{
  "_id": "6a5a1f4809eb0996dd69035c",
  "Package": "MorphoRegions",
  "Type": "Package",
  "Title": "Analysis of Regionalization Patterns in Serially Homologous\nStructures",
  "Version": "0.2.0",
  "Date": "2026-07-17",
  "Authors@R": "c(\nperson(\"Amandine\", \"Gillet\", role = c(\"cre\", \"aut\"),\nemail = \"gillet.aman@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9763-6061\")),\nperson(\"Katrina\", \"Jones\", role = c(\"aut\"),\nemail = \"katrina.jones@bristol.ac.uk\",\ncomment = c(ORCID=\"0000-0003-1088-0497\")),\nperson(\"Noah\", \"Greifer\", role = c(\"aut\"),\nemail = \"ngreifer@iq.harvard.edu\",\ncomment = c(ORCID=\"0000-0003-3067-7154\")),\nperson(\"Stephanie\", \"Pierce\", role = c(\"aut\"),\nemail = \"spierce@oeb.harvard.edu\",\ncomment = c(ORCID = \"0000-0003-0717-1841\"))\n)",
  "Description": "Computes the optimal number of regions (or subdivisions)\nand their position in serial structures without a priori\nassumptions and to visualize the results. After reducing data\ndimensionality with the built-in function for data ordination,\nregions are fitted as segmented linear regressions along the\nserial structure. Every region boundary position and increasing\nnumber of regions are iteratively fitted and the best model\n(number of regions and boundary positions) is selected with an\ninformation criterion. This package expands on the previous\n'regions' package (Jones et al. (2018)\n<doi:10.1126/science.aar3126>) with improved computation and\nmore fitting and plotting options.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "URL": "https://aagillet.github.io/MorphoRegions/,\nhttps://github.com/aagillet/MorphoRegions",
  "BugReports": "https://github.com/aagillet/MorphoRegions/issues",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://aagillet.r-universe.dev",
  "Date/Publication": "2026-07-17 10:25:36 UTC",
  "RemoteUrl": "https://github.com/aagillet/morphoregions",
  "RemoteRef": "HEAD",
  "RemoteSha": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-17 12:22:01 UTC",
    "User": "root"
  },
  "Author": "Amandine Gillet [cre, aut] (ORCID:\n<https://orcid.org/0000-0001-9763-6061>),\nKatrina Jones [aut] (ORCID: <https://orcid.org/0000-0003-1088-0497>),\nNoah Greifer [aut] (ORCID: <https://orcid.org/0000-0003-3067-7154>),\nStephanie Pierce [aut] (ORCID: <https://orcid.org/0000-0003-0717-1841>)",
  "Maintainer": "Amandine Gillet <gillet.aman@gmail.com>",
  "_user": "aagillet",
  "_type": "src",
  "_file": "MorphoRegions_0.2.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/8c8be345a81b494afbd60d6141e1f0d434bc66d901fd8ca72528757387995528",
  "_filesize": 4804206,
  "_sha256": "8c8be345a81b494afbd60d6141e1f0d434bc66d901fd8ca72528757387995528",
  "_expires": "2026-10-25T12:25:41.000Z",
  "_created": "2026-07-17T12:22:01.000Z",
  "_published": "2026-07-17T12:25:43.871Z",
  "_jobs": [
    {
      "job": 87883129256,
      "time": 174,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8406654585"
    },
    {
      "job": 87883129243,
      "time": 164,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8406650607"
    },
    {
      "job": 87883129283,
      "time": 177,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8406647084"
    },
    {
      "job": 87883129268,
      "time": 158,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8406634137"
    },
    {
      "job": 87882388143,
      "time": 238,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8406588721"
    },
    {
      "job": 87883129251,
      "time": 127,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8406636533"
    },
    {
      "job": 87883129265,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8406624695"
    },
    {
      "job": 87883129300,
      "time": 97,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8406625239"
    },
    {
      "job": 87883129280,
      "time": 130,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8406637676"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482",
  "_status": "success",
  "_upstream": "https://github.com/aagillet/morphoregions",
  "_commit": {
    "id": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
    "author": "AaGillet <53935650+AaGillet@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge developGMM into Master\n\nEdit data file",
    "time": 1784283936
  },
  "_maintainer": {
    "name": "Amandine Gillet",
    "email": "gillet.aman@gmail.com",
    "login": "aagillet",
    "description": "",
