{
  "_id": "6a1146e1acfb0bcc41ce7bd1",
  "Package": "shapeR",
  "Type": "Package",
  "Title": "Collection and Analysis of Otolith Shape Data",
  "Version": "0.1-5",
  "Date": "2015-05-19",
  "Authors@R": "c(person(\"Lisa Anne\", \"Libungan\", role = c(\"aut\", \"cre\"), \nemail = \"lisa.libungan@gmail.com\"),\nperson(\"Snaebjorn\", \"Palsson\", role = c(\"aut\", \"ths\"),\nemail = \"snaebj@hi.is\"))",
  "Maintainer": "Lisa Anne Libungan <lisa.libungan@gmail.com>",
  "Description": "Studies otolith shape variation among fish populations.\nOtoliths are calcified structures found in the inner ear of\nteleost fish and their shape has been known to vary among\nseveral fish populations and stocks, making them very useful in\ntaxonomy, species identification and to study geographic\nvariations. The package extends previously described software\nused for otolith shape analysis by allowing the user to\nautomatically extract closed contour outlines from a large\nnumber of images, perform smoothing to eliminate pixel noise,\nchoose from conducting either a Fourier or wavelet transform to\nthe outlines and visualize the mean shape. The output of the\npackage are independent Fourier or wavelet coefficients which\ncan be directly imported into a wide range of statistical\npackages in R. The package might prove useful in studies of any\ntwo dimensional objects.",
  "License": "GPL(>=2)",
  "URL": "https://github.com/lisalibungan/shapeR,\nhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121102",
  "LazyDataCompression": "yes",
  "Config/pak/sysreqs": "libjpeg-dev",
  "Repository": "https://lisalibungan.r-universe.dev",
  "Date/Publication": "2018-03-14 11:03:52 UTC",
  "RemoteUrl": "https://github.com/lisalibungan/shaper",
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  "Packaged": {
    "Date": "2026-05-23 06:15:49 UTC",
    "User": "root"
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  "Author": "Lisa Anne Libungan [aut, cre],\nSnaebjorn Palsson [aut, ths]",
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  "_tags": [],
  "_stars": 9,
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/shapeR"
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  "_devurl": "https://github.com/lisalibungan/shaper",
  "_searchresults": 29,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
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    "manual.pdf"
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  "_realowner": "lisalibungan",
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      "date": "2015-04-03"
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      "date": "2015-05-20"
    },
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      "date": "2022-11-22"
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    {
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      "date": "2025-10-28"
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    "cluster.plot",
    "detect.outline",
    "enrich.master.list",
    "estimate.outline.reconstruction",
    "generateShapeCoefficients",
    "getFourier",
    "getMasterlist",
    "getMeasurements",
    "getStdFourier",
    "getStdMeasurements",
    "getStdWavelet",
    "getWavelet",
    "outline.reconstruction.plot",
    "plotFourier",
    "plotFourierShape",
    "plotWavelet",
    "plotWaveletShape",
    "read.master.list",
    "remove.outline",
    "setFilter",
    "shapeR",
    "show",
    "show.original.with.outline",
    "smoothout",
    "stdCoefs",
    "write.image.with.outline"
  ],
  "_datasets": [
    {
      "name": "FISH",
      "title": "An example data file",
      "object": "FISH",
      "file": "FISH.csv.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "country",
        "station",
        "pop",
        "stockID",
        "day",
        "month",
        "year",
        "lat",
        "lon",
        "fishno",
        "length_cm",
        "weight_g",
        "age",
        "sex",
        "maturity",
        "folder",
        "picname",
        "cal"
      ],
      "rows": 240,
      "table": true,
      "tojson": true
    },
    {
      "name": "shape",
      "title": "An example shapeR instance including 160 images.",
      "object": "otoliths",
      "file": "otoliths.RData",
      "class": [
        "shapeR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "shape",
      "title": "An example shapeR instance including 160 images.",
      "object": "shape",
      "file": "shape.RData",
      "class": [
        "shapeR"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "cluster.plot",
      "title": "Plot data clusters",
