{
  "_id": "6a10577aacfb0bcc41ca2fd7",
  "Package": "yaps",
  "Title": "Track Estimation using YAPS (Yet Another Positioning Solver)",
  "Version": "1.2.5",
  "Authors@R": "c(\tperson(\"Henrik\", \"Baktoft\", email = \"hba@aqua.dtu.dk\", role = c(\"cre\", \"aut\"), comment=c(ORCID = \"0000-0002-3644-4960\")),\nperson(\"Karl\", \"Gjelland\", role=c(\"aut\"), comment=c(ORCID = \"0000-0003-4036-4207\")),\nperson(\"Uffe H.\", \"Thygesen\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-4311-6324\")),\nperson(\"Finn\", \"Økland\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-1938-5460\"))\n)",
  "Description": "Estimate tracks of animals tagged with acoustic\ntransmitters. 'yaps' was introduced in 2017 as a transparent\nopen-source tool to estimate positions of fish (and other\naquatic animals) tagged with acoustic transmitters. Based on\nregistrations of acoustic transmitters on hydrophones\npositioned in a fixed array, 'yaps' enables users to\nsynchronize the collected data (i.e. correcting for drift in\nthe internal clocks of the hydrophones/receivers) and\nsubsequently to estimate tracks of the tagged animals. The\npaper introducing 'yaps' is available in open access at\nBaktoft, Gjelland, Økland & Thygesen (2017)\n<doi:10.1038/s41598-017-14278-z>. Also check out our cookbook\nwith a completely worked through example at Baktoft, Gjelland,\nØkland, Rehage, Rodemann, Corujo, Viadero & Thygesen (2019)\n<DOI:10.1101/2019.12.16.877688>. Additional tutorials will\neventually make their way onto the project website at\n<https://baktoft.github.io/yaps/>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.1.1",
  "Remotes": [
    "spkaluzny/splusTimeSeries",
    "spkaluzny/splusTimeDate"
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  "URL": "https://github.com/baktoft/yaps, https://baktoft.github.io/yaps/",
  "BugReports": "https://github.com/baktoft/yaps/issues",
  "Config/pak/sysreqs": "cmake libicu-dev",
  "Repository": "https://mhpob.r-universe.dev",
  "Date/Publication": "2023-11-07 12:14:40 UTC",
  "RemoteUrl": "https://github.com/baktoft/yaps",
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  "Packaged": {
    "Date": "2026-05-09 07:20:20 UTC",
    "User": "root"
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  "Author": "Henrik Baktoft [cre, aut] (ORCID:\n<https://orcid.org/0000-0002-3644-4960>),\nKarl Gjelland [aut] (ORCID: <https://orcid.org/0000-0003-4036-4207>),\nUffe H. Thygesen [aut] (ORCID: <https://orcid.org/0000-0002-4311-6324>),\nFinn Økland [aut] (ORCID: <https://orcid.org/0000-0002-1938-5460>)",
  "Maintainer": "Henrik Baktoft <hba@aqua.dtu.dk>",
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  "_user": "mhpob",
  "_type": "src",
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  "_created": "2026-05-09T07:20:20.000Z",
  "_published": "2026-05-22T13:17:46.228Z",
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    "name": "Mike O'Brien",
    "description": "Faculty Research Assistant at the Chesapeake Biological Laboratory"
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    "applySync",
    "checkInp",
    "checkInpSync",
    "fineTuneSyncModel",
    "getBbox",
    "getInp",
    "getInpSync",
    "getSyncCoverage",
    "getSyncModel",
    "getToaYaps",
    "plotBbox",
    "plotSyncModelCheck",
    "plotSyncModelHydros",
    "plotSyncModelResids",
    "plotYaps",
    "prepDetections",
    "runTmb",
    "runYaps",
    "simHydros",
    "simTelemetryTrack",
    "simToa",
    "simTrueTrack",
    "tempToSs",
    "testYaps"
  ],
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      "name": "dat_align",
      "title": "Example data for showcasing yaps function alignBurstSeq()",
      "object": "dat_align",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "title": "Test data from Florida Bay",
      "object": "ssu1",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
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  "_help": [
    {
      "page": "alignBurstSeq",
      "title": "Align synced data with known burst sequence",
      "topics": [
        "alignBurstSeq"
      ]
    },
    {
      "page": "applySync",
      "title": "Apply sync model to toa matrix to obtain synced data",
      "topics": [
        "applySync"
      ]
    },
    {
      "page": "checkInp",
      "title": "Check consistency of 'inp' object obtained from 'getInp()'",
      "topics": [
        "checkInp"
      ]
    },
    {
      "page": "checkInpSync",
      "title": "Check consistency of 'inp_sync' object obtained from 'getInpSync()'",
      "topics": [
        "checkInpSync"
      ]
    },
    {
      "page": "dat_align",
      "title": "Example data for showcasing yaps function alignBurstSeq()",
      "topics": [
        "dat_align"
      ]
    },
    {
      "page": "fineTuneSyncModel",
      "title": "Fine-tune an already fitted sync_model Wrapper function to re-run getSyncModel() using the same data, but excluding outliers. Note dimensions of data might change if eps_threshold results in empty rows in the TOA-matrix.",
      "topics": [
        "fineTuneSyncModel"
      ]
    },
    {
      "page": "getBbox",
      "title": "Get a standard bounding box to impose spatial constraints",
      "topics": [
        "getBbox"
      ]
    },
    {
      "page": "getInp",
      "title": "Get prepared inp-object for use in TMB-call",
      "topics": [
        "getInp"
      ]
    },
    {
      "page": "getInpSync",
      "title": "Get object inp for synchronization",
      "topics": [
        "getInpSync"
      ]
    },
    {
      "page": "getSyncCoverage",
      "title": "Quick overview to check if all hydros have enough data within each offset period.",
      "topics": [
        "getSyncCoverage"
      ]
    },
    {
      "page": "getSyncModel",
      "title": "Get sync model from inp_sync object obtained by 'getInpSync()'",
      "topics": [
        "getSyncModel"
      ]
    },
    {
      "page": "getToaYaps",
      "title": "Build TOA matrix from synced data.table - also do some pre-filtering of severe MP, pruning loose ends etc",
      "topics": [
        "getToaYaps"
      ]
    },
    {
      "page": "plotBbox",
      "title": "Graphical representation of spatial constraints",
      "topics": [
        "plotBbox"
      ]
    },
    {
      "page": "plotSyncModelCheck",
      "title": "Plot to check how well the sync model is working",
      "topics": [
        "plotSyncModelCheck"
      ]
    },
    {
      "page": "plotSyncModelHydros",
      "title": "Plot hydrophone positions. Especially useful if some hydro re-positioned as part of the sync model.",
      "topics": [
        "plotSyncModelHydros"
      ]
    },
    {
      "page": "plotSyncModelResids",
      "title": "Plot residuals of sync_model to enable check of model",
      "topics": [
        "plotSyncModelResids"
      ]
    },
    {
      "page": "plotYaps",
      "title": "Basic plots of yaps output",
      "topics": [
        "plotYaps"
      ]
    },
    {
      "page": "prepDetections",
      "title": "Experimental! Prepare detections data.table from raw data - csv-files exported from vendor software",
      "topics": [
        "prepDetections"
      ]
    },
    {
      "page": "runYaps",
      "title": "Function to run TMB to estimate track",
      "topics": [
        "runTmb",
        "runYaps"
      ]
    },
    {
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      "title": "Sim hydrophone array configuration",
      "topics": [
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      ]
    },
    {
      "page": "simTelemetryTrack",
      "title": "Simulate telemetry track based on known true track obtained using simTrueTrack",
      "topics": [
        "simTelemetryTrack"
      ]
    },
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      "title": "Sim TOA matrix for the supplied telemetryTrack",
      "topics": [
        "simToa"
      ]
    },
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      "title": "Simulate a known movement track for subsequent estimation using YAPS",
      "topics": [
        "simTrueTrack"
      ]
    },
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      "title": "Test data from Florida Bay",
      "topics": [
        "ssu1"
      ]
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      "page": "tempToSs",
      "title": "Calculate speed of sound from water temperature, salinity and depth Based on H. Medwin (1975) Speed of sound in water: A simple equation for realistic parameters. (https://doi.org/10.1121/1.380790)",
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      ]
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      "title": "Test YAPS core functionality",
      "topics": [
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      ]
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