    "uuid": 53935650,
    "orcid": "0000-0001-9763-6061"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "version": ">= 1.1-3",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "version": ">= 2.1.4",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 1.3.0",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 4.0.0",
      "role": "Imports"
    },
    {
      "package": "arg",
      "version": ">= 0.1.1",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "version": ">= 1.7-2",
      "role": "Imports"
    },
    {
      "package": "viridisLite",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "version": ">= 1.1.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "aagillet",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-29",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "ngreifer",
      "count": 57,
      "uuid": 20465600
    },
    {
      "user": "aagillet",
      "count": 27,
      "uuid": 53935650
    }
  ],
  "_userbio": {
    "uuid": 53935650,
    "type": "user",
    "name": "AaGillet",
    "followers": 1
  },
  "_downloads": {
    "count": 204,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MorphoRegions"
  },
  "_devurl": "https://github.com/aagillet/morphoregions",
  "_pkgdown": "https://aagillet.github.io/MorphoRegions/",
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MorphoRegions.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/aagillet/morphoregions",
  "_realowner": "aagillet",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2024-08-21"
    }
  ],
  "_exports": [
    "addregions",
    "calcBPvar",
    "calcmodel",
    "calcregions",
    "modelperf",
    "modelselect",
    "modelsupport",
    "ncombos",
    "PCOload",
    "PCOselect",
    "plotsegreg",
    "plotvertmap",
    "process_gmPC",
    "process_measurements",
    "process_PC",
    "simregions",
    "subsample",
    "svdPCO"
  ],
  "_datasets": [
    {
      "name": "alligator",
      "title": "Measurements from the vertebral column of an alligator",
      "object": "alligator",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebra",
        "CL",
        "Chpost",
        "Cwpost",
        "Chant",
        "Cwant",
        "ArchH",
        "ArchW",
        "Mid.LW",
        "NSL",
        "NSH",
        "totH",
        "totW",
        "PreZW",
        "InterZL",
        "TPL",
        "NSA",
        "PreZA",
        "TPDV",
        "TPAP"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "dolphin",
      "title": "Measurements from the vertebral column of a dolphin",
      "object": "dolphin",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebra",
        "Lc",
        "Wc",
        "Hc",
        "Hnp",
        "Wnp",
        "Inp",
        "Ha",
        "Wa",
        "Lm",
        "Wm",
        "Hm",
        "Hch",
        "Wch",
        "Ltp",
        "Wtp",
        "Itp"
      ],
      "rows": 40,
      "table": true,
      "tojson": true
    },
    {
      "name": "musm",
      "title": "Measurements from the vertebral column of a mouse",
      "object": "musm",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebral.number",
        "CL",
        "Chpost",
        "Cwpost",
        "chant",
        "cwant",
        "ArchH",
        "ArchW",
        "Mid.LW",
        "NSL",
        "NSH",
        "totH",
        "totW",
        "PreZW",
        "InterZL",
        "TPL",
        "PreZA",
        "TPDV",
        "NSA",
        "TPAP"
      ],
      "rows": 23,
      "table": true,
      "tojson": true
    },
    {
      "name": "porpoise1",
      "title": "Measurements from the vertebral column of three porpoises",
      "object": "porpoise",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebra",
        "Lc",
        "Wc",
        "Hc",
        "Hnp",
        "Wnp",
        "Inp",
        "Ha",
        "Wa",
        "Lm",
        "Wm",
        "Hm",
        "Hch",
        "Wch",
        "Ltp",
        "Wtp",
        "Itp"
      ],
      "rows": 58,
      "table": true,
      "tojson": true
    },
    {
      "name": "porpoise2",
      "title": "Measurements from the vertebral column of three porpoises",
      "object": "porpoise",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebra",
        "Lc",
        "Wc",
        "Hc",
        "Hnp",
        "Wnp",
        "Inp",
        "Ha",
        "Wa",
        "Lm",
        "Wm",
        "Hm",
        "Hch",
        "Wch",
        "Ltp",
        "Wtp",
        "Itp"
      ],
      "rows": 56,
      "table": true,
      "tojson": true
    },
    {
      "name": "porpoise3",
      "title": "Measurements from the vertebral column of three porpoises",
      "object": "porpoise",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Vertebra",
        "Lc",
        "Wc",
        "Hc",
        "Hnp",
        "Wnp",
        "Inp",
        "Ha",
        "Wa",
        "Lm",
        "Wm",
        "Hm",
        "Hch",
        "Wch",
        "Ltp",
        "Wtp",
        "Itp"
      ],
      "rows": 59,
      "table": true,
      "tojson": true
    },
    {
      "name": "seal_gmm",
      "title": "Geometric morphometric data and PC scores of the vertebral column a seal",
      "object": "seal_gmm",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "wolves_gmm",
      "title": "Geometric morphometric data and PC scores of the vertebral column two wolves",
      "object": "wolves_gmm",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "alligator",
      "title": "Measurements from the vertebral column of an alligator",
      "topics": [
        "alligator"
      ]
    },
    {
      "page": "calcBPvar",
      "title": "Calculate variability of breakpoints",
      "topics": [
        "calcBPvar"
      ]
    },
    {
      "page": "calcmodel",
      "title": "Calculate results of a single segmented regression model",
      "topics": [
        "calcmodel"
      ]
    },
    {
      "page": "calcregions",
      "title": "Fit segmented regression models for all combinations of breakpoints",
      "topics": [
        "addregions",
        "calcregions",
        "ncombos",
        "summary.regions_results"
      ]
    },
    {
      "page": "dolphin",
      "title": "Measurements from the vertebral column of a dolphin",
      "topics": [
        "dolphin"
      ]
    },
    {
      "page": "modelperf",
      "title": "Assess model performance",
      "topics": [
        "modelperf",
        "modelperf.regions_pco",
        "modelperf.regions_results_single",
        "modelperf.regions_sim"
      ]
    },
    {
      "page": "modelselect",
      "title": "Select the best models",
      "topics": [
        "modelselect"
      ]
    },
    {
      "page": "modelsupport",
      "title": "Evaluate model support",
      "topics": [
        "modelsupport"
      ]
    },
    {
      "page": "musm",
      "title": "Measurements from the vertebral column of a mouse",
      "topics": [
        "musm"
      ]
    },
    {
      "page": "PCOload",
      "title": "Calculate PCO loadings",
      "topics": [
        "PCOload",
        "plot.regions_pco_load"
      ]
    },
    {
      "page": "PCOselect",
      "title": "Select PCO scores",
      "topics": [
        "PCOselect",
        "plot.regions_pco_select",
        "summary.regions_pco_select"
      ]
    },
    {
      "page": "plot.regions_pco",
      "title": "Plot PC axes",
      "topics": [
        "plot.regions_pco"
      ]
    },
    {
      "page": "plotsegreg",
      "title": "Plot a segmented regression model",
      "topics": [
        "plotsegreg",
        "plotsegreg.regions_pco",
        "plotsegreg.regions_results_single",
        "plotsegreg.regions_sim"
      ]
    },
    {
      "page": "plotvertmap",
      "title": "Plot a vertebra map",
      "topics": [
        "plotvertmap"
      ]
    },
    {
      "page": "porpoise",
      "title": "Measurements from the vertebral column of three porpoises",
      "topics": [
        "porpoise",
        "porpoise1",
        "porpoise2",
        "porpoise3"
      ]
    },
    {
      "page": "process_gmPC",
      "title": "Process vertebral measurements and PC scores of 2D or 3D geometric morphometric data",
      "topics": [
        "process_gmPC"
      ]
    },
    {
      "page": "process_measurements",
      "title": "Process vertebral measurements",
      "topics": [
        "process_measurements"
      ]
    },
    {
      "page": "process_PC",
      "title": "Process vertebral measurements and PC scores of traditional morphometric data",
      "topics": [
        "process_PC"
      ]
    },
    {
      "page": "seal_gmm",
      "title": "Geometric morphometric data and PC scores of the vertebral column a seal",
      "topics": [
        "seal_gmm"
      ]
    },
    {
      "page": "simregions",
      "title": "Simulate regions data",
      "topics": [
        "plot.regions_sim",
        "simregions"
      ]
    },
    {
      "page": "subsample",
      "title": "Subsample a dataset",
      "topics": [