      "topics": [
        "cluster.plot"
      ]
    },
    {
      "page": "detect.outline",
      "title": "Detect otolith outline",
      "topics": [
        "detect.outline"
      ]
    },
    {
      "page": "enrich.master.list",
      "title": "Link information in the info.file to the coefficients obtained from the otolith images",
      "topics": [
        "enrich.master.list"
      ]
    },
    {
      "page": "estimate.outline.reconstruction",
      "title": "Estimate the outline reconstruction based on Fourier/wavelet compared to the outlines that have not been transformed",
      "topics": [
        "estimate.outline.reconstruction"
      ]
    },
    {
      "page": "FISH",
      "title": "An example data file",
      "topics": [
        "FISH"
      ]
    },
    {
      "page": "generateShapeCoefficients",
      "title": "Get wavelet/Fourier coefficients and basic shape variables",
      "topics": [
        "generateShapeCoefficients"
      ]
    },
    {
      "page": "getFourier",
      "title": "Get Fourier coefficients, filtered according to filter",
      "topics": [
        "getFourier"
      ]
    },
    {
      "page": "getMasterlist",
      "title": "Get filtered master.list values",
      "topics": [
        "getMasterlist"
      ]
    },
    {
      "page": "getMeasurements",
      "title": "Get simple shape variables, filtered according to filter",
      "topics": [
        "getMeasurements"
      ]
    },
    {
      "page": "getStdFourier",
      "title": "Get standardized Fourier coefficients, filtered according to filter",
      "topics": [
        "getStdFourier"
      ]
    },
    {
      "page": "getStdMeasurements",
      "title": "Get simple shape variables after standardization, filtered according to filter",
      "topics": [
        "getStdMeasurements"
      ]
    },
    {
      "page": "getStdWavelet",
      "title": "Get standardized wavelet coefficients, filtered according to filter",
      "topics": [
        "getStdWavelet"
      ]
    },
    {
      "page": "getWavelet",
      "title": "Get wavelet coefficients, filtered according to filter",
      "topics": [
        "getWavelet"
      ]
    },
    {
      "page": "outline.reconstruction.plot",
      "title": "Plot outline reconstruction",
      "topics": [
        "outline.reconstruction.plot"
      ]
    },
    {
      "page": "plotFourier",
      "title": "Mean and standard deviation of the Fourier coefficients",
      "topics": [
        "plotFourier"
      ]
    },
    {
      "page": "plotFourierShape",
      "title": "Mean otolith shape based on Fourier reconstruction",
      "topics": [
        "plotFourierShape"
      ]
    },
    {
      "page": "plotWavelet",
      "title": "Mean and standard deviation of the wavelet coefficients",
      "topics": [
        "plotWavelet"
      ]
    },
    {
      "page": "plotWaveletShape",
      "title": "Mean otolith shape based on wavelet reconstruction",
      "topics": [
        "plotWaveletShape"
      ]
    },
    {
      "page": "read.master.list",
      "title": "Read updated master list",
      "topics": [
        "read.master.list"
      ]
    },
    {
      "page": "remove.outline",
      "title": "Remove otolith outline",
      "topics": [
        "remove.outline"
      ]
    },
    {
      "page": "setFilter",
      "title": "Set a filter to analyze the shape data",
      "topics": [
        "setFilter"
      ]
    },
    {
      "page": "shape",
      "title": "An example shapeR instance including 160 images.",
      "topics": [
        "shape"
      ]
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        "shapeR-package",
        "shapeR",
        "shapeR-class"
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        "show,shapeR-method"
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      "title": "Show the extracted outline on top of the original image",
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      ]
    },
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      "page": "smoothout",
      "title": "Contour smoothing",
      "topics": [
        "smoothout"
      ]
    },
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      "page": "stdCoefs",
      "title": "Standardize coefficients",
      "topics": [
        "stdCoefs"
      ]
    },
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      "page": "write.image.with.outline",
      "title": "Write outlines on top of the original images for quality checking",
      "topics": [
        "write.image.with.outline"
      ]
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