# Spatially Explicit Capture-Recapture

## Documentation for package ‘secr’ version 5.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N O P R S T U V W X misc

secr-package | Spatially Explicit Capture-Recapture Models

## -- A --

addCovariates | Add Covariates to Mask or Traps
addSightings | Mark-resight Data
addTelemetry | Combine Telemetry and Detection Data
adjustVarD | Overdispersion of Activity Centres
AIC.secr | Compare SECR Models
AIC.secrlist | Compare SECR Models
AICcompatible | Model Compatibility
AICcompatible.secr | Model Compatibility
AICcompatible.secrlist | Model Compatibility
alive | Dissect Spatial Capture History Object
alongtransect | Dissect Spatial Capture History Object
animalID | Dissect Spatial Capture History Object
append.capthist | Combine capthist Objects
ARL | Home Range Statistics
as.array | Coerce capthist to Data Frame or Array
as.array.capthist | Coerce capthist to Data Frame or Array
as.data.frame | Coerce capthist to Data Frame or Array
as.data.frame.capthist | Coerce capthist to Data Frame or Array
as.data.frame.traps | Coerce capthist to Data Frame or Array
as.mask | Coerce traps object to mask
as.popn | Coerce ppp object to popn
attenuationplot | Plot Detection Functions
autoini | Initial Parameter Values for SECR

## -- B --

bias.D | Mask Buffer Width
binCovariate | Add Binned Covariate
blackbear | Black Bear Hair Snag Dataset
blackbear.0 | Black Bear Hair Snag Dataset
blackbear.h2bk | Black Bear Hair Snag Dataset
blackbearCH | Black Bear Hair Snag Dataset
boundarytoSF | Internal Functions
buffer.contour | Deprecated Functions in Package 'secr'
bufferBiasCheck | Mask Buffer Width
bufferContour | Contour Detection Probability

## -- C --

capped | Detector Type
captdata | SECR Models Fitted to Demonstration Data
capthist | Spatial Capture History Object
captXY | SECR Models Fitted to Demonstration Data
centroids | Home Range Statistics
chat.nj | Overdispersion of Activity Centres
chat.nk | Number per detector
circular.p | Circular Probability
circular.r | Circular Probability
clip.hex | Build Detector Array on Triangular or Hexagonal Grid
clone | Replicate Rows
clone.capthist | Replicate Rows
clone.default | Replicate Rows
clone.popn | Replicate Rows
closedN | Closed population estimates
closure.test | Closure tests
cluster | Detector Clustering
cluster.centres | Complex Detector Layouts
cluster.counts | Complex Detector Layouts
clusterID | Detector Clustering
clusterID<- | Detector Clustering
clustertrap | Detector Clustering
clustertrap<- | Detector Clustering
coef.secr | Coefficients of secr Object
collate | Array of Parameter Estimates
collate.ipsecr | Array of Parameter Estimates
collate.secr | Array of Parameter Estimates
collate.secrlist | Array of Parameter Estimates
confint.secr | Profile Likelihood Confidence Intervals
Coulombe | House mouse live trapping data
count | Detector Type
counts | Summarise Detections
covariates | Covariates Attribute
covariates<- | Covariates Attribute
CV | Coefficient of Variation
CVa | Coefficient of Variation
CVa0 | Coefficient of Variation
CVpdot | Net Detection Probability

## -- D --

D.designdata | Construct Density Design Data
dbar | Home Range Statistics
deermouse | Deermouse Live-trapping Datasets
deermouse.ESG | Deermouse Live-trapping Datasets
deermouse.WSG | Deermouse Live-trapping Datasets
defunct | Defunct Functions in Package 'secr'
deleteMaskPoints | Edit Mask Points
derived | Derived Parameters of Fitted SECR Model
derived.secr | Derived Parameters of Fitted SECR Model
derived.secrlist | Derived Parameters of Fitted SECR Model
derivedCluster | Empirical Variance of H-T Density Estimate
derivedDcoef | Derived Absolute Density
derivedDcoef.secr | Derived Absolute Density
derivedDcoef.secrlist | Derived Absolute Density
derivedDfit | Derived Absolute Density
derivedDsurface | Derived Absolute Density
derivedExternal | Empirical Variance of H-T Density Estimate
derivedMash | Empirical Variance of H-T Density Estimate
derivednj | Empirical Variance of H-T Density Estimate
derivedSession | Empirical Variance of H-T Density Estimate
derivedSystematic | Defunct Functions in Package 'secr'
details | Detail Specification for secr.fit
detectfn | Detection Functions
detectfnplot | Plot Detection Functions
Detection functions | Detection Functions
detector | Detector Type
detector<- | Detector Type
detectpar | SECR Model Predictions
detectpar.secr | SECR Model Predictions
deviance | Deviance of fitted secr model and residual degrees of freedom
deviance.secr | Deviance of fitted secr model and residual degrees of freedom
df.residual | Deviance of fitted secr model and residual degrees of freedom
df.residual.secr | Deviance of fitted secr model and residual degrees of freedom
Dfn2 | Internal Functions
discretize | Rasterize Area Search or Transect Data
distancetotrap | Distance To Nearest Detector
Dsurface | Density Surfaces
Dsurface-class | Density Surfaces

## -- E --

edist | Utility Functions
effort | Detector Usage
ellipse.bvn | Confidence Ellipses
ellipse.secr | Confidence Ellipses
empirical.varD | Empirical Variance of H-T Density Estimate
Enk | Number per detector
esa | Derived Parameters of Fitted SECR Model
esa.plot | Deprecated Functions in Package 'secr'
esa.secr | Derived Parameters of Fitted SECR Model
esaPlot | Mask Buffer Diagnostic Plot
expected.n | Expected Number of Individuals
extractMoves | Simulated Movements

## -- F --

FAQ | Frequently Asked Questions, And Others
fixedbeta | Detail Specification for secr.fit
Fletcher.chat | Estimate overdispersion
flip | Transform Point Array
flip.popn | Transform Point Array
flip.traps | Transform Point Array
fx.total | Deprecated Functions in Package 'secr'
fxi | Probability Density of Activity Centre
fxi.contour | Deprecated Functions in Package 'secr'
fxi.mode | Deprecated Functions in Package 'secr'
fxi.secr | Probability Density of Activity Centre
fxiContour | Probability Density of Activity Centre
fxiMode | Probability Density of Activity Centre
fxTotal | Activity Centres of Detected and Undetected Animals
fxTotal.secr | Activity Centres of Detected and Undetected Animals

## -- G --

getMeanSD | Utility Functions
gridCells | Construct Grid Cells
GSM | Black Bear Hair Snag Dataset

## -- H --

hcov | Hybrid Mixture Model
head.capthist | First or Last Part of an Object
head.Dsurface | First or Last Part of an Object
head.mask | First or Last Part of an Object
head.traps | First or Last Part of an Object
hist.MCgof | Methods for MCgof Objects
hornedlizard | Flat-tailed Horned Lizard Dataset
hornedlizardCH | Flat-tailed Horned Lizard Dataset
housemouse | House mouse live trapping data

## -- I --

infraCH | Skink Pitfall Data
insertdim | Construct Detection Model Design Matrices and Lookups
interference | Non-target Data
intervals | Work with Open Population data
intervals<- | Work with Open Population data
invlogit | Logit Transformation
ip.secr | Defunct Functions in Package 'secr'

## -- J --

join | Combine or Split Sessions of capthist Object

## -- K --

kfn | Overlap Index

## -- L --

lineoCH | Skink Pitfall Data
list.secr.fit | Fit Multiple SECR Models
LLonly | Detail Specification for secr.fit
LLsurface | Plot Likelihood Surface
LLsurface.secr | Plot Likelihood Surface
logit | Logit Transformation
logLik.secr | Compare SECR Models
logmultinom | Multinomial Coefficient of SECR Likelihood
LR.test | Likelihood Ratio Test
LStraps | Skink Pitfall Data

## -- M --

make.capthist | Construct capthist Object
make.circle | Build Detector Array
make.grid | Build Detector Array
make.lacework | Construct Lacework Detector Design
make.lookup | Construct Detection Model Design Matrices and Lookups
make.mask | Build Habitat Mask
make.newdata | Defunct Functions in Package 'secr'
make.poly | Build Detector Array
make.spcosa | Construct Spatial Coverage Design
make.systematic | Construct Systematic Detector Design
make.telemetry | Build Detector Array
make.transect | Build Detector Array
make.tri | Build Detector Array on Triangular or Hexagonal Grid
makeNewData | Create Default Design Data
makeNewData.default | Create Default Design Data
makeNewData.secr | Create Default Design Data
makeStart | Initial Parameter Values
markocc | Sighting Attributes
markocc<- | Sighting Attributes
mash | Complex Detector Layouts
mask | Mask Object
mask-class | Mask Object
mask.check | Mask Diagnostics
maskarea | Utility Functions
masklength | Utility Functions
masksize | Utility Functions
maxdistance | Detail Specification for secr.fit
MCgof | Monte Carlo Goodness-of-fit for SECR Models
MCgof.secr | Monte Carlo Goodness-of-fit for SECR Models
MCgof.secrlist | Monte Carlo Goodness-of-fit for SECR Models
miscparm | Detail Specification for secr.fit
MMDM | Home Range Statistics
model.average | Defunct Functions in Package 'secr'
modelAverage | Averaging of SECR Models Using Akaike's Information Criterion
modelAverage.secr | Averaging of SECR Models Using Akaike's Information Criterion
modelAverage.secrlist | Averaging of SECR Models Using Akaike's Information Criterion
moves | Home Range Statistics
ms | Multi-session Objects
MS.capthist | Combine capthist Objects
ms.default | Multi-session Objects
ms.mask | Multi-session Objects
ms.secr | Multi-session Objects
multi | Detector Type
Multi-core processing | Multi-core Processing

## -- N --

ncores | Multi-core Processing
nearesttrap | Distance To Nearest Detector
nedist | Utility Functions
newdata | Create Default Design Data
nk | Number per detector
noise | Signal Fields
noise.capthist | Signal Fields
noise<- | Signal Fields
noneuc | Non-Euclidean Distances
nontarget | Non-target Data
nontarget<- | Non-target Data

## -- O --

occasion | Dissect Spatial Capture History Object
occasionKey | Key to Petal Plot
ORL | Home Range Statistics
ovenbird | Ovenbird Mist-netting Dataset
ovenbird.model.1 | Ovenbird Mist-netting Dataset
ovenbird.model.D | Ovenbird Mist-netting Dataset
ovenCH | Ovenbird Mist-netting Dataset
ovenCHp | Ovenbird Mist-netting Dataset
ovenmask | Ovenbird Mist-netting Dataset
ovensong | Ovenbird Acoustic Dataset
ovensong.model.1 | Ovenbird Acoustic Dataset
ovensong.model.2 | Ovenbird Acoustic Dataset
OVpossum | Orongorongo Valley Brushtail Possums
OVpossumCH | Orongorongo Valley Brushtail Possums

## -- P --

par.derived | Deprecated Functions in Package 'secr'
par.region.N | Deprecated Functions in Package 'secr'
par.secr.fit | Deprecated Functions in Package 'secr'
Parallel | Multi-core Processing
param | Detail Specification for secr.fit
pdot | Net Detection Probability
pdot.contour | Deprecated Functions in Package 'secr'
pdotContour | Contour Detection Probability
pfn | Defunct Functions in Package 'secr'
PG | Telemetry Fixes in Polygons
plot.capthist | Plot Detection Histories
plot.Dsurface | Plot Habitat Mask, Density or Resource Surface
plot.mask | Plot Habitat Mask, Density or Resource Surface
plot.MCgof | Methods for MCgof Objects
plot.popn | Plot Population Object
plot.Rsurface | Plot Habitat Mask, Density or Resource Surface
plot.secr | Plot Detection Functions
plot.secrlist | Plot Detection Functions
plot.secrtest | Goodness-of-fit Test Results
plot.traps | Plot traps Object
plotMaskEdge | Outline Around Mask Cells
plotMCP | Plot Detection Histories
pmixProfileLL | Mixture Model Check
pointsInPolygon | Points Inside Polygon
polyarea | Area of Polygon(s)
polygon | Detector Type
polygonX | Detector Type
polyID | Detector Attributes
polyID<- | Detector Attributes
popn | Population Object
population size | Population Size
possum | Brushtail Possum Trapping Dataset
possum.model.0 | Brushtail Possum Trapping Dataset
possum.model.Ds | Brushtail Possum Trapping Dataset
possumarea | Brushtail Possum Trapping Dataset
possumCH | Brushtail Possum Trapping Dataset
possummask | Brushtail Possum Trapping Dataset
possumremovalarea | Brushtail Possum Trapping Dataset
predict.secr | SECR Model Predictions
predict.secrlist | SECR Model Predictions
predictDlambda | Density Trend
predictDsurface | Predict Density Surface
print.capthist | Print Detections
print.Dsurface | Density Surfaces
print.MCgof | Methods for MCgof Objects
print.secr | Print or Summarise secr Object
print.secrtest | Goodness-of-fit Test Results
print.summary.capthist | Summarise Detections
print.summary.mask | Summarise Habitat Mask
print.summary.popn | Summarise Simulated Population
print.summary.traps | Summarise Detector Array
print.traps | Print Detectors
proximity | Detector Type

