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secr (version 2.5.0)

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

2.5.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

January 23rd, 2013

Functions in secr (2.5.0)

addCovariates

Add Covariates to Mask or Traps
reduce

Combine Columns
ovenbird

Ovenbird Mist-netting Dataset
closedN

Closed population estimates
closure.test

Closure tests
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
head

First or Last Part of an Object
esa.plot

Mask Buffer Diagnostic Plot
sort.capthist

Sort Rows of capthist Object
D.designdata

Construct Density Design Data
hornedlizard

Flat-tailed Horned Lizard Dataset
derived

Derