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  "Description": "Functions to estimate the density and size of a spatially\ndistributed animal population sampled with an array of passive\ndetectors, such as traps, or by searching polygons or\ntransects. Models incorporating distance-dependent detection\nare fitted by maximizing the likelihood. Tools are included for\ndata manipulation and model selection.",
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    "make.transect",
    "make.tri",
    "makeNewData",
    "makeStart",
    "markocc",
    "markocc<-",
    "mash",
    "mask.check",
    "maskarea",
    "masklength",
    "masksize",
    "MCgof",
    "MMDM",
    "model.average",
    "modelAverage",
    "moves",
    "ms",
    "MS.capthist",
    "nearesttrap",
    "nedist",
    "nk",
    "noise",
    "noise<-",
    "nontarget",
    "nontarget<-",
    "occasion",
    "occasionKey",
    "ORL",
    "par.derived",
    "par.region.N",
    "par.secr.fit",
    "pdot",
    "pdot.contour",
    "pdotContour",
    "PG",
    "plotMaskEdge",
    "plotMCP",
    "pmixProfileLL",
    "pointsInPolygon",
    "polyarea",
    "polyID",
    "polyID<-",
    "predictDlambda",
    "predictDsurface",
    "randomDensity",
    "randomHabitat",
    "rast",
    "raster",
    "read.capthist",
    "read.DA",
    "read.mask",
    "read.telemetry",
    "read.traps",
    "rectangularMask",
    "reduce",
    "region.N",
    "rlnormCV",
    "RMarkInput",
    "rotate",
    "RPSV",
    "RSE",
    "Rsurface",
    "score.table",
    "score.test",
    "searcharea",
    "secr.design.MS",
    "secr.fit",
    "secr.refit",
    "secr.test",
    "secrlist",
    "session",
    "session<-",
    "sessionlabels",
    "sessionlabels<-",
    "setNumThreads",
    "shareFactorLevels",
    "shift",
    "sighting",
    "sightingPlot",
    "signal",
    "signal<-",
    "signalframe",
    "signalframe<-",
    "signalmatrix",
    "sim.capthist",
    "sim.detect",
    "sim.popn",
    "sim.resight",
    "sim.secr",
    "simOU",
    "simOU.capthist",
    "snip",
    "spacing",
    "spacing<-",
    "spotHeight",
    "strip.legend",
    "suggest.buffer",
    "t2r2",
    "telemetered",
    "telemetrytype",
    "telemetrytype<-",
    "telemetryxy",
    "telemetryxy<-",
    "tile",
    "timevaryingcov",
    "timevaryingcov<-",
    "Tm",
    "Tm<-",
    "Tn",
    "Tn<-",
    "transectID",
    "transectID<-",
    "transectlength",
    "trap",
    "trap.builder",
    "traps",
    "traps<-",
    "trapsPerAnimal",
    "trim",
    "Tu",
    "Tu<-",
    "unjoin",
    "unRMarkInput",
    "updateCH",
    "usage",
    "usage<-",
    "usagePlot",
    "verify",
    "write.capthist",
    "write.captures",
    "write.DA",
    "write.mask",
    "write.traps",
    "writeGPS",
    "xy",
    "xy<-",
    "xy2CH"
  ],
  "_datasets": [
    {
      "name": "blackbear.0",
      "title": "Black Bear Hair Snag Dataset",
      "object": "blackbear",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blackbear.h2bk",
      "title": "Black Bear Hair Snag Dataset",
      "object": "blackbear",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "blackbearCH",
      "title": "Black Bear Hair Snag Dataset",
      "object": "blackbear",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "captdata",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "captXY",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Session",
        "ID",
        "Occasion",
        "X",
        "Y"
      ],
      "rows": 235,
      "table": true,
      "tojson": true
    },
    {
      "name": "deermouse.ESG",
      "title": "Deermouse Live-trapping Datasets",
      "object": "deermouse",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "deermouse.WSG",
      "title": "Deermouse Live-trapping Datasets",
      "object": "deermouse",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "FTHL.0",
      "title": "Flat-tailed Horned Lizard Dataset",
      "object": "hornedlizard",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "FTHL.CL",
      "title": "Flat-tailed Horned Lizard Dataset",
      "object": "hornedlizard",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "GSM",
      "title": "Black Bear Hair Snag Dataset",
      "object": "blackbear",
      "class": [
        "sfc_POLYGON",
        "sfc"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "hornedlizardCH",
      "title": "Flat-tailed Horned Lizard Dataset",
      "object": "hornedlizard",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "housemouse",
      "title": "House mouse live trapping data",
      "object": "housemouse",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "infraCH",
      "title": "Skink Pitfall Data",
      "object": "skink",
