{
  "_id": "6a21f6aacd65a98ecbd43471",
  "Package": "PAMpal",
  "Type": "Package",
  "Title": "Load and Process Passive Acoustic Data",
  "Version": "1.5.2",
  "Authors@R": "c(\nTS = person(\"Taiki\", \"Sakai\", email = \"taiki.sakai@noaa.gov\", role = c(\"aut\", \"cre\")),\nJB = person(\"Jay\", \"Barlow\", role = c(\"ctb\")),\nEG = person(\"Emily\", \"Griffiths\", role = c(\"ctb\")),\nMO = person(\"Michael\", \"Oswald\", role = c(\"ctb\")),\nSB = person(\"Simone\", \"Baumann-Pickering\", role = c(\"ctb\")),\nJO = person(\"Julie\", \"Oswald\", role = c(\"ctb\")))",
  "Maintainer": "Taiki Sakai <taiki.sakai@noaa.gov>",
  "Description": "Tools for loading and processing passive acoustic data.\nRead in data that has been processed in 'Pamguard'\n(<https://www.pamguard.org/>), apply a suite processing\nfunctions, and export data for reports or external modeling\ntools. Parameter calculations implement methods by Oswald et al\n(2007) <doi:10.1121/1.2743157>, Griffiths et al (2020)\n<doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)\n<doi:10.1121/1.3479549>.",
  "License": "GNU General Public License",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "cmake libfftw3-dev make libicu-dev libpng-dev\nlibsndfile1-dev libuv1-dev libxml2-dev libnetcdf-dev libssl-dev\npython3 zlib1g-dev",
  "Repository": "https://taikisan21.r-universe.dev",
  "Date/Publication": "2026-02-26 20:04:14 UTC",
  "RemoteUrl": "https://github.com/taikisan21/pampal",
  "RemoteRef": "HEAD",
  "RemoteSha": "8f800f35cf48425dd574d09e6cb01626f22f2f98",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 21:59:55 UTC",
    "User": "root"
  },
  "Author": "Taiki Sakai [aut, cre],\nJay Barlow [ctb],\nEmily Griffiths [ctb],\nMichael Oswald [ctb],\nSimone Baumann-Pickering [ctb],\nJulie Oswald [ctb]",
  "MD5sum": "79e74b64026a4dc02377645e8cad34c7",
  "_user": "taikisan21",
  "_type": "src",
  "_file": "PAMpal_1.5.2.tar.gz",
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  "_filesize": 684279,
  "_sha256": "c4c7fd6d5bb45dc6c4ac651007e006d3435963978fc51443b56b375237c5f48e",
  "_created": "2026-06-04T21:59:55.000Z",
  "_published": "2026-06-04T22:05:30.101Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/taikisan21/actions/runs/26981980043",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/taikisan21/pampal",
  "_commit": {
    "id": "8f800f35cf48425dd574d09e6cb01626f22f2f98",
    "author": "Taiki <tnsakai@gmail.com>",
    "committer": "Taiki <tnsakai@gmail.com>",
    "message": "wrapping some process examples in donttest to avoid going ever example time limit\n",
    "time": 1772136254
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  "_maintainer": {
    "name": "Taiki Sakai",
    "email": "taiki.sakai@noaa.gov",
    "login": "taiki-sakai",
    "description": "",
    "uuid": 186210537
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.1.1",
      "role": "Depends"
    },
    {
      "package": "PamBinaries",
      "version": ">= 1.3.0",
      "role": "Imports"
    },
    {
      "package": "PAMmisc",
      "version": ">= 1.12.0",
      "role": "Imports"
    },
    {
      "package": "tuneR",
      "role": "Imports"
    },
    {
      "package": "seewave",
      "role": "Imports"
    },
    {
      "package": "gam",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "RSQLite",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "signal",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
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    },
    {
      "package": "knitr",
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    },
    {
      "package": "xml2",
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    },
    {
      "package": "rlang",
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    },
    {
      "package": "reticulate",
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    {
      "package": "geosphere",
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    },
    {
      "package": "shiny",
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    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "taikisan21",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-24",
      "n": 1
    },
    {
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  ],
  "_tags": [],
  "_stars": 11,
  "_contributors": [
    {
      "user": "taikisan21",
      "count": 284,
      "uuid": 13296556
    },
    {
      "user": "taiki-sakai",
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      "uuid": 186210537
    }
  ],
  "_userbio": {
    "uuid": 13296556,
    "type": "user",
    "name": "Taiki Sakai"
  },
  "_downloads": {
    "count": 216,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PAMpal"
  },
  "_devurl": "https://github.com/taikisan21/pampal",
  "_searchresults": 94,
  "_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/PAMpal.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/taikisan21/pampal",
