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secr (version 1.4.1)

Spatially explicit capture-recapture

Description

Estimate animal population density with capture--recapture data from an array of passive detectors (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

1,565

Version

1.4.1

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

August 30th, 2010

Functions in secr (1.4.1)

pdot

Net Detection Probability
logit

Logit Transformation
make.capthist

Construct capthist Object
make.mask

Build Habitat Mask
plot.mask

Plot Habitat Mask
D.designdata

Construct Density Design Data
AIC.secr

Compare SECR Models
closedN

Closed population estimates
deermouse

Deermouse Live-trapping Datasets
make.tri

Build Detector Array on Triangular Grid
LLsurface.secr

Plot likelihood surface
predict.secr

SECR Model Predictions
secr.make.newdata

Create Default Design Data
rotate

Rotate Points
traps.info

Detector Attributes
capthist

Spatial Capture History Object
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
capthist.parts

Dissect Spatial Capture History Object
secr.model.detection

Models for Detection Parameters
summary.capthist

Summarise Detections
confint.secr

Profile Likelihood Confidence Intervals
flip.traps

Flip Detector Array
closure.test

Closure tests
model.average

Model averaging for SECR Models
subset.traps

Subset traps Object
plot.capthist

Plot Detection Histories
detector

Detector Type
shift.traps

Shift Detectors
coef.secr

Coefficients of secr Object
verify

Check SECR Data
derived

Derived Parameters of Fitted SECR Model
usage

Detector Usage
read.capthist

Import or export data
print.secr

Print secr Object
covariates

Covariates Attribute
FAQ

Frequently Asked Questions, And Others
summary.mask

Summarise Habitat Mask
print.capthist

Print Detections
plot.secr

Plot Detection Functions
possum

Brushtail Possum Trapping Dataset
sim.capthist

Simulate Detection Histories
secrdemo

SECR Models Fitted to Demonstration Data
rbind.popn

Combine popn Objects
rbind.capthist

Combine capthist Objects
subset.capthist

Subset or Split capthist Object
rotate.traps

Rotate Detectors
distancetotrap

Distance To Nearest Detector
secr-package

Spatially Explicit Capture--Recapture Models
rbind.traps

Combine traps Objects
ellipse.secr

Confidence ellipse
skink

Skink Pitfall Data
sim.popn

Simulate 2-D Population
trim

Drop Unwanted List Components
vcov.secr

Variance - Covariance Matrix of SECR Parameters
subset.mask

Subset Mask Object
LR.test

Likelihood Ratio Test for SECR Models
secr.fit

Spatially Explicit Capture--Recapture
flip

Flip Points
mask

Mask Object
plot.popn

Plot popn Object
print.traps

Print Detectors
read.mask

Read Habitat Mask From File
session

Session Vector
write.captures

Write Data to Text File
secr.design.MS

Construct Detection Model Design Matrices and Lookups
housemouse

House mouse live trapping data
plot.traps

Plot traps Object
SPACECAP

Exchange data with SPACECAP package
make.traps

Build Detector Array
ovensong

Ovenbird Acoustic Dataset
stoatDNA

Stoat DNA data
reduce

Combine Columns
logmultinom

Multinomial Coefficient of SECR Likelihood
ovenbird

Ovenbird Mist-netting Dataset
traps

Detector Array
autoini

Initial Parameter Values for SECR
homerange

Home Range Statistics
shift

Shift Points
summary.traps

Summarise Detector Array
secr.model

Spatially Explicit Capture--Recapture Models
deviance

Deviance of fitted secr model and residual degrees of freedom
popn

Population Object
reduce.capthist

Combine Occasions
sim.secr

Simulate From Fitted secr Model
read.traps

Read Detector Data From File
score.test

Score Test for SECR Models
empirical.varD

Design-based Variance of Density
detectfn

Detection Functions
secr.model.density

Density Models