      "class": [
        "capthist",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "lineoCH",
      "title": "Skink Pitfall Data",
      "object": "skink",
      "class": [
        "capthist",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "LStraps",
      "title": "Skink Pitfall Data",
      "object": "skink",
      "class": [
        "traps",
        "data.frame"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 462,
      "table": true,
      "tojson": true
    },
    {
      "name": "ovenbird.model.1",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovenbird.model.D",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovenbird.model.Dl",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovenCH",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "capthist",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovenCHp",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "capthist",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovenmask",
      "title": "Ovenbird Mist-netting Dataset",
      "object": "ovenbird",
      "class": [
        "mask",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "ovensong.model.1",
      "title": "Ovenbird Acoustic Dataset",
      "object": "ovensong",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ovensong.model.2",
      "title": "Ovenbird Acoustic Dataset",
      "object": "ovensong",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "OVpossumCH",
      "title": "Orongorongo Valley Brushtail Possums",
      "object": "OVpossum",
      "class": [
        "capthist",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "possum.model.0",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "possum.model.Ds",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "possumarea",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 152,
      "table": true,
      "tojson": true
    },
    {
      "name": "possumCH",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "possummask",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "mask",
        "data.frame"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 5120,
      "table": true,
      "tojson": true
    },
    {
      "name": "possumremovalarea",
      "title": "Brushtail Possum Trapping Dataset",
      "object": "possum",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x",
        "y"
      ],
      "rows": 116,
      "table": true,
      "tojson": true
    },
    {
      "name": "secrdemo.0",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "secrdemo.b",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "secrdemo.CL",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "signalCH",
      "title": "Ovenbird Acoustic Dataset",
      "object": "ovensong",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "stoat.model.EX",
      "title": "Stoat DNA Data",
      "object": "stoatDNA",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "stoat.model.HN",
      "title": "Stoat DNA Data",
      "object": "stoatDNA",
      "class": [
        "secr"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "stoatCH",
      "title": "Stoat DNA Data",
      "object": "stoatDNA",
      "class": [
        "capthist"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "trapXY",
      "title": "SECR Models Fitted to Demonstration Data",
      "object": "secrdemo",
      "class": [
        "data.frame"
      ],
      "fields": [
        "trapID",
        "x",
        "y"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "secr-package",
      "title": "Spatially Explicit Capture-Recapture Models",
      "topics": [
        "secr-package",
        "secr"
      ]
    },
    {
      "page": "addCovariates",
      "title": "Add Covariates to Mask or Traps",
      "topics": [
        "addCovariates"
      ]
    },
    {
      "page": "addSightings",
      "title": "Mark-resight Data",
      "topics": [
        "addSightings"
      ]
    },
    {
      "page": "addTelemetry",
      "title": "Combine Telemetry and Detection Data",
      "topics": [
        "addTelemetry",
        "telemetrytype",
        "telemetrytype<-",
        "xy2CH"
      ]
    },
    {
      "page": "AIC.secr",
      "title": "Compare SECR Models",
      "topics": [
        "AIC.secr",
        "AIC.secrlist",
        "logLik.secr",
        "secrlist",
        "[.secrlist"
      ]
    },
    {
      "page": "AICcompatible",
      "title": "Model Compatibility",
      "topics": [
        "AICcompatible",
        "AICcompatible.secr",
        "AICcompatible.secrlist"
      ]
    },
    {
      "page": "as.data.frame",
      "title": "Coerce capthist to Data Frame or Array",
      "topics": [
        "as.array",
        "as.array.capthist",
        "as.data.frame",
        "as.data.frame.capthist",
        "as.data.frame.traps"
      ]
    },
    {
      "page": "as.mask",
      "title": "Coerce traps object to mask",
      "topics": [
        "as.mask"
      ]
    },
    {
      "page": "as.popn",
      "title": "Coerce ppp object to popn",
      "topics": [
        "as.popn"
      ]
    },
    {
      "page": "autoini",
      "title": "Initial Parameter Values for SECR",
      "topics": [
        "autoini"
      ]
    },
    {
      "page": "binCovariate",
      "title": "Add Binned Covariate",
      "topics": [
        "binCovariate"
      ]
    },
    {
      "page": "blackbear",
      "title": "Black Bear Hair Snag Dataset",
      "topics": [
        "blackbear",
        "blackbear.0",
        "blackbear.h2bk",
        "blackbearCH",
        "GSM"
      ]
    },
    {
      "page": "DA",
      "title": "Convert Data To Or From BUGS Format",
      "topics": [
        "read.DA",
        "write.DA"
      ]
    },
    {
      "page": "capthist",
      "title": "Spatial Capture History Object",
      "topics": [
        "capthist"
      ]
    },
    {
      "page": "capthistfn",
      "title": "Dissect Spatial Capture History Object",
      "topics": [
        "alive",
        "alongtransect",
        "animalID",
        "occasion",
        "telemetered",
        "telemetryxy",
        "telemetryxy<-",
        "trap",
        "xy",
        "xy<-"
      ]
    },
    {
      "page": "chatnj",
      "title": "Overdispersion of Activity Centres",
      "topics": [
        "adjustVarD",
        "chat.nj"
      ]
    },
    {
      "page": "circular",
      "title": "Circular Probability",
      "topics": [
        "circular.p",
        "circular.r"
      ]
    },
    {
      "page": "clone",
      "title": "Replicate Rows",
      "topics": [
        "clone",
        "clone.capthist",
        "clone.default",
        "clone.popn"
      ]
    },
    {
      "page": "closedN",
      "title": "Closed population estimates",
      "topics": [
        "closedN"
      ]
    },
    {
      "page": "closure",
      "title": "Closure tests",
      "topics": [
        "closure.test"
      ]
    },
    {
      "page": "cluster",
      "title": "Detector Clustering",
      "topics": [
        "cluster",
        "clusterID",
        "clusterID<-",
        "clustertrap",
        "clustertrap<-"
      ]
    },
    {
      "page": "coef.secr",
      "title": "Coefficients of secr Object",
      "topics": [
        "coef.secr"
      ]
    },
    {
      "page": "collate",
      "title": "Array of Parameter Estimates",
      "topics": [
        "collate",
        "collate.ipsecr",
        "collate.secr",
        "collate.secrlist"
      ]
    },
    {
      "page": "confint.secr",
      "title": "Profile Likelihood Confidence Intervals",
      "topics": [
        "confint.secr"
      ]
    },
    {
      "page": "contour",
      "title": "Contour Detection Probability",
      "topics": [
        "bufferContour",
        "pdotContour"
      ]
    },
    {
      "page": "covariates",
      "title": "Covariates Attribute",
      "topics": [
        "covariates",
        "covariates<-"
      ]
    },
    {
      "page": "CV",
      "title": "Coefficient of Variation",
      "topics": [
        "CV",
        "CVa",
        "CVa0"
      ]
    },
    {
      "page": "D.designdata",
      "title": "Construct Density Design Data",
      "topics": [
        "D.designdata"
      ]
    },
    {
      "page": "deermouse",
      "title": "Deermouse Live-trapping Datasets",
      "topics": [
        "deermouse",
        "deermouse.ESG",
        "deermouse.WSG"
      ]
    },
    {
      "page": "deletemaskpoints",
      "title": "Edit Mask Points",
      "topics": [
        "deleteMaskPoints"
      ]
    },
    {
      "page": "derivedMS",
      "title": "Derived Parameters of Fitted SECR Model",
      "topics": [
        "derived",
        "derived.secr",
        "derived.secrlist",
        "esa",
        "esa.secr"
      ]
    },
    {
      "page": "derivedDsurface",
      "title": "Derived Absolute Density",
      "topics": [
        "derivedDcoef",
        "derivedDcoef.secr",
        "derivedDcoef.secrlist",
        "derivedDfit",
        "derivedDsurface"
      ]
    },
    {
      "page": "details",
      "title": "Detail Specification for secr.fit",
      "topics": [
        "details",
        "fixedbeta",
        "LLonly",
        "maxdistance",
        "miscparm",
        "param",
        "saveprogress"
      ]
    },
    {
      "page": "detectfn",
      "title": "Detection Functions",
      "topics": [
        "detectfn",
        "Detection functions"
      ]