  "_realowner": "taikisan21",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.9.14",
      "date": "2020-12-17"
    },
    {
      "version": "0.13.0",
      "date": "2021-06-21"
    },
    {
      "version": "0.14.4",
      "date": "2021-10-09"
    },
    {
      "version": "0.15.0",
      "date": "2022-01-11"
    },
    {
      "version": "0.16.0",
      "date": "2022-03-07"
    },
    {
      "version": "0.17.0",
      "date": "2022-11-08"
    },
    {
      "version": "0.19.1",
      "date": "2023-04-20"
    },
    {
      "version": "1.0.0",
      "date": "2023-08-12"
    },
    {
      "version": "1.2.1",
      "date": "2024-07-11"
    },
    {
      "version": "1.4.4",
      "date": "2025-03-04"
    },
    {
      "version": "1.5.2",
      "date": "2026-02-26"
    }
  ],
  "_exports": [
    "addAnnotation",
    "addBinaries",
    "addCalibration",
    "addDatabase",
    "addFPOD",
    "addFunction",
    "addGps",
    "addHydrophoneDepth",
    "addMeasures",
    "addNote",
    "addRecordings",
    "addSettings",
    "addWaveHeight",
    "ancillary",
    "ancillary<-",
    "applyCalibration",
    "bindStudies",
    "calculateAverageSpectra",
    "calculateEchoDepth",
    "calculateICI",
    "checkAnnotation",
    "checkStudy",
    "detectors",
    "detectors<-",
    "effort",
    "effort<-",
    "events",
    "events<-",
    "export_annomate",
    "export_banter",
    "files",
    "files<-",
    "filterEchoDepths",
    "getAnnotation",
    "getBinaryData",
    "getCepstrumData",
    "getClickData",
    "getClipData",
    "getDetectorData",
    "getFPODData",
    "getGPLData",
    "getICI",
    "getMeasures",
    "getNotes",
    "getWarnings",
    "getWhistleData",
    "gps",
    "gps<-",
    "id",
    "id<-",
    "is.AcousticEvent",
    "is.AcousticStudy",
    "is.PAMpalSettings",
    "loadPamguardXML",
    "localizations",
    "localizations<-",
    "mapWavFolder",
    "markAnnotated",
    "matchEnvData",
    "matchRecordingUrl",
    "matchTimeData",
    "models",
    "models<-",
    "nCepstrum",
    "nClicks",
    "nDetections",
    "nGPL",
    "nWhistles",
    "PAMpalSettings",
    "parseEventClipName",
    "plotDataExplorer",
    "plotGram",
    "plotSpectrogram",
    "plotWaveform",
    "plotWigner",
    "pps",
    "pps<-",
    "prepAnnotation",
    "processPgDetections",
    "removeBinaries",
    "removeCalibration",
    "removeDatabase",
    "removeFunction",
    "removeNote",
    "removeSettings",
    "roccaWhistleCalcs",
    "runDepthReview",
    "runIciReview",
    "sampleDetector",
    "setSpecies",
    "settings",
    "settings<-",
    "species",
    "species<-",
    "standardCepstrumCalcs",
    "standardClickCalcs",
    "summariseDiveDepth",
    "timeJoin",
    "updateFiles",
    "updatePamObject",
    "writeEventClips",
    "writeWignerData"
  ],
  "_datasets": [
    {
      "name": "exStudy",
      "title": "Example AcousticStudy Object",
      "object": "exStudy",
      "class": [
        "AcousticStudy"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "testCeps",
      "title": "A fake cepstrum contour",
      "object": "testCeps",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "testClick",
      "title": "A two-channel recording of a delphinid click",
      "object": "testClick",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "testGPL",
      "title": "A fake GPL detection",
      "object": "testGPL",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "testWhistle",
      "title": "A fake whistle contour",
      "object": "testWhistle",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AcousticEvent-class",
      "title": "'AcousticEvent' Class",
      "topics": [
        "AcousticEvent-class"
      ]
    },
    {
      "page": "AcousticStudy-class",
      "title": "'AcousticStudy' Class",
      "topics": [
        "AcousticStudy-class"
      ]
    },
    {
      "page": "addAnnotation",
      "title": "Add Annotation Data to an AcousticStudy Object",
      "topics": [
        "addAnnotation",
        "checkAnnotation",
        "export_annomate",
        "getAnnotation",
        "matchRecordingUrl",
        "prepAnnotation"
      ]
    },
    {
      "page": "addBinaries",
      "title": "Add Binaries to a PAMpalSettings Object",
      "topics": [
        "addBinaries"
      ]
    },
    {
      "page": "addCalibration",
      "title": "Add a Calibration File to a PAMpalSettings Object",
      "topics": [
        "addCalibration",
        "applyCalibration"
      ]
    },
    {
      "page": "addDatabase",
      "title": "Add a Database to a PAMpalSettings Object",
      "topics": [
        "addDatabase"
      ]
    },
    {
      "page": "addFPOD",
      "title": "Add FPOD Detector to an AcousticStudy",
      "topics": [
        "addFPOD"
      ]
    },
    {
      "page": "addFunction",
