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secr (version 2.4.0)

Spatially explicit capture-recapture

Description

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. 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

2,295

Version

2.4.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

November 5th, 2012

Functions in secr (2.4.0)

AIC.secr

Compare SECR Models
LR.test

Likelihood Ratio Test
deermouse

Deermouse Live-trapping Datasets
print.capthist

Print Detections
read.mask

Read Habitat Mask From File
BUGS

Convert Data To Or From BUGS Format
subset.popn

Subset popn Object
subset.traps

Subset traps Object
homerange

Home Range Statistics
coef.secr

Coefficients of secr Object
covariates

Covariates Attribute
join

Combine or Split Sessions of capthist Object
detector

Detector Type
make.capthist

Construct capthist Object
expected.n

Expected Number of Individuals
cluster

Detector Clustering
fxi

Probability Density of Home Range Centre
polyarea

Area of Polygon(s)
popn

Population Object
secr.model.detection

Models for Detection Parameters
reduce.capthist

Combine Occasions Or Convert Detector Types
read.capthist

Import or export data
plot.secr

Plot Detection Functions
secr.design.MS

Construct Detection Model Design Matrices and Lookups
rectangularMask

Rectangular Mask
usage

Detector Usage
randomHabitat

Random Landscape
closedN

Closed population estimates
pdot

Net Detection Probability
Dsurface

Density Surfaces
housemouse

House mouse live trapping data
print.secr

Print secr Object
derived

Derived Parameters of Fitted SECR Model
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
Parallel

Multi-core Processing
SPACECAP

Exchange data with SPACECAP package
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
make.tri

Build Detector Array on Triangular or Hexagonal Grid
make.mask

Build Habitat Mask
traps.info

Detector Attributes
trim

Drop Unwanted List Components
vcov.secr

Variance - Covariance Matrix of SECR Parameters
mask.check

Mask Diagnostics
plot.mask

Plot Habitat Mask or Density Surface
trap.builder

Complex Detector Layouts
ellipse.secr

Confidence ellipse
logit

Logit Transformation
make.systematic

Construct Systematic Detector Design
logmultinom

Multinomial Coefficient of SECR Likelihood
pointsInPolygon

Points Inside Polygon
ovensong

Ovenbird Acoustic Dataset
capthist.parts

Dissect Spatial Capture History Object
LLsurface.secr

Plot likelihood surface
region.N

Population Size
score.test

Score Test for SECR Models
summary.traps

Summarise Detector Array
FAQ

Frequently Asked Questions, And Others
empirical.varD

Empirical Variance of H-T Density Estimate
signalmatrix

Reformat Signal Data
confint.secr

Profile Likelihood Confidence Intervals
print.traps

Print Detectors
possum

Brushtail Possum Trapping Dataset
make.traps

Build Detector Array
write.captures

Write Data to Text File
plot.capthist

Plot Detection Histories
secr.make.newdata

Create Default Design Data
secrdemo

SECR Models Fitted to Demonstration Data
head

First or Last Part of an Object
rbind.popn

Combine popn Objects
suggest.buffer

Mask Buffer Width
predict.secr

SECR Model Predictions
stoatDNA

Stoat DNA Data
sort.capthist

Sort Rows of capthist Object
reduce

Combine Columns
secr-package

Spatially Explicit Capture--Recapture Models
rbind.traps

Combine traps Objects
sim.popn

Simulate 2-D Population
detectfn

Detection Functions
secr.fit

Spatially Explicit Capture--Recapture
sim.capthist

Simulate Detection Histories
sim.secr

Simulate From Fitted secr Model
spacing

Detector or Mask Spacing
addTelemetry

Combine Telemetry and Detection Data
addCovariates

Add Covariates to Mask or Traps
session

Session Vector
timevaryingcov

Time-varying Detector Covariates
autoini

Initial Parameter Values for SECR
summary.mask

Summarise Habitat Mask
verify

Check SECR Data
RMarkInput

Convert Data to RMark Input Format
capthist

Spatial Capture History Object
traps

Detector Array
circular

Circular Probability
closure.test

Closure tests
writeGPS

Upload to GPS
subset.capthist

Subset or Split capthist Object
esa.plot

Mask Buffer Diagnostic Plot
mask

Mask Object
ovenbird

Ovenbird Mist-netting Dataset
plot.traps

Plot traps Object
ms

Multi-session Objects
plot.popn

Plot popn Object
read.traps

Read Detector Data From File
predictDsurface

Predict Density Surface
secr.model.density

Density Models
hornedlizard

Flat-tailed Horned Lizard Dataset
rbind.capthist

Combine capthist Objects
skink

Skink Pitfall Data
secr.model

Spatially Explicit Capture--Recapture Models
summary.capthist

Summarise Detections
D.designdata

Construct Density Design Data
contour

Contour Detection Probability
deviance

Deviance of fitted secr model and residual degrees of freedom
distancetotrap

Distance To Nearest Detector
model.average

Model averaging for SECR Models
subset.mask

Subset Mask Object
transformations

Transform Point Array
troubleshooting

Problems in Fitting SECR Models