    },
    {
      "page": "detector",
      "title": "Detector Type",
      "topics": [
        "capped",
        "count",
        "detector",
        "detector<-",
        "multi",
        "polygon",
        "polygonX",
        "proximity",
        "single",
        "transect",
        "transectX"
      ]
    },
    {
      "page": "deviance.secr",
      "title": "Deviance of fitted secr model and residual degrees of freedom",
      "topics": [
        "deviance",
        "deviance.secr",
        "df.residual",
        "df.residual.secr"
      ]
    },
    {
      "page": "discretize",
      "title": "Rasterize Area Search or Transect Data",
      "topics": [
        "discretize"
      ]
    },
    {
      "page": "distancetotrap",
      "title": "Distance To Nearest Detector",
      "topics": [
        "distancetotrap",
        "nearesttrap"
      ]
    },
    {
      "page": "Dsurface",
      "title": "Density Surfaces",
      "topics": [
        "Dsurface",
        "Dsurface-class",
        "print.Dsurface",
        "summary.Dsurface"
      ]
    },
    {
      "page": "ellipse.secr",
      "title": "Confidence Ellipses",
      "topics": [
        "ellipse.bvn",
        "ellipse.secr"
      ]
    },
    {
      "page": "empirical",
      "title": "Empirical Variance of H-T Density Estimate",
      "topics": [
        "derivedCluster",
        "derivedExternal",
        "derivedMash",
        "derivednj",
        "derivedSession",
        "empirical.varD"
      ]
    },
    {
      "page": "esaplot",
      "title": "Mask Buffer Diagnostic Plot",
      "topics": [
        "esaPlot"
      ]
    },
    {
      "page": "expected.n",
      "title": "Expected Number of Individuals",
      "topics": [
        "expected.n"
      ]
    },
    {
      "page": "extractMoves",
      "title": "Simulated Movements",
      "topics": [
        "extractMoves"
      ]
    },
    {
      "page": "FAQ",
      "title": "Frequently Asked Questions, And Others",
      "topics": [
        "FAQ"
      ]
    },
    {
      "page": "fillNA",
      "title": "Fill Missing Covariate Values",
      "topics": [
        "fillNA"
      ]
    },
    {
      "page": "Fletcher.chat",
      "title": "Estimate overdispersion",
      "topics": [
        "Fletcher.chat"
      ]
    },
    {
      "page": "fxi",
      "title": "Probability Density of Activity Centre",
      "topics": [
        "fxi",
        "fxi.secr",
        "fxiContour",
        "fxiMode"
      ]
    },
    {
      "page": "fxTotal",
      "title": "Activity Centres of Detected and Undetected Animals",
      "topics": [
        "fxTotal",
        "fxTotal.secr"
      ]
    },
    {
      "page": "gridcells",
      "title": "Construct Grid Cells",
      "topics": [
        "gridCells"
      ]
    },
    {
      "page": "hcov",
      "title": "Hybrid Mixture Model",
      "topics": [
        "hcov"
      ]
    },
    {
      "page": "head",
      "title": "First or Last Part of an Object",
      "topics": [
        "head.capthist",
        "head.Dsurface",
        "head.mask",
        "head.traps",
        "tail.capthist",
        "tail.Dsurface",
        "tail.mask",
        "tail.traps"
      ]
    },
    {
      "page": "homerange",
      "title": "Home Range Statistics",
      "topics": [
        "ARL",
        "centroids",
        "dbar",
        "MMDM",
        "moves",
        "ORL",
        "RPSV",
        "t2r2",
        "trapsPerAnimal"
      ]
    },
    {
      "page": "hornedlizard",
      "title": "Flat-tailed Horned Lizard Dataset",
      "topics": [
        "FTHL.0",
        "FTHL.CL",
        "hornedlizard",
        "hornedlizardCH"
      ]
    },
    {
      "page": "coulombe",
      "title": "House mouse live trapping data",
      "topics": [
        "Coulombe",
        "housemouse"
      ]
    },
    {
      "page": "secr-internal",
      "title": "Internal Functions",
      "topics": [
        "boundarytoSF",
        "Dfn2"
      ]
    },
    {
      "page": "manip",
      "title": "Work with Open Population data",
      "topics": [
        "intervals",
        "intervals<-",
        "sessionlabels",
        "sessionlabels<-"
      ]
    },
    {
      "page": "join",
      "title": "Combine or Split Sessions of capthist Object",
      "topics": [
        "join",
        "unjoin"
      ]
    },
    {
      "page": "kfn",
      "title": "Overlap Index",
      "topics": [
        "kfn"
      ]
    },
    {
      "page": "list.secr.fit",
      "title": "Fit Multiple SECR Models",
      "topics": [
        "list.secr.fit"
      ]
    },
    {
      "page": "LLsurface",
      "title": "Plot Likelihood Surface",
      "topics": [
        "LLsurface",
