AIC.secr                Compare SECR Models
AICcompatible           Model Compatibility
CV                      Coefficient of Variation
D.designdata            Construct Density Design Data
Dsurface                Density Surfaces
FAQ                     Frequently Asked Questions, And Others
Fletcher.chat           Estimate overdispersion
LLsurface               Plot Likelihood Surface
LR.test                 Likelihood Ratio Test
MCgof                   Monte Carlo Goodness-of-fit for SECR Models
OVpossum                Orongorongo Valley Brushtail Possums
PG                      Telemetry Fixes in Polygons
Parallel                Multi-core Processing
RMarkInput              Convert Data to RMark Input Format
RSE                     RSE from Fitted Model
Rsurface                Smoothed Resource Surface
Troubleshooting         Problems in Fitting SECR Models
addCovariates           Add Covariates to Mask or Traps
addSightings            Mark-resight Data
addTelemetry            Combine Telemetry and Detection Data
animalID                Dissect Spatial Capture History Object
as.data.frame           Coerce capthist to Data Frame or Array
as.mask                 Coerce traps object to mask
as.popn                 Coerce ppp object to popn
autoini                 Initial Parameter Values for SECR
binCovariate            Add Binned Covariate
blackbear               Black Bear Hair Snag Dataset
boundarytoSF            Internal Functions
capthist                Spatial Capture History Object
chat.nj                 Overdispersion of Activity Centres
circular.r              Circular Probability
clone                   Replicate Rows
closedN                 Closed population estimates
closure.test            Closure tests
cluster                 Detector Clustering
coef.secr               Coefficients of secr Object
collate                 Array of Parameter Estimates
confint.secr            Profile Likelihood Confidence Intervals
covariates              Covariates Attribute
dbar                    Home Range Statistics
deermouse               Deermouse Live-trapping Datasets
deleteMaskPoints        Edit Mask Points
derived                 Derived Parameters of Fitted SECR Model
derivedDsurface         Derived Absolute Density
details                 Detail Specification for secr.fit
detectfn                Detection Functions
detector                Detector Type
deviance                Deviance of fitted secr model and residual
                        degrees of freedom
discretize              Rasterize Area Search or Transect Data
distancetotrap          Distance To Nearest Detector
ellipse.secr            Confidence Ellipses
empirical.varD          Empirical Variance of H-T Density Estimate
esaPlot                 Mask Buffer Diagnostic Plot
expected.n              Expected Number of Individuals
extractMoves            Simulated Movements
fillNA                  Fill Missing Covariate Values
fxTotal                 Activity Centres of Detected and Undetected
                        Animals
fxi                     Probability Density of Activity Centre
getMeanSD               Utility Functions
gridCells               Construct Grid Cells
hcov                    Hybrid Mixture Model
head.mask               First or Last Part of an Object
hornedlizard            Flat-tailed Horned Lizard Dataset
housemouse              House mouse live trapping data
intervals               Work with Open Population data
join                    Combine or Split Sessions of capthist Object
kfn                     Overlap Index
list.secr.fit           Fit Multiple SECR Models
logit                   Logit Transformation
logmultinom             Multinomial Coefficient of SECR Likelihood
make.capthist           Construct capthist Object
make.grid               Build Detector Array
make.lacework           Construct Lacework Detector Design
make.mask               Build Habitat Mask
make.spcosa             Construct Spatial Coverage Design
make.systematic         Construct Systematic Detector Design
make.tri                Build Detector Array on Triangular or Hexagonal
                        Grid
makeStart               Initial Parameter Values
mask                    Mask Object
mask.check              Mask Diagnostics
modelAverage            Averaging of SECR Models Using Akaike's
                        Information Criterion
ms                      Multi-session Objects
newdata                 Create Default Design Data
nk                      Number per detector
nontarget               Non-target Data
