Man pages for secr
Spatially Explicit Capture-Recapture

addCovariatesAdd Covariates to Mask or Traps
addSightingsMark-resight Data
addTelemetryCombine Telemetry and Detection Data
AICcompatibleModel Compatibility
AIC.secrCompare SECR Models capthist to Data Frame
as.maskCoerce traps object to mask
as.popnCoerce ppp object to popn
autoiniInitial Parameter Values for SECR
capthistSpatial Capture History Object
capthistfnDissect Spatial Capture History Object
chatOverdispersion of Activity Centres
circularCircular Probability
cloneReplicate Rows
closedNClosed population estimates
closureClosure tests
clusterDetector Clustering
coef.secrCoefficients of secr Object
collateArray of Parameter Estimates
confint.secrProfile Likelihood Confidence Intervals
contourContour Detection Probability
coulombeHouse mouse live trapping data
covariatesCovariates Attribute
CVCoefficient of Variation
DAConvert Data To Or From BUGS Format
D.designdataConstruct Density Design Data
deermouseDeermouse Live-trapping Datasets
deletemaskpointsEdit Mask Points
DENSITYImport or export data
derivedMSDerived Parameters of Fitted SECR Model
detailsDetail Specification for
detectfnDetection Functions
detectorDetector Type
deviance.secrDeviance of fitted secr model and residual degrees of freedom
discretizeRasterize Area Search or Transect Data
distancetotrapDistance To Nearest Detector
DsurfaceDensity Surfaces
ellipse.secrConfidence Ellipses
empiricalEmpirical Variance of H-T Density Estimate
esaplotMask Buffer Diagnostic Plot
esaplotsecrMask Buffer Diagnostic Plot (internal)
expected.nExpected Number of Individuals
extractMovesSimulated Movements
FAQFrequently Asked Questions, And Others
Fletcher.chatEstimate overdispersion
fxiProbability Density of Home Range Centre
fx.totalActivity Centres of Detected and Undetected Animals
gridcellsConstruct Grid Cells
hcovHybrid Mixture Model
headFirst or Last Part of an Object
homerangeHome Range Statistics
hornedlizardFlat-tailed Horned Lizard Dataset
joinCombine or Split Sessions of capthist Object
kfnOverlap Index
LLsurfacePlot Likelihood Surface
logitLogit Transformation
logmultinomMultinomial Coefficient of SECR Likelihood
LRtestLikelihood Ratio Test
make.capthistConstruct capthist Object
make.laceworkConstruct Lacework Detector Design
make.maskBuild Habitat Mask
makeStartInitial Parameter Values
make.systematicConstruct Systematic Detector Design
make.trapsBuild Detector Array
make.triBuild Detector Array on Triangular or Hexagonal Grid
manipWork with Open Population data
maskMask Object
mask.checkMask Diagnostics
modelAverageAveraging of SECR Models Using Akaike's Information Criterion
msMulti-session Objects
nontargetNon-target Data
occasionKeyKey to Petal Plot
ovenbirdOvenbird Mist-netting Dataset
ovensongOvenbird Acoustic Dataset
OVpossumOrongorongo Valley Brushtail Possums
ParallelMulti-core Processing
par.secr.fitFit Multiple SECR Models
pdotNet Detection Probability
PGTelemetry Fixes in Polygons
plot.capthistPlot Detection Histories
plot.maskPlot Habitat Mask, Density or Resource Surface
plotmaskedgeOutline Around Mask Cells
plot.popnPlot Population Object
plot.secrPlot Detection Functions
plot.trapsPlot traps Object
pmixProfileLLMixture Model Check
pointsInPolygonPoints Inside Polygon
polyareaArea of Polygon(s)
popnPopulation Object
possumBrushtail Possum Trapping Dataset
predictDsurfacePredict Density Surface
predict.secrSECR Model Predictions
print.capthistPrint Detections
print.secrPrint or Summarise secr Object
print.trapsPrint Detectors
randomHabitatRandom Landscape
raster2Create a RasterLayer Object from Mask or Dsurface
rbind.capthistCombine capthist Objects
rbind.popnCombine popn Objects
rbind.trapsCombine traps Objects
read.maskRead Habitat Mask From File
read.telemetryImport Telemetry Fixes
read.trapsRead Detector Data From File
rectangularMaskRectangular Mask
reduceCombine Columns
reduce.capthistCombine Occasions Or Detectors
region.NPopulation Size
RMarkInputConvert Data to RMark Input Format
RSERSE from Fitted Model
RsurfaceSmoothed Resource Surface
score.testScore Test for SECR Models
secr-defunctDefunct Functions in Package 'secr'
secrdemoSECR Models Fitted to Demonstration Data
secr-deprecatedDeprecated Functions in Package 'secr' Detection Model Design Matrices and Lookups
secr.fitSpatially Explicit Capture-Recapture
secr-internalInternal Functions
secr.make.newdataCreate Default Design Data
secr-packageSpatially Explicit Capture-Recapture Models
secrRNGRandom Number Seed
secrtestGoodness-of-fit Test Results
secr.testGoodness-of-Fit Test
sessionSession Vector
setNumThreadsNumber of Threads
sharefactorlevelsFix Inconsistent Covariates
sightingSighting Attributes
signalSignal Fields
signalmatrixReformat Signal Data
sim.capthistSimulate Detection Histories
sim.popnSimulate 2-D Population
sim.secrSimulate From Fitted secr Model
skinkSkink Pitfall Data
smoothsSmooth Terms in SECR Models
snipSlice Transect Into Shorter Sections
sortSort Rows of capthist or mask Object
spacingDetector or Mask Spacing
speedSpeed Tips
stoatDNAStoat DNA Data
strip.legendColour Strip Legend
subset.capthistSubset or Split capthist Object
subset.maskSubset, Split or Combine Mask Objects
subset.popnSubset popn Object
subset.trapsSubset traps Object
suggest.bufferMask Buffer Width
summary.capthistSummarise Detections
summary.maskSummarise Habitat Mask
summary.popnSummarise Simulated Population
summary.trapsSummarise Detector Array
timevaryingcovTime-varying Covariates
transformationsTransform Point Array
trap.builderComplex Detector Layouts
trapsDetector Array
trapsfnDetector Attributes
trendDensity Trend
trimDrop Unwanted List Components
troubleshootingProblems in Fitting SECR Models
turnoverSpecifying a Dynamic Population
updateCHUpdate Old capthist Format
usageDetector Usage
usagePlotPlot usage, detections or sightings.
userdistNon-Euclidean Distances
utilityUtility Functions
vcov.secrVariance - Covariance Matrix of SECR Parameters
verifyCheck SECR Data
writeWrite Data to Text File
writeGPSUpload to GPS
secr documentation built on Oct. 18, 2023, 1:07 a.m.