        "LLsurface.secr"
      ]
    },
    {
      "page": "logit",
      "title": "Logit Transformation",
      "topics": [
        "invlogit",
        "logit"
      ]
    },
    {
      "page": "logmultinom",
      "title": "Multinomial Coefficient of SECR Likelihood",
      "topics": [
        "logmultinom"
      ]
    },
    {
      "page": "LRtest",
      "title": "Likelihood Ratio Test",
      "topics": [
        "LR.test"
      ]
    },
    {
      "page": "make.capthist",
      "title": "Construct capthist Object",
      "topics": [
        "make.capthist"
      ]
    },
    {
      "page": "make.lacework",
      "title": "Construct Lacework Detector Design",
      "topics": [
        "make.lacework"
      ]
    },
    {
      "page": "make.mask",
      "title": "Build Habitat Mask",
      "topics": [
        "make.mask"
      ]
    },
    {
      "page": "make.spcosa",
      "title": "Construct Spatial Coverage Design",
      "topics": [
        "make.spcosa"
      ]
    },
    {
      "page": "make.systematic",
      "title": "Construct Systematic Detector Design",
      "topics": [
        "make.systematic"
      ]
    },
    {
      "page": "make.traps",
      "title": "Build Detector Array",
      "topics": [
        "make.circle",
        "make.grid",
        "make.poly",
        "make.telemetry",
        "make.transect"
      ]
    },
    {
      "page": "make.tri",
      "title": "Build Detector Array on Triangular or Hexagonal Grid",
      "topics": [
        "clip.hex",
        "make.tri"
      ]
    },
    {
      "page": "makeStart",
      "title": "Initial Parameter Values",
      "topics": [
        "makeStart"
      ]
    },
    {
      "page": "mask",
      "title": "Mask Object",
      "topics": [
        "mask",
        "mask-class"
      ]
    },
    {
      "page": "mask.check",
      "title": "Mask Diagnostics",
      "topics": [
        "mask.check"
      ]
    },
    {
      "page": "MCgof",
      "title": "Monte Carlo Goodness-of-fit for SECR Models",
      "topics": [
        "MCgof",
        "MCgof.secr",
        "MCgof.secrlist"
      ]
    },
    {
      "page": "modelAverage",
      "title": "Averaging of SECR Models Using Akaike's Information Criterion",
      "topics": [
        "modelAverage",
        "modelAverage.secr",
        "modelAverage.secrlist"
      ]
    },
    {
      "page": "ms",
      "title": "Multi-session Objects",
      "topics": [
        "ms",
        "ms.default",
        "ms.mask",
        "ms.secr"
      ]
    },
    {
      "page": "makeNewData",
      "title": "Create Default Design Data",
      "topics": [
        "makeNewData",
        "makeNewData.default",
        "makeNewData.secr",
        "newdata"
      ]
    },
    {
      "page": "chatnk",
      "title": "Number per detector",
      "topics": [
        "chat.nk",
        "Enk",
        "nk"
      ]
    },
    {
      "page": "nontarget",
      "title": "Non-target Data",
      "topics": [
        "interference",
        "nontarget",
        "nontarget<-"
      ]
    },
    {
      "page": "occasionKey",
      "title": "Key to Petal Plot",
      "topics": [
        "occasionKey"
      ]
    },
    {
      "page": "ovenbird",
      "title": "Ovenbird Mist-netting Dataset",
      "topics": [
        "ovenbird",
        "ovenbird.model.1",
        "ovenbird.model.D",
        "ovenbird.model.Dl",
        "ovenCH",
        "ovenCHp",
        "ovenmask"
      ]
    },
    {
      "page": "ovensong",
      "title": "Ovenbird Acoustic Dataset",
      "topics": [
        "ovensong",
        "ovensong.model.1",
        "ovensong.model.2",
        "signalCH"
      ]
    },
    {
      "page": "OVpossum",
      "title": "Orongorongo Valley Brushtail Possums",
      "topics": [
        "OVpossum",
        "OVpossumCH"
      ]
    },
    {
      "page": "Parallel",
      "title": "Multi-core Processing",
      "topics": [
        "Multi-core processing",
        "ncores",
        "Parallel"
      ]
    },
    {
      "page": "pdot",
      "title": "Net Detection Probability",
      "topics": [
        "CVpdot",
        "pdot"
      ]
    },
    {
      "page": "PG",
      "title": "Telemetry Fixes in Polygons",
      "topics": [
        "PG"
      ]
    },
    {
      "page": "plot.capthist",
      "title": "Plot Detection Histories",
      "topics": [
        "plot.capthist",
        "plotMCP"
      ]
    },
    {
      "page": "plot.mask",
      "title": "Plot Habitat Mask, Density or Resource Surface",
      "topics": [
        "plot.Dsurface",
        "plot.mask",
        "plot.Rsurface",
        "spotHeight"
      ]
    },
    {
      "page": "MCgof.methods",
      "title": "Methods for MCgof Objects",