occasionKey             Key to Petal Plot
ovenbird                Ovenbird Mist-netting Dataset
ovensong                Ovenbird Acoustic Dataset
pdot                    Net Detection Probability
pdotContour             Contour Detection Probability
plot.MCgof              Methods for MCgof Objects
plot.capthist           Plot Detection Histories
plot.mask               Plot Habitat Mask, Density or Resource Surface
plot.popn               Plot Population Object
plot.secr               Plot Detection Functions
plot.traps              Plot traps Object
plotMaskEdge            Outline Around Mask Cells
pmixProfileLL           Mixture Model Check
pointsInPolygon         Points Inside Polygon
polyarea                Area of Polygon(s)
popn                    Population Object
possum                  Brushtail Possum Trapping Dataset
predict.secr            SECR Model Predictions
predictDlambda          Density Trend
predictDsurface         Predict Density Surface
print.capthist          Print Detections
print.secr              Print or Summarise secr Object
print.traps             Print Detectors
randomHabitat           Random Landscape
raster                  Create a RasterLayer Object from Mask or
                        Dsurface
rbind.capthist          Combine capthist Objects
rbind.popn              Combine popn Objects
rbind.traps             Combine traps Objects
read.DA                 Convert Data To Or From BUGS Format
read.capthist           Import or export data
read.mask               Read Habitat Mask From File
read.telemetry          Import Telemetry Fixes
read.traps              Read Detector Data From File
rectangularMask         Rectangular Mask
reduce                  Combine Columns
reduce.capthist         Combine Occasions Or Detectors
region.N                Population Size
score.test              Score Test for SECR Models
searcharea              Detector Attributes
secr-defunct            Defunct Functions in Package 'secr'
secr-deprecated         Deprecated Functions in Package 'secr'
secr-package            Spatially Explicit Capture-Recapture Models
secr-version5           Changes in 'secr' 5.0
secr.design.MS          Construct Detection Model Design Matrices and
                        Lookups
secr.fit                Spatially Explicit Capture-Recapture
secr.refit              Repeat or Resume Model Fit
secr.test               Goodness-of-Fit Test
secrRNG                 Random Number Seed
secrdemo                SECR Models Fitted to Demonstration Data
secrtest                Goodness-of-fit Test Results
session                 Session Vector
setNumThreads           Number of Threads
shareFactorLevels       Fix Inconsistent Covariates
sighting                Sighting Attributes
signal                  Signal Fields
signalmatrix            Reformat Signal Data
sim.capthist            Simulate Detection Histories
sim.popn                Simulate 2-D Population
sim.secr                Simulate From Fitted secr Model
simOU.capthist          Simulate Detections For Ornstein-Uhlenbeck
                        Movement
skink                   Skink Pitfall Data
smooths                 Smooth Terms in SECR Models
snip                    Slice Transect Into Shorter Sections
sort.capthist           Sort Rows of capthist or mask Object
spacing                 Detector or Mask Spacing
speed                   Speed Tips
stoatDNA                Stoat DNA Data
strip.legend            Colour Strip Legend
subset.capthist         Subset or Split capthist Object
subset.mask             Subset, Split or Combine Mask Objects
subset.popn             Subset popn Object
subset.traps            Subset traps Object
suggest.buffer          Mask Buffer Width
summary.capthist        Summarise Detections
summary.mask            Summarise Habitat Mask
summary.popn            Summarise Simulated Population
summary.traps           Summarise Detector Array
timevaryingcov          Time-varying Covariates
transformations         Transform Point Array
trap.builder            Complex Detector Layouts
traps                   Detector Array
trim                    Drop Unwanted List Components
turnover                Specifying a Dynamic Population
updateCH                Update Old capthist Format
usage                   Detector Usage
usagePlot               Plot usage, detections or sightings.
userdist                Non-Euclidean Distances
vcov.secr               Variance - Covariance Matrix of SECR Parameters
verify                  Check SECR Data
write.captures          Write Data to Text File
writeGPS                Upload to GPS