## -- R --

random numbers | Random Number Seed
randomDensity | Random Landscape
randomHabitat | Random Landscape
rast | Create a RasterLayer Object from Mask or Dsurface
rast-method | Create a RasterLayer Object from Mask or Dsurface
raster | Create a RasterLayer Object from Mask or Dsurface
raster-method | Create a RasterLayer Object from Mask or Dsurface
rbind.capthist | Combine capthist Objects
rbind.mask | Subset, Split or Combine Mask Objects
rbind.popn | Combine popn Objects
rbind.traps | Combine traps Objects
read.capthist | Import or export data
read.DA | Convert Data To Or From BUGS Format
read.mask | Read Habitat Mask From File
read.SPACECAP | Defunct Functions in Package 'secr'
read.telemetry | Import Telemetry Fixes
read.traps | Read Detector Data From File
rectangularMask | Rectangular Mask
reduce | Combine Columns
reduce.capthist | Combine Occasions Or Detectors
reduce.default | Combine Columns
reduce.traps | Combine Occasions Or Detectors
region.N | Population Size
region.N.secr | Population Size
region.N.secrlist | Population Size
rlnormCV | Utility Functions
RMarkInput | Convert Data to RMark Input Format
rotate | Transform Point Array
rotate.popn | Transform Point Array
rotate.traps | Transform Point Array
RPSV | Home Range Statistics
RSE | RSE from Fitted Model
Rsurface | Smoothed Resource Surface

## -- S --

saveprogress | Detail Specification for secr.fit
score.table | Score Test for SECR Models
score.test | Score Test for SECR Models
searcharea | Detector Attributes
secr | Spatially Explicit Capture-Recapture Models
secr-defunct | Defunct Functions in Package 'secr'
secr-deprecated | Deprecated Functions in Package 'secr'
secr-version5 | Changes in 'secr' 5.0
secr.design.MS | Construct Detection Model Design Matrices and Lookups
secr.fit | Spatially Explicit Capture-Recapture
secr.make.newdata | Defunct Functions in Package 'secr'
secr.refit | Repeat or Resume Model Fit
secr.test | Goodness-of-Fit Test
secrdemo | SECR Models Fitted to Demonstration Data
secrdemo.0 | SECR Models Fitted to Demonstration Data
secrdemo.b | SECR Models Fitted to Demonstration Data
secrdemo.CL | SECR Models Fitted to Demonstration Data
secrlist | Compare SECR Models
secrRNG | Random Number Seed
secrtest | Goodness-of-fit Test Results
seed | Random Number Seed
session | Session Vector
session<- | Session Vector
sessionlabels | Work with Open Population data
sessionlabels<- | Work with Open Population data
setNumThreads | Number of Threads
shareFactorLevels | Fix Inconsistent Covariates
shift | Transform Point Array
shift.mask | Transform Point Array
shift.popn | Transform Point Array
shift.traps | Transform Point Array
sighting | Sighting Attributes
sightingPlot | Plot usage, detections or sightings.
sightings | Sighting Attributes
signal | Signal Fields
signal.capthist | Signal Fields
signal<- | Signal Fields
signalCH | Ovenbird Acoustic Dataset
signalframe | Signal Fields
signalframe<- | Signal Fields
signalmatrix | Reformat Signal Data
sim.capthist | Simulate Detection Histories
sim.detect | Simulate From Fitted secr Model
sim.popn | Simulate 2-D Population
sim.resight | Simulate Detection Histories
sim.secr | Simulate From Fitted secr Model
simOU | Simulate Detections For Ornstein-Uhlenbeck Movement
simOU.capthist | Simulate Detections For Ornstein-Uhlenbeck Movement
simulate | Simulate From Fitted secr Model
simulate.secr | Simulate From Fitted secr Model
single | Detector Type
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
sort.mask | Sort Rows of capthist or mask Object
spacing | Detector or Mask Spacing
spacing.mask | Detector or Mask Spacing
spacing.traps | Detector or Mask Spacing
spacing<- | Detector or Mask Spacing
speed | Speed Tips
Speed tips | Speed Tips
split.capthist | Subset or Split capthist Object
split.mask | Subset, Split or Combine Mask Objects
split.traps | Subset traps Object
spotHeight | Plot Habitat Mask, Density or Resource Surface
stoat.model.EX | Stoat DNA Data
stoat.model.HN | Stoat DNA Data
stoatCH | Stoat DNA Data
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.Dsurface | Density Surfaces
summary.mask | Summarise Habitat Mask
summary.MCgof | Methods for MCgof Objects
summary.popn | Summarise Simulated Population
summary.secr | Print or Summarise secr Object
summary.traps | Summarise Detector Array