      "topics": [
        "hist.MCgof",
        "plot.MCgof",
        "print.MCgof",
        "summary.MCgof"
      ]
    },
    {
      "page": "plot.popn",
      "title": "Plot Population Object",
      "topics": [
        "plot.popn"
      ]
    },
    {
      "page": "plot.secr",
      "title": "Plot Detection Functions",
      "topics": [
        "attenuationplot",
        "detectfnplot",
        "plot.secr",
        "plot.secrlist"
      ]
    },
    {
      "page": "plot.traps",
      "title": "Plot traps Object",
      "topics": [
        "plot.traps"
      ]
    },
    {
      "page": "plotmaskedge",
      "title": "Outline Around Mask Cells",
      "topics": [
        "plotMaskEdge"
      ]
    },
    {
      "page": "pmixProfileLL",
      "title": "Mixture Model Check",
      "topics": [
        "pmixProfileLL"
      ]
    },
    {
      "page": "pointsInPolygon",
      "title": "Points Inside Polygon",
      "topics": [
        "pointsInPolygon"
      ]
    },
    {
      "page": "polyarea",
      "title": "Area of Polygon(s)",
      "topics": [
        "polyarea"
      ]
    },
    {
      "page": "popn",
      "title": "Population Object",
      "topics": [
        "popn"
      ]
    },
    {
      "page": "possum",
      "title": "Brushtail Possum Trapping Dataset",
      "topics": [
        "possum",
        "possum.model.0",
        "possum.model.Ds",
        "possumarea",
        "possumCH",
        "possummask",
        "possumremovalarea"
      ]
    },
    {
      "page": "predict.secr",
      "title": "SECR Model Predictions",
      "topics": [
        "detectpar",
        "detectpar.secr",
        "predict.secr",
        "predict.secrlist"
      ]
    },
    {
      "page": "predictDsurface",
      "title": "Predict Density Surface",
      "topics": [
        "predictDsurface"
      ]
    },
    {
      "page": "print.capthist",
      "title": "Print Detections",
      "topics": [
        "print.capthist"
      ]
    },
    {
      "page": "print.secr",
      "title": "Print or Summarise secr Object",
      "topics": [
        "print.secr",
        "summary.secr"
      ]
    },
    {
      "page": "print.traps",
      "title": "Print Detectors",
      "topics": [
        "print.traps"
      ]
    },
    {
      "page": "randomHabitat",
      "title": "Random Landscape",
      "topics": [
        "randomDensity",
        "randomHabitat"
      ]
    },
    {
      "page": "raster2",
      "title": "Create a RasterLayer Object from Mask or Dsurface",
      "topics": [
        "rast",
        "rast,Dsurface-method",
        "rast,mask-method",
        "raster",
        "raster,Dsurface-method",
        "raster,mask-method"
      ]
    },
    {
      "page": "rbind.capthist",
      "title": "Combine capthist Objects",
      "topics": [
        "append.capthist",
        "MS.capthist",
        "rbind.capthist"
      ]
    },
    {
      "page": "rbind.popn",
      "title": "Combine popn Objects",
      "topics": [
        "rbind.popn"
      ]
    },
    {
      "page": "rbind.traps",
      "title": "Combine traps Objects",
      "topics": [
        "rbind.traps"
      ]
    },
    {
      "page": "DENSITY",
      "title": "Import or export data",
      "topics": [
        "read.capthist",
        "write.capthist"
      ]
    },
    {
      "page": "read.mask",
      "title": "Read Habitat Mask From File",
      "topics": [
        "read.mask"
      ]
    },
    {
      "page": "read.telemetry",
      "title": "Import Telemetry Fixes",
      "topics": [
        "read.telemetry"
      ]
    },
    {
      "page": "read.traps",
      "title": "Read Detector Data From File",
      "topics": [
        "read.traps"
      ]
    },
    {
      "page": "rectangularMask",
      "title": "Rectangular Mask",
      "topics": [
        "rectangularMask"
      ]
    },
    {
      "page": "reduce",
      "title": "Combine Columns",
      "topics": [
        "reduce",
        "reduce.default"
      ]
    },
    {
      "page": "reduce.capthist",
      "title": "Combine Occasions Or Detectors",
      "topics": [
        "reduce.capthist",
        "reduce.traps"
      ]
    },
    {
      "page": "region.N",
      "title": "Population Size",
      "topics": [
        "population size",
        "region.N",
        "region.N.secr",
        "region.N.secrlist"
      ]
    },
    {
      "page": "RMarkInput",
      "title": "Convert Data to RMark Input Format",
      "topics": [
        "RMarkInput",
        "unRMarkInput"
      ]
    },
    {
      "page": "RSE",
      "title": "RSE from Fitted Model",
      "topics": [
        "RSE"
      ]
    },
    {
      "page": "Rsurface",
      "title": "Smoothed Resource Surface",
