# Spatially explicit capture-recapture

## Documentation for package ‘secr’ version 2.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

## -- --

secr-package | Spatially Explicit Capture-Recapture Models

## -- A --

AIC.secr | Compare SECR Models
AIC.secrlist | Compare SECR Models
alive | Dissect Spatial Capture History Object
animalID | Dissect Spatial Capture History Object
ARL | Home Range Statistics
attenuationplot | Plot Detection Functions
autoini | Initial Parameter Values for SECR

## -- B --

bias.D | Mask Buffer Width
binomN | Spatially Explicit Capture-Recapture
buffer.contour | Contour Detection Probability

## -- C --

captdata | SECR Models Fitted to Demonstration Data
capthist | Spatial Capture History Object
captXY | SECR Models Fitted to Demonstration Data
clip.hex | Build Detector Array on Triangular or Hexagonal Grid
closedN | Closed population estimates
closure.test | Closure tests
coef.secr | Coefficients of secr Object
collate | Model averaging for SECR Models
confint.secr | Profile Likelihood Confidence Intervals
Coulombe | House mouse live trapping data
count | Detector Type
counts | Summarise Detections
covariates | Covariates Attribute
covariates<- | Covariates Attribute

## -- 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
derived | Derived Parameters of Fitted SECR Model
detectfn | Detection Functions
detectfnplot | Plot Detection Functions
detection functions | Detection Functions
detector | Detector Type
detector<- | Detector Type
detectpar | 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
distancetotrap | Distance To Nearest Detector

## -- E --

ellipse.secr | Confidence ellipse
empirical.varD | Design-based Variance of Density
esa | Derived Parameters of Fitted SECR Model
esa.plot | Mask Buffer Diagnostic Plot
esa.plot.secr | Mask Buffer Diagnostic Plot (internal)
ESG.0 | Deermouse Live-trapping Datasets
ESG.b | Deermouse Live-trapping Datasets
ESG.h2 | Deermouse Live-trapping Datasets
ESG.t | Deermouse Live-trapping Datasets

## -- F --

FAQ | Frequently Asked Questions, And Others
flip | Transform Point Array
flip.traps | Transform Point Array
fxi | Probability Density of Home Range Centre
fxi.contour | Probability Density of Home Range Centre
fxi.mode | Probability Density of Home Range Centre
fxi.secr | Probability Density of Home Range Centre

## -- H --

hornedlizard | Flat-tailed Horned Lizard Dataset
hornedlizardCH | Flat-tailed Horned Lizard Dataset
housemouse | House mouse live trapping data
housemouse.0 | House mouse live trapping data
housemouse.ampm | House mouse live trapping data
housemouse.ampmh2h2 | House mouse live trapping data

## -- I --

infraCH | Skink Pitfall Data
invlogit | Logit Transformation
ip.secr | Spatially Explicit Capture-Recapture by Inverse Prediction

## -- L --

lineoCH | Skink Pitfall Data
LLsurface.secr | Plot likelihood surface
logit | Logit Transformation
logLik.secr | Compare SECR Models
logmultinom | Multinomial Coefficient of SECR Likelihood
LR.test | Likelihood Ratio Test for SECR Models
LStraps | Skink Pitfall Data

## -- M --

make.capthist | Construct capthist Object
make.circle | Build Detector Array
make.grid | Build Detector Array
make.mask | Build Habitat Mask
make.poly | Build Detector Array
make.transect | Build Detector Array
make.tri | Build Detector Array on Triangular or Hexagonal Grid
mask | Mask Object
mask.check | Mask Diagnostics
MMDM | Home Range Statistics
model.average | Model averaging for SECR Models
morning.0 | House mouse live trapping data
morning.0h2 | House mouse live trapping data
morning.b | House mouse live trapping data
morning.h2 | House mouse live trapping data
morning.h2h2 | House mouse live trapping data
morning.t | House mouse live trapping data
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

## -- N --

nearesttrap | Distance To Nearest Detector

## -- O --

occasion | Dissect Spatial Capture History Object
ovenbird | Ovenbird Mist-netting Dataset
ovenbird.model.1 | Ovenbird Mist-netting Dataset
ovenbird.model.1b | Ovenbird Mist-netting Dataset
ovenbird.model.1T | Ovenbird Mist-netting Dataset
ovenbird.model.h2 | Ovenbird Mist-netting Dataset
ovenCH | 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