        "subsample"
      ]
    },
    {
      "page": "svdPCO",
      "title": "Calculate PCO (principal co-ordinates analysis) based on SVD",
      "topics": [
        "svdPCO"
      ]
    },
    {
      "page": "wolves_gmm",
      "title": "Geometric morphometric data and PC scores of the vertebral column two wolves",
      "topics": [
        "wolves_gmm"
      ]
    }
  ],
  "_readme": "https://github.com/aagillet/morphoregions/raw/HEAD/README.md",
  "_rundeps": [
    "arg",
    "cli",
    "cluster",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "pbapply",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "MorphoRegions.Rmd",
      "filename": "MorphoRegions.html",
      "title": "MorphoRegions",
      "engine": "knitr::rmarkdown_notangle",
      "headings": [
        "About MorphoRegions",
        "Package installation",
        "Overview of MorphoRegions worflow",
        "Preparing the data",
        "Raw morphometrics (Pipeline 1)",
        "Data input",
        "Data ordination",
        "PCs from traditional morphometrics  (Pipeline 2)",
        "PCs from geometric morphometrics  (Pipeline 3)",
        "Data reduction",
        "Manual selection:",
        "Variance cutoff:",
        "Maximizing the number of regions:",
        "Bootstrap:",
        "Variable loadings",
        "Regionalization analysis",
        "Fitting segmented linear regressions",
        "Selecting best model for each number of regions",
        "Selecting best overall model and region score",
        "Adding more regions",
        "Model performance",
        "Breakpoint position variability",
        "Visualizing results",
        "Segmented linear regression plots",
        "Vertebral maps",
        "Model fitting parameters",
        "Continuous vs. discontinuous fit",
        "Minimum number of elements per region",
        "Forcing or preventing specific breakpoint positions",
        "Exhaustive vs. non-exhaustive search",
        "Parallel computing",
        "Intraspecific variability",
        "Raw morphometrics (Pipeline 1):",
        "PCs from traditional morphometrics (Pipeline 2):",
        "PCs from geometric morphometrics (Pipeline 3):",
        "Perform regionalization analysis:",
        "Other useful options",
        "Fitting a specific model",
        "Subsampling elements",
        "Simulating data",
        "References"
      ],
      "created": "2024-07-23 19:37:58",
      "modified": "2026-07-17 10:09:43",
      "commits": 5
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "morphoregions",
  "_universes": [
    "aagillet"
  ],
  "_previous": "0.1.1",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-07-17T12:24:41.000Z",
      "distro": "resolute",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/a32214b463fc5f680316cfb11ef68f0fc03315f475f36422c62890ef9fd426ac",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.2.0",
      "date": "2026-07-17T12:24:33.000Z",
      "distro": "resolute",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/f57dfea15ed9b58569b827920ae29813269ea25cbd8f3025eaac5d4dc13ed7f3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-07-17T12:24:33.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/c8efb6b79fa0c5bfba70ea4a5517e555ec4c38742dcfd648798d2a480582471d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.2.0",
      "date": "2026-07-17T12:23:55.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/0673273a49a59b29e8f1ebfbbd693911e8091cfc1472949d5458f5c054c9f964",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.0",
      "date": "2026-07-17T12:24:26.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/9469ea4c771f63d20b3b79f84bee2264d579d9370fb5a9667206d06e6f65ba38",
      "status": "success",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-07-17T12:23:15.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/400c3abe17ec650803807bdcada1c7555a07a50d5214bd9a45ccff4ada2ccc12",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-07-17T12:23:19.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/f8c82edbe6412d9cdf64500f2c09e27fcec309eb291928b9dbe63b3c496626f0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.2.0",
      "date": "2026-07-17T12:23:57.000Z",
      "commit": "b27f2f3089b6536c0fa623dbb0068c4157b30935",
      "fileid": "https://r2.ropensci.org/3b86202890df246db36aca2c2a8a02945995fb065fd7a97cda5bcea69000c950",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/aagillet/actions/runs/29579744482"
    }
  ]
}