      "topics": [
        "Rsurface"
      ]
    },
    {
      "page": "score.test",
      "title": "Score Test for SECR Models",
      "topics": [
        "score.table",
        "score.test"
      ]
    },
    {
      "page": "secr-defunct",
      "title": "Defunct Functions in Package 'secr'",
      "topics": [
        "defunct",
        "derivedSystematic",
        "ip.secr",
        "make.newdata",
        "model.average",
        "pfn",
        "read.SPACECAP",
        "secr-defunct",
        "secr.make.newdata",
        "write.SPACECAP"
      ]
    },
    {
      "page": "secr-deprecated",
      "title": "Deprecated Functions in Package 'secr'",
      "topics": [
        "buffer.contour",
        "esa.plot",
        "fx.total",
        "fxi.contour",
        "fxi.mode",
        "par.derived",
        "par.region.N",
        "par.secr.fit",
        "pdot.contour",
        "secr-deprecated"
      ]
    },
    {
      "page": "secr-version5",
      "title": "Changes in 'secr' 5.0",
      "topics": [
        "secr-version5",
        "version5"
      ]
    },
    {
      "page": "secr.design.MS",
      "title": "Construct Detection Model Design Matrices and Lookups",
      "topics": [
        "insertdim",
        "make.lookup",
        "secr.design.MS"
      ]
    },
    {
      "page": "secr.fit",
      "title": "Spatially Explicit Capture-Recapture",
      "topics": [
        "secr.fit"
      ]
    },
    {
      "page": "secr.refit",
      "title": "Repeat or Resume Model Fit",
      "topics": [
        "secr.refit"
      ]
    },
    {
      "page": "secr.test",
      "title": "Goodness-of-Fit Test",
      "topics": [
        "secr.test"
      ]
    },
    {
      "page": "secrdemo",
      "title": "SECR Models Fitted to Demonstration Data",
      "topics": [
        "captdata",
        "captXY",
        "secrdemo",
        "secrdemo.0",
        "secrdemo.b",
        "secrdemo.CL",
        "trapXY"
      ]
    },
    {
      "page": "secrRNG",
      "title": "Random Number Seed",
      "topics": [
        "random numbers",
        "secrRNG",
        "seed"
      ]
    },
    {
      "page": "secrtest",
      "title": "Goodness-of-fit Test Results",
      "topics": [
        "plot.secrtest",
        "print.secrtest",
        "secrtest"
      ]
    },
    {
      "page": "session",
      "title": "Session Vector",
      "topics": [
        "session",
        "session<-"
      ]
    },
    {
      "page": "setNumThreads",
      "title": "Number of Threads",
      "topics": [
        "setNumThreads"
      ]
    },
    {
      "page": "sharefactorlevels",
      "title": "Fix Inconsistent Covariates",
      "topics": [
        "shareFactorLevels"
      ]
    },
    {
      "page": "sighting",
      "title": "Sighting Attributes",
      "topics": [
        "markocc",
        "markocc<-",
        "sighting",
        "sightings",
        "Tm",
        "Tm<-",
        "Tn",
        "Tn<-",
        "Tu",
        "Tu<-"
      ]
    },
    {
      "page": "signal",
      "title": "Signal Fields",
      "topics": [
        "noise",
        "noise.capthist",
        "noise<-",
        "signal",
        "signal.capthist",
        "signal<-",
        "signalframe",
        "signalframe<-"
      ]
    },
    {
      "page": "signalmatrix",
      "title": "Reformat Signal Data",
      "topics": [
        "signalmatrix"
      ]
    },
    {
      "page": "sim.capthist",
      "title": "Simulate Detection Histories",
      "topics": [
        "sim.capthist",
        "sim.resight"
      ]
    },
    {
      "page": "sim.popn",
      "title": "Simulate 2-D Population",
      "topics": [
        "sim.popn",
        "tile"
      ]
    },
    {
      "page": "sim.secr",
      "title": "Simulate From Fitted secr Model",
      "topics": [
        "sim.detect",
        "sim.secr",
        "simulate",
        "simulate.secr"
      ]
    },
    {
      "page": "simOU.capthist",
      "title": "Simulate Detections For Ornstein-Uhlenbeck Movement",
      "topics": [
        "simOU",
        "simOU.capthist"
      ]
    },
    {
      "page": "skink",
      "title": "Skink Pitfall Data",
      "topics": [
        "infraCH",
        "lineoCH",
        "LStraps",
        "skink"
      ]
    },
    {
      "page": "smooths",
      "title": "Smooth Terms in SECR Models",
      "topics": [
        "smooths"
      ]
    },
    {
      "page": "snip",
      "title": "Slice Transect Into Shorter Sections",
      "topics": [
        "snip"
      ]
    },
    {
      "page": "sort",
      "title": "Sort Rows of capthist or mask Object",
      "topics": [
        "sort.capthist",
        "sort.mask"
      ]
    },
    {
      "page": "spacing",