      "title": "Add a Function to a PAMpalSettings Object",
      "topics": [
        "addFunction"
      ]
    },
    {
      "page": "addGps",
      "title": "Add GPS Locations to an AcousticStudy",
      "topics": [
        "addGps",
        "addGps,AcousticEvent-method",
        "addGps,AcousticStudy-method",
        "addGps,ANY-method",
        "addGps,data.frame-method",
        "addGps,list-method"
      ]
    },
    {
      "page": "addHydrophoneDepth",
      "title": "Add Hydrophone Depth Data to an AcousticStudy",
      "topics": [
        "addHydrophoneDepth"
      ]
    },
    {
      "page": "addMeasures",
      "title": "Add Measures",
      "topics": [
        "addMeasures",
        "getMeasures"
      ]
    },
    {
      "page": "addNote",
      "title": "addNote",
      "topics": [
        "addNote",
        "getNotes"
      ]
    },
    {
      "page": "addRecordings",
      "title": "Add Recordings to an AcousticStudy Object",
      "topics": [
        "addRecordings",
        "mapWavFolder"
      ]
    },
    {
      "page": "addSettings",
      "title": "Add Settingss to a PAMpalSettings Object",
      "topics": [
        "addSettings"
      ]
    },
    {
      "page": "addWaveHeight",
      "title": "Add Wave Height Data to an AcousticStudy",
      "topics": [
        "addWaveHeight"
      ]
    },
    {
      "page": "bindStudies",
      "title": "Combine AcousticStudy Objects",
      "topics": [
        "bindStudies"
      ]
    },
    {
      "page": "calculateAverageSpectra",
      "title": "Calculate Average Spectra of Clicks",
      "topics": [
        "calculateAverageSpectra"
      ]
    },
    {
      "page": "calculateEchoDepth",
      "title": "Calculate Depth from Echoes",
      "topics": [
        "calculateEchoDepth"
      ]
    },
    {
      "page": "calculateICI",
      "title": "Calculate Inter-Click Interval",
      "topics": [
        "calculateICI",
        "calculateICI,AcousticEvent-method",
        "calculateICI,AcousticStudy-method",
        "getICI"
      ]
    },
    {
      "page": "calculateModuleData",
      "title": "Run Custom Calculations on Pamguard Module Data",
      "topics": [
        "calculateModuleData"
      ]
    },
    {
      "page": "checkStudy",
      "title": "Check an AcousticStudy Object for Issues",
      "topics": [
        "checkStudy"
      ]
    },
    {
      "page": "export_banter",
      "title": "Export Data for a BANTER Model",
      "topics": [
        "export_banter"
      ]
    },
    {
      "page": "exStudy",
      "title": "Example AcousticStudy Object",
      "topics": [
        "exStudy"
      ]
    },
    {
      "page": "filter",
      "title": "Filter an AcousticStudy or AcousticEvent Object",
      "topics": [
        "filter.AcousticStudy"
      ]
    },
    {
      "page": "filterEchoDepths",
      "title": "Filter Candidate Echo Depths",
      "topics": [
        "filterEchoDepths"
      ]
    },
    {
      "page": "getBinaryData",
      "title": "Get Raw Binary Data for Detections",
      "topics": [
        "getBinaryData"
      ]
    },
    {
      "page": "getClipData",
      "title": "Get Wav Clips of Data",
      "topics": [
        "getClipData"
      ]
    },
    {
      "page": "getDetectorData",
      "title": "Extract and Combine Detector Data",
      "topics": [
        "getCepstrumData",
        "getClickData",
        "getDetectorData",
        "getFPODData",
        "getGPLData",
        "getWhistleData",
        "nCepstrum",
        "nClicks",
        "nDetections",
        "nGPL",
        "nWhistles"
      ]
    },
    {
      "page": "getWarnings",
      "title": "Get Warning Messages",
      "topics": [
        "getWarnings"
      ]
    },
    {
      "page": "is.AcousticEvent",
      "title": "Check if an Object is an AcousticEvent",
      "topics": [
        "is.AcousticEvent"
      ]
    },
    {
      "page": "is.AcousticStudy",
      "title": "Check if an Object is an AcousticStudy",
      "topics": [
        "is.AcousticStudy"
      ]
    },
    {
      "page": "is.PAMpalSettings",
      "title": "Check if an Object is a PAMpalSettings",
      "topics": [
        "is.PAMpalSettings"
      ]
    },
    {
      "page": "loadPamguardXML",
      "title": "Load Pamguard XML Settings",
      "topics": [
        "loadPamguardXML"
      ]
    },
    {
      "page": "markAnnotated",
      "title": "Mark Detections as Annotated",
      "topics": [
        "markAnnotated"
      ]
    },
    {
      "page": "matchEnvData",
      "title": "Match Environmental Data to an AcousticStudy Object",
      "topics": [
        "matchEnvData,AcousticEvent-method",
        "matchEnvData,AcousticStudy-method"
      ]
    },
    {
      "page": "matchTimeData",
      "title": "Match time-based data to PAMpal objects",
      "topics": [
        "matchTimeData",
        "timeJoin"
      ]
    },
    {