## -- P --

pdot | Net Detection Probability
pdot.contour | Contour Detection Probability
pfn | Spatially Explicit Capture-Recapture by Inverse Prediction
plot.capthist | Plot Detection Histories
plot.mask | Plot Habitat Mask
plot.popn | Plot popn Object
plot.secr | Plot Detection Functions
plot.secrlist | Plot Detection Functions
plot.traps | Plot traps Object
polyarea | Area of simple polygon
polygon | Detector Type
polygonX | Detector Type
polyID | Detector Attributes
polyID<- | Detector Attributes
popn | Population Object
possum | Brushtail Possum Trapping Dataset
possum.model.1 | Brushtail Possum Trapping Dataset
possum.model.1b | Brushtail Possum Trapping Dataset
possumarea | Brushtail Possum Trapping Dataset
possumCH | Brushtail Possum Trapping Dataset
possummask | Brushtail Possum Trapping Dataset
predict.secr | SECR Model Predictions
predict.secrlist | SECR Model Predictions
print.capthist | Print Detections
print.secr | Print secr Object
print.summary.capthist | Summarise Detections
print.summary.mask | Summarise Habitat Mask
print.summary.traps | Summarise Detector Array
print.traps | Print Detectors
proximity | Detector Type

## -- R --

rbind.capthist | Combine capthist Objects
rbind.mask | Subset Mask Object
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 | Exchange data with SPACECAP package
read.traps | Read Detector Data From File
reduce | Combine Columns
reduce.capthist | Combine Occasions Or Convert Detector Types
rotate | Transform Point Array
rotate.traps | Transform Point Array
RPSV | Home Range Statistics

## -- S --

score.table | Score Test for SECR Models
score.test | Score Test for SECR Models
searcharea | Detector Attributes
secr | Spatially Explicit Capture-Recapture Models
secr density models | Density Models
secr detection models | Models for Detection Parameters
secr FAQ | Frequently Asked Questions, And Others
secr models | Spatially Explicit Capture-Recapture Models
secr.design.MS | Construct Detection Model Design Matrices and Lookups
secr.fit | Spatially Explicit Capture-Recapture
secr.make.newdata | Create Default Design Data
secr.model | Spatially Explicit Capture-Recapture Models
secr.model.density | Density Models
secr.model.detection | Models for Detection Parameters
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
session | Session Vector
session<- | Session Vector
shift | Transform Point Array
shift.traps | Transform Point Array
signal | Dissect Spatial Capture History Object
signal<- | Dissect Spatial Capture History Object
signalCH | Ovenbird Acoustic Dataset
sim.capthist | Simulate Detection Histories
sim.popn | Simulate 2-D Population
sim.resight | Simulate Detection Histories
sim.secr | Simulate From Fitted secr Model
simulate | Simulate From Fitted secr Model
simulate.secr | Simulate From Fitted secr Model
single | Detector Type
skink | Skink Pitfall Data
sort.capthist | Sort Rows of capthist Object
spacing | Detector or Mask Spacing
spacing<- | Detector or Mask Spacing
split.capthist | Subset or Split capthist Object
split.traps | Subset traps Object
stoat.model.EX | Stoat DNA Data
stoat.model.HN | Stoat DNA Data
stoat.model.HZ | Stoat DNA Data
stoatCH | Stoat DNA Data
stoatDNA | Stoat DNA Data
subset.capthist | Subset or Split capthist Object
subset.mask | Subset Mask Object
subset.traps | Subset traps Object
suggest.buffer | Mask Buffer Width
summary.capthist | Summarise Detections
summary.mask | Summarise Habitat Mask
summary.traps | Summarise Detector Array

## -- T --

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
traps | Detector Array
traps object | Detector Array
traps<- | Detector Array
trapXY | SECR Models Fitted to Demonstration Data
trim | Drop Unwanted List Components
trim.default | Drop Unwanted List Components
trim.secr | Drop Unwanted List Components

## -- U --

usage | Detector Usage
usage<- | Detector Usage

## -- 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

## -- W --

write.capthist | Import or export data
write.captures | Write Data to Text File
write.DA | Convert Data To Or From BUGS Format
write.SPACECAP | Exchange data with SPACECAP package
write.traps | Write Data to Text File
WSG.0 | Deermouse Live-trapping Datasets
WSG.b | Deermouse Live-trapping Datasets
WSG.h2 | Deermouse Live-trapping Datasets
WSG.t | Deermouse Live-trapping Datasets

## -- X --

xy | Dissect Spatial Capture History Object
xy<- | Dissect Spatial Capture History Object