## -- T --

t2r2 | Home Range Statistics
tail.capthist | First or Last Part of an Object
tail.Dsurface | First or Last Part of an Object
tail.mask | First or Last Part of an Object
tail.traps | First or Last Part of an Object
telemetered | Dissect Spatial Capture History Object
telemetrytype | Combine Telemetry and Detection Data
telemetrytype<- | Combine Telemetry and Detection Data
telemetryxy | Dissect Spatial Capture History Object
telemetryxy<- | Dissect Spatial Capture History Object
tile | Simulate 2-D Population
timevaryingcov | Time-varying Covariates
timevaryingcov<- | Time-varying Covariates
Tm | Sighting Attributes
Tm<- | Sighting Attributes
Tn | Sighting Attributes
Tn<- | Sighting Attributes
transect | Detector Type
transectID | Detector Attributes
transectID<- | Detector Attributes
transectlength | Detector Attributes
transectX | Detector Type
transformations | Transform Point Array
trap | Dissect Spatial Capture History Object
trap.builder | Complex Detector Layouts
traps | Detector Array
traps object | Detector Array
traps<- | Detector Array
trapsPerAnimal | Home Range Statistics
trapXY | SECR Models Fitted to Demonstration Data
trim | Drop Unwanted List Components
trim.default | Drop Unwanted List Components
trim.secr | Drop Unwanted List Components
trim.secrlist | Drop Unwanted List Components
Troubleshooting | Problems in Fitting SECR Models
Tu | Sighting Attributes
Tu<- | Sighting Attributes
turnover | Specifying a Dynamic Population

## -- U --

unjoin | Combine or Split Sessions of capthist Object
unRMarkInput | Convert Data to RMark Input Format
updateCH | Update Old capthist Format
usage | Detector Usage
usage.traps | Detector Usage
usage<- | Detector Usage
usagePlot | Plot usage, detections or sightings.
userdist | Non-Euclidean Distances

## -- V --

vcov.secr | Variance - Covariance Matrix of SECR Parameters
verify | Check SECR Data
verify.capthist | Check SECR Data
verify.default | Check SECR Data
verify.mask | Check SECR Data
verify.traps | Check SECR Data
version5 | Changes in 'secr' 5.0

## -- W --

write.capthist | Import or export data
write.captures | Write Data to Text File
write.DA | Convert Data To Or From BUGS Format
write.mask | Write Data to Text File
write.SPACECAP | Defunct Functions in Package 'secr'
write.traps | Write Data to Text File
writeGPS | Upload to GPS

## -- X --

xy | Dissect Spatial Capture History Object
xy2CH | Combine Telemetry and Detection Data
xy<- | Dissect Spatial Capture History Object

## -- misc --

[.secrlist | Compare SECR Models