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secr (version 1.3.0)

Spatially explicit capture-recapture

Description

Estimate animal population density with capture--recapture data from an array of passive dectors (traps). Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

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Version

Install

install.packages('secr')

Monthly Downloads

1,505

Version

1.3.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

March 11th, 2010

Functions in secr (1.3.0)

model.average

Model averaging for SECR Models
print.mask

Print Habitat Mask
secr.model

Spatially Explicit Capture--Recapture Models
score.test

Score Test for SECR Models
possum

Brushtail Possum Trapping Dataset
predict.secr

SECR Model Predictions
capthist

Spatial Capture History Object
write.capthist

Write Data to Text File
make.traps

Build Detector Array
secr.model.density

Density Models
rbind.popn

Combine popn Objects
popn

Population Object
mask

Mask Object
distancetotrap

Distance To Nearest Detector
rawdata

Demonstration Data
LLsurface.secr

Plot likelihood surface
AIC.secr

Compare SECR Models
traps.info

Detector Attributes
read.captures

Read Capture Data From File
read.traps

Read Detector Data From File
sim.popn

Simulate 2-D Population
capthist.parts

Dissect Spatial Capture History Object
print.capthist

Print Detections
plot.traps

Plot traps Object
rotate

Rotate Points
secr.fit

Spatially Explicit Capture--Recapture
D.designdata

Construct Density Design Data
secr-package

Spatially Explicit Capture--Recapture Models
secrdemo

SECR Models Fitted to Demonstration Data
rbind.capthist

Combine capthist Objects
usage

Detector Usage
flip

Flip Points
deviance

Deviance of fitted secr model and residual degrees of freedom
subset.capthist

Subset or Split capthist Object
detectfn

Detection Functions
ovenbird

Ovenbird Mist-netting Dataset
ellipse.secr

Confidence ellipse
autoini

Initial Parameter Values for SECR
read.mask

Read Habitat Mask From File
session

Session Vector
subset.mask

Subset Mask Object
rotate.traps

Rotate Detectors
trim

Drop Unwanted List Components
derived

Derived Parameters of Fitted SECR Model
reduce

Combine Columns
secr.make.newdata

Create Default Design Data
secr.model.detection

Models for Detection Parameters
verify

Check SECR Data
vcov.secr

Variance - Covariance Matrix of SECR Parameters
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
sim.secr

Simulate From Fitted secr Model
shift.traps

Shift Detectors
plot.mask

Plot Habitat Mask
print.secr

Print secr Object
reduce.capthist

Combine Occasions
summary.mask

Summarise Habitat Mask
summary.capthist

Summarise Detections
make.mask

Build Habitat Mask
flip.traps

Flip Detector Array
secr.design.MS

Construct Detection Model Design Matrices and Lookups
subset.traps

Subset traps Object
print.traps

Print Detectors
summary.traps

Summarise Detector Array
LR.test

Likelihood Ratio Test for SECR Models
make.capthist

Construct capthist Object
confint.secr

Profile Likelihood Confidence Intervals
detector

Detector Type
logit

Logit Transformation
plot.capthist

Plot Detection Histories
shift

Shift Points
sim.capthist

Simulate Detection Histories
traps

Detector Array
coef.secr

Coefficients of secr Object
covariates

Covariates Attribute
ovensong

Ovenbird Acoustic Dataset
pdot

Net Detection Probability
homerange

Home Range Statistics
rbind.traps

Combine traps Objects
FAQ

Frequently Asked Questions, And Others
captdata

Detection Dataset
plot.popn

Plot popn Object
plot.secr

Plot Detection Functions