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  "Title": "Read, Plot and Analyse Output from the DEPONS Model",
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  "Description": "Methods for analyzing population dynamics and movement\ntracks simulated using the DEPONS model <https://www.depons.eu>\n(v.3.0), for manipulating input raster files, shipping routes\nand for analyzing sound propagated from ships.",
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  "Date/Publication": "2026-03-27 14:25:54 UTC",
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  "_releases": [
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      "date": "2020-10-26"
    },
    {
      "version": "1.0.3",
      "date": "2021-04-26"
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    {
      "version": "1.1.4",
      "date": "2022-07-03"
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    {
      "version": "1.1.6",
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  "_exports": [
    "aggregate.dpm.sim.dat",
    "ais.to.DeponsShips",
    "as.data.frame",
    "as.DeponsRaster",
    "as.raster",
    "bbox",
    "calib_01",
    "calib_02",
    "calib_03_make_sim_dpm",
    "calib_03_ssd",
    "check.DeponsShips",
    "crs",
    "crs<-",
    "dyn",
    "find.nearest.piling",
    "get.latest.sim",
    "get.pods.at.dist.sim.dat",
    "get.simtime",
    "interpolate.ais.data",
    "interpolate.maps",
    "landscape",
    "landscape<-",
    "make.blocksraster",
    "make.clip.poly",
    "make.construction.traffic",
    "make.DeponsDyn",
    "make.stationary.ships",
    "make.windfarms",
    "plot",
    "plot_calib02",
    "read.DeponsBlockdyn",
    "read.DeponsDyn",
    "read.DeponsDynBatch",
    "read.DeponsParam",
    "read.DeponsRaster",
    "read.DeponsShips",
    "read.DeponsTrack",
    "read.DeponsTrackBatch",
    "routes",
    "routes<-",
    "set.ship.type",
    "ships",
    "ships<-",
    "startday",
    "startday<-",
    "summarise.aggregated.dpm.dat",
    "summary",
    "tick.to.time",
    "time.to.tick",
    "title",
    "title<-",
    "write"
  ],
  "_datasets": [
    {
      "name": "aisdata",
      "title": "Position for three ships in the inner Danish waters",
      "object": "aisdata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "id",
        "time",
        "speed",
        "type",
        "length",
        "x",
        "y"
      ],
      "rows": 144,
      "table": true,
      "tojson": true
    },
    {
      "name": "argosmetrics",
      "title": "Fine and Large-scale metrics of Argos data",
      "object": "argosmetrics",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "bathymetry",
      "title": "Bathymetry of the Kattegat area",
      "object": "bathymetry",
      "class": [
        "DeponsRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "coastline",
      "title": "Coastline of Northern Europe",
      "object": "coastline",
      "class": [
        "SpatialPolygons"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "geminidata",
      "title": "Observed and simulated data from Gemini windfarm construction",
      "object": "geminidata",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "porpoisebdyn",
      "title": "Simulated porpoise population dynamics",
      "object": "porpoisebdyn",
      "class": [
        "DeponsBlockdyn"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "porpoisedyn",
      "title": "Simulated porpoise population dynamics",
      "object": "porpoisedyn",
      "class": [
        "DeponsDyn"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "porpoisetrack",
      "title": "Simulated porpoise track",
      "object": "porpoisetrack",
      "class": [
        "DeponsTrack"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "shipdata",
      "title": "Ships on example routes through the Kattegat",
      "object": "shipdata",
      "class": [
        "DeponsShips"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "aggregate.dpm.sim.dat",
      "title": "Aggregate simulated porpoise detections by piling event and hour",
      "topics": [
        "aggregate.dpm.sim.dat"
      ]
    },
    {
      "page": "ais.to.DeponsShips",
      "title": "Convert ship tracks to DeponsShips object",
      "topics": [
        "ais.to.DeponsShips"
      ]
    },
    {
      "page": "aisdata",
      "title": "Position for three ships in the inner Danish waters",
      "topics": [
        "aisdata"
      ]
    },
    {
      "page": "argosmetrics",
      "title": "Fine and Large-scale metrics of Argos data",
      "topics": [
        "argosmetrics"
      ]
    },
    {
      "page": "as.data.frame-DeponsDyn-method",
      "title": "Convert DeponsDyn object to data frame",
      "topics": [
        "as.data.frame,DeponsDyn-method"
      ]
    },
    {
      "page": "as.data.frame-DeponsTrack-method",
      "title": "Convert DeponsTrack to data frame",
      "topics": [
        "as.data.frame,DeponsTrack-method"
      ]
    },
    {
      "page": "as.DeponsRaster",
      "title": "Convert a RasterLayer into a DeponsRaster",
      "topics": [
        "as.DeponsRaster",
        "as.DeponsRaster,RasterLayer-method"
      ]
    },
    {
      "page": "as.raster",
      "title": "Convert a DeponsRaster into a RasterLayer",
      "topics": [
        "as.raster",
        "as.raster,DeponsRaster-method"
      ]
    },
    {
      "page": "bathymetry",
      "title": "Bathymetry of the Kattegat area",
      "topics": [
        "bathymetry"
      ]
    },
    {
      "page": "bbox",
      "title": "Get bbox from Depons* object",
      "topics": [
        "bbox",
        "bbox,DeponsRaster-method",
        "bbox,DeponsTrack-method"
      ]
    },
    {
      "page": "calib_01",
      "title": "Plot distribution of turning angles, step lengths and speed of tracked simulated porpoises.",
      "topics": [
        "calib_01"
      ]
    },
    {
      "page": "calib_02",
      "title": "Calculate calibration metrics of previously filtered tracks (fine-scale or large-scale)",
      "topics": [
        "calib_02"
      ]
    },
    {
      "page": "calib_03_make_sim_dpm",
      "title": "Create piling-response table from simulated porpoise counts",
      "topics": [
        "calib_03_make_sim_dpm"
      ]
    },
    {
      "page": "calib_03_ssd",
      "title": "Compute SSD for one response to piling simulation",
      "topics": [
        "calib_03_ssd"
      ]
    },
    {
      "page": "check.DeponsShips",
      "title": "Check if ships move at unrealistic speeds or are outside the map boundary",
      "topics": [
        "check.DeponsShips"
      ]
    },
    {
      "page": "coastline",
      "title": "Coastline of Northern Europe",
      "topics": [
        "coastline"
      ]
    },
    {
      "page": "crs",
      "title": "Get or set map projection in Depons* objects",
      "topics": [
        "crs",
        "crs,DeponsRaster-method",
        "crs,DeponsShips-method",
        "crs,DeponsTrack-method",
        "crs<-",
        "crs<-,DeponsRaster-method",
        "crs<-,DeponsShips-method",
        "crs<-,DeponsTrack-method"
      ]
    },
    {
      "page": "DEPONS2R",
      "title": "Package for analyzing DEPONS simulation output",
      "topics": [
        "DEPONS2R"
      ]
    },
    {
      "page": "DeponsBlockdyn-class",
      "title": "DeponsBlockdyn-class",
      "topics": [
        "DeponsBlockdyn-class"
      ]
    },
    {
      "page": "DeponsDyn-class",
      "title": "DeponsDyn-class",
      "topics": [
        "DeponsDyn-class"
      ]
    },
    {
      "page": "DeponsRaster-class",
      "title": "DeponsRaster-class",
      "topics": [
        "DeponsRaster-class"
      ]
    },
    {
      "page": "DeponsShips-class",
      "title": "DeponsShips-class",
      "topics": [
        "DeponsShips-class"
      ]
    },
    {
      "page": "DeponsTrack-class",
      "title": "DeponsTrack-class",
      "topics": [
        "DeponsTrack-class"
      ]
    },
    {
      "page": "dyn",
      "title": "Extract population dynamics from objects",
      "topics": [
        "dyn",
        "dyn,DeponsBlockdyn-method",
        "dyn,DeponsDyn-method"
      ]
    },
    {
      "page": "find.nearest.piling",
      "title": "Find nearest active piling from simulated CPOD blocks",
      "topics": [
        "find.nearest.piling"
      ]
    },
    {
      "page": "geminidata",
      "title": "Observed and simulated data from Gemini windfarm construction",
      "topics": [
        "geminidata"
      ]
    },
    {
      "page": "get.latest.sim",
      "title": "Get name of newest file",
      "topics": [
        "get.latest.sim"
      ]
    },
    {
      "page": "get.pods.at.dist.sim.dat",
      "title": "Assign hours since piling for detections within a distance interval",
      "topics": [
        "get.pods.at.dist.sim.dat"
      ]
    },
    {
      "page": "get.simtime",