      "page": "PAMpal.accessors",
      "title": "'AcousticEvent' and 'AcousticStudy' accessors",
      "topics": [
        "$,AcousticEvent-method",
        "$,AcousticStudy-method",
        "$<-,AcousticEvent-method",
        "$<-,AcousticStudy-method",
        "ancillary",
        "ancillary,AcousticEvent-method",
        "ancillary,AcousticStudy-method",
        "ancillary<-",
        "ancillary<-,AcousticEvent-method",
        "ancillary<-,AcousticStudy-method",
        "detectors",
        "detectors,AcousticEvent-method",
        "detectors,AcousticStudy-method",
        "detectors<-",
        "detectors<-,AcousticEvent-method",
        "effort",
        "effort,AcousticStudy-method",
        "effort<-",
        "effort<-,AcousticStudy-method",
        "events",
        "events,AcousticStudy-method",
        "events<-",
        "events<-,AcousticStudy-method",
        "files",
        "files,AcousticEvent-method",
        "files,AcousticStudy-method",
        "files<-",
        "files<-,AcousticEvent-method",
        "files<-,AcousticStudy-method",
        "gps",
        "gps,AcousticStudy-method",
        "gps<-",
        "gps<-,AcousticStudy-method",
        "id",
        "id,AcousticEvent-method",
        "id,AcousticStudy-method",
        "id<-",
        "id<-,AcousticEvent-method",
        "id<-,AcousticStudy-method",
        "localizations",
        "localizations,AcousticEvent-method",
        "localizations<-",
        "localizations<-,AcousticEvent-method",
        "models",
        "models,AcousticStudy-method",
        "models<-",
        "models<-,AcousticStudy-method",
        "PAMpal.accessors",
        "pps",
        "pps,AcousticStudy-method",
        "pps<-",
        "pps<-,AcousticStudy-method",
        "settings",
        "settings,AcousticEvent-method",
        "settings,AcousticStudy-method",
        "settings<-",
        "settings<-,AcousticEvent-method",
        "settings<-,AcousticStudy-method",
        "species",
        "species,AcousticEvent-method",
        "species,AcousticStudy-method",
        "species<-",
        "species<-,AcousticEvent-method",
        "[,AcousticEvent,ANY,ANY,ANY-method",
        "[,AcousticStudy,ANY,ANY,ANY-method",
        "[<-,AcousticEvent,ANY,ANY,ANY-method",
        "[<-,AcousticStudy,ANY,ANY,ANY-method",
        "[[,AcousticEvent,ANY,ANY-method",
        "[[,AcousticStudy,ANY,missing-method",
        "[[<-,AcousticEvent,ANY,ANY,ANY-method",
        "[[<-,AcousticStudy,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "PAMpalSettings",
      "title": "Constructor for PAMpalSettings Object",
      "topics": [
        "PAMpalSettings"
      ]
    },
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      "page": "PAMpalSettings-class",
      "title": "'PAMpalSettings' Class",
      "topics": [
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    {
      "page": "plotDataExplorer",
      "title": "Explore Data in an Interactive Shiny Plot",
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    },
    {
      "page": "plotGram",
      "title": "Plot Spectrogram or Cepstrogram",
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    },
    {
      "page": "plotWaveform",
      "title": "Plot Graphical Representations of Waveforms",
      "topics": [
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    {
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      "title": "Load and Process Detections from Pamguard",
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      "page": "removeBinaries",
      "title": "Remove Binaries from a PAMpalSettings Object",
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      "page": "removeCalibration",
      "title": "Remove a Calibration Function from a PAMpalSettings Object",
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      "title": "Remove a Database from a PAMpalSettings Object",
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      "page": "removeFunction",
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      "page": "removeSettings",
      "title": "Remove Settings from a PAMpalSettings Object",
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      "page": "roccaWhistleCalcs",
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      "page": "runDepthReview",
      "title": "Run Echo Depth Review App",
      "topics": [
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      "topics": [
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      "page": "setSpecies",
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      "topics": [
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      "page": "standardCepstrumCalcs",
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      "page": "standardClickCalcs",
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      "page": "testWhistle",
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