",
    "digest",
    "dplyr",
    "farver",
    "generics",
    "ggmap",
    "ggplot2",
    "glue",
    "gridBase",
    "gtable",
    "httr",
    "igraph",
    "isoband",
    "jpeg",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "mime",
    "network",
    "nlme",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "S7",
    "scales",
    "statnet.common",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_score": 1.5563025007672873,
  "_indexed": true,
  "_nocasepkg": "sidier",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.1.1",
      "date": "2026-06-01T11:13:34.000Z",
      "distro": "noble",
      "commit": "a2bb46e2b439e7cb13f8db81d3b9222393c11440",
      "fileid": "b1f33e2cc4a1afcc00d5e038456fb4eb4947d0fcadc90bde06707e0f944b12da",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26751194557"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "4.1.1",
      "date": "2026-06-01T11:13:29.000Z",
      "distro": "noble",
      "commit": "a2bb46e2b439e7cb13f8db81d3b9222393c11440",
      "fileid": "15bd8ae70c15380330e2409926d372095aa21109c374d96d9a020b7323b27c8f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26751194557"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "4.1.1",
      "date": "2026-06-01T11:13:49.000Z",
      "commit": "a2bb46e2b439e7cb13f8db81d3b9222393c11440",
      "fileid": "2910554441ff22c2d3461d3c34bd0a7c22b192d50fbcffe62576cc65651f2680",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26751194557"
    }
  ]
}