      "title": "Detector or Mask Spacing",
      "topics": [
        "spacing",
        "spacing.mask",
        "spacing.traps",
        "spacing<-"
      ]
    },
    {
      "page": "speed",
      "title": "Speed Tips",
      "topics": [
        "speed",
        "Speed tips"
      ]
    },
    {
      "page": "stoatDNA",
      "title": "Stoat DNA Data",
      "topics": [
        "stoat.model.EX",
        "stoat.model.HN",
        "stoatCH",
        "stoatDNA"
      ]
    },
    {
      "page": "strip.legend",
      "title": "Colour Strip Legend",
      "topics": [
        "strip.legend"
      ]
    },
    {
      "page": "subset.capthist",
      "title": "Subset or Split capthist Object",
      "topics": [
        "split.capthist",
        "subset.capthist"
      ]
    },
    {
      "page": "subset.mask",
      "title": "Subset, Split or Combine Mask Objects",
      "topics": [
        "rbind.mask",
        "split.mask",
        "subset.mask"
      ]
    },
    {
      "page": "subset.popn",
      "title": "Subset popn Object",
      "topics": [
        "subset.popn"
      ]
    },
    {
      "page": "subset.traps",
      "title": "Subset traps Object",
      "topics": [
        "split.traps",
        "subset.traps"
      ]
    },
    {
      "page": "suggest.buffer",
      "title": "Mask Buffer Width",
      "topics": [
        "bias.D",
        "bufferBiasCheck",
        "suggest.buffer"
      ]
    },
    {
      "page": "summary.capthist",
      "title": "Summarise Detections",
      "topics": [
        "counts",
        "print.summary.capthist",
        "summary.capthist"
      ]
    },
    {
      "page": "summary.mask",
      "title": "Summarise Habitat Mask",
      "topics": [
        "print.summary.mask",
        "summary.mask"
      ]
    },
    {
      "page": "summary.popn",
      "title": "Summarise Simulated Population",
      "topics": [
        "print.summary.popn",
        "summary.popn"
      ]
    },
    {
      "page": "summary.traps",
      "title": "Summarise Detector Array",
      "topics": [
        "print.summary.traps",
        "summary.traps"
      ]
    },
    {
      "page": "timevaryingcov",
      "title": "Time-varying Covariates",
      "topics": [
        "timevaryingcov",
        "timevaryingcov<-"
      ]
    },
    {
      "page": "transformations",
      "title": "Transform Point Array",
      "topics": [
        "flip",
        "flip.popn",
        "flip.traps",
        "rotate",
        "rotate.popn",
        "rotate.traps",
        "shift",
        "shift.mask",
        "shift.popn",
        "shift.traps",
        "transformations"
      ]
    },
    {
      "page": "trap.builder",
      "title": "Complex Detector Layouts",
      "topics": [
        "cluster.centres",
        "cluster.counts",
        "mash",
        "trap.builder"
      ]
    },
    {
      "page": "traps",
      "title": "Detector Array",
      "topics": [
        "traps",
        "traps object",
        "traps<-"
      ]
    },
    {
      "page": "trapsfn",
      "title": "Detector Attributes",
      "topics": [
        "polyID",
        "polyID<-",
        "searcharea",
        "transectID",
        "transectID<-",
        "transectlength"
      ]
    },
    {
      "page": "trend",
      "title": "Density Trend",
      "topics": [
        "predictDlambda"
      ]
    },
    {
      "page": "trim",
      "title": "Drop Unwanted List Components",
      "topics": [
        "trim",
        "trim.default",
        "trim.secr",
        "trim.secrlist"
      ]
    },
    {
      "page": "troubleshooting",
      "title": "Problems in Fitting SECR Models",
      "topics": [
        "Troubleshooting"
      ]
    },
    {
      "page": "turnover",
      "title": "Specifying a Dynamic Population",
      "topics": [
        "turnover"
      ]
    },
    {
      "page": "updateCH",
      "title": "Update Old capthist Format",
      "topics": [
        "updateCH"
      ]
    },
    {
      "page": "usage",
      "title": "Detector Usage",
      "topics": [
        "effort",
        "usage",
        "usage.traps",
        "usage<-"
      ]
    },
    {
      "page": "usagePlot",
      "title": "Plot usage, detections or sightings.",
      "topics": [
        "sightingPlot",
        "usagePlot"
      ]
    },
    {
      "page": "userdist",
      "title": "Non-Euclidean Distances",
      "topics": [
        "noneuc",
        "userdist"
      ]
    },
    {
      "page": "utility",
      "title": "Utility Functions",
      "topics": [
        "edist",
        "getMeanSD",
        "maskarea",
        "masklength",
        "masksize",
        "nedist",
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