Spatially explicit capture-recapture


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Documentation for package ‘secr’ version 1.3.0

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A C D E F 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
animalID Dissect Spatial Capture History Object
attenuationplot Plot Detection Functions
autoini Initial Parameter Values for SECR

-- C --

captdata Detection Dataset
capthist Spatial Capture History Object
captXY Demonstration Data
coef.secr Coefficients of secr Object
collate Model averaging for SECR Models
confint.secr Profile Likelihood Confidence Intervals
counts Summarise Detections
covariates Covariates Attribute
covariates<- Covariates Attribute

-- D --

D.designdata Construct Density Design Data
dbar Home Range Statistics
derived Derived Parameters of Fitted SECR Model
detectfnplot Plot Detection Functions
detection functions Detection Functions
detector Detector Type
detector<- Detector Type
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
esa Derived Parameters of Fitted SECR Model

-- F --

FAQ Frequently Asked Questions, And Others
flip Flip Points
flip.traps Flip Detector Array

-- I --

invlogit Logit Transformation
ip.secr Spatially Explicit Capture-Recapture by Inverse Prediction

-- L --

LLsurface.secr Plot likelihood surface
logit Logit Transformation
LR.test Likelihood Ratio Test for SECR Models

-- 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
mask Mask Object
model.average Model averaging for SECR Models
MS.capthist Combine capthist Objects

-- 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
ovenCH Ovenbird Mist-netting Dataset
ovensong Ovenbird Acoustic Dataset

-- P --

pdot Net 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.traps Plot traps Object
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
possumCH Brushtail Possum Trapping Dataset
possummask Brushtail Possum Trapping Dataset
predict.secr SECR Model Predictions
print.capthist Print Detections
print.mask Print Habitat Mask
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

-- R --

rawdata Demonstration Data
rbind.capthist Combine capthist Objects
rbind.mask Subset Mask Object
rbind.popn Combine popn Objects
rbind.traps Combine traps Objects
read.captures Read Capture Data From File
read.mask Read Habitat Mask From File
read.traps Read Detector Data From File
reduce Combine Columns
reduce.capthist Combine Occasions
rotate Rotate Points
rotate.traps Rotate Detectors
RPSV Home Range Statistics

-- S --

score.table Score Test for SECR Models
score.test Score Test for SECR Models
searcharea Detector Attributes
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 Shift Points
shift.traps Shift Detectors
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
split.capthist Subset or Split capthist Object
split.traps Subset traps Object
subset.capthist Subset or Split capthist Object
subset.mask Subset Mask Object
subset.traps Subset traps Object
summary.capthist Summarise Detections
summary.mask Summarise Habitat Mask
summary.traps Summarise Detector Array

-- T --

transectID Detector Attributes
transectID<- Detector Attributes
transectlength Detector Attributes
trap Dissect Spatial Capture History Object
traps Detector Array
traps object Detector Array
traps<- Detector Array
trapXY 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 Write Data to Text File
write.traps Write Data to Text File

-- X --

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