      "title": "Get simulation date",
      "topics": [
        "get.simtime"
      ]
    },
    {
      "page": "interpolate.ais.data",
      "title": "Interpolate AIS data",
      "topics": [
        "interpolate.ais.data"
      ]
    },
    {
      "page": "interpolate.maps",
      "title": "Interpolate missing entries in a series of maps",
      "topics": [
        "interpolate.maps"
      ]
    },
    {
      "page": "landscape",
      "title": "Get or set the landscape name",
      "topics": [
        "landscape",
        "landscape,DeponsBlockdyn-method",
        "landscape,DeponsDyn-method",
        "landscape,DeponsTrack-method",
        "landscape<-",
        "landscape<-,DeponsBlockdyn-method",
        "landscape<-,DeponsDyn-method",
        "landscape<-,DeponsTrack-method"
      ]
    },
    {
      "page": "make.blocksraster",
      "title": "Makes new file with blocks",
      "topics": [
        "make.blocksraster",
        "make.blocksraster,DeponsRaster-method"
      ]
    },
    {
      "page": "make.clip.poly",
      "title": "Make clipping polygon from bbox",
      "topics": [
        "make.clip.poly",
        "make.clip.poly,matrix-method"
      ]
    },
    {
      "page": "make.construction.traffic",
      "title": "Generate artificial AIS data representing ship traffic during wind farm construction",
      "topics": [
        "make.construction.traffic"
      ]
    },
    {
      "page": "make.DeponsDyn",
      "title": "Make DeponsDyn object from data stored in data frame",
      "topics": [
        "make.DeponsDyn"
      ]
    },
    {
      "page": "make.stationary.ships",
      "title": "Identify and parameterize stationary active ships in a DeponsShips object",
      "topics": [
        "make.stationary.ships"
      ]
    },
    {
      "page": "make.windfarms",
      "title": "Make wind farm construction scenario",
      "topics": [
        "make.windfarms"
      ]
    },
    {
      "page": "plot_calib02",
      "title": "Plotting of simulated fine or large-scale metrics against argos data",
      "topics": [
        "plot_calib02"
      ]
    },
    {
      "page": "plot-DeponsBlockdyn-missing-method",
      "title": "Plot a DeponsBlockdyn object",
      "topics": [
        "plot,DeponsBlockdyn,missing-method",
        "plot.DeponsBlockdyn"
      ]
    },
    {
      "page": "plot-DeponsDyn-missing-method",
      "title": "Plot a DeponsDyn object",
      "topics": [
        "plot,DeponsDyn,missing-method",
        "plot.DeponsDyn"
      ]
    },
    {
      "page": "plot-DeponsRaster-ANY-method",
      "title": "Plot a DeponsRaster object",
      "topics": [
        "plot,DeponsRaster,ANY-method",
        "plot,DeponsRaster,DeponsTrack-method",
        "plot.DeponsRaster"
      ]
    },
    {
      "page": "plot-DeponsShips-missing-method",
      "title": "Plot a DeponsShips object",
      "topics": [
        "plot,DeponsShips,missing-method",
        "plot.DeponsShips"
      ]
    },
    {
      "page": "plot-DeponsTrack-missing-method",
      "title": "Plot a DeponsTrack object",
      "topics": [
        "plot,DeponsTrack,missing-method",
        "plot.DeponsTrack"
      ]
    },
    {
      "page": "porpoisebdyn",
      "title": "Simulated porpoise population dynamics",
      "topics": [
        "porpoisebdyn"
      ]
    },
    {
      "page": "porpoisedyn",
      "title": "Simulated porpoise population dynamics",
      "topics": [
        "porpoisedyn"
      ]
    },
    {
      "page": "porpoisetrack",
      "title": "Simulated porpoise track",
      "topics": [
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      "page": "read.DeponsBlockdyn",
      "title": "Reading simulated population count for blocks",
      "topics": [
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      "title": "Reading DEPONS simulation output",
      "topics": [
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      "topics": [
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      "topics": [
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        "summary,DeponsRaster-method",
        "summary,DeponsShips-method",
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      "title": "Get or set the title of Depons* objects",
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        "title,DeponsShips-method",
        "title,DeponsTrack-method",
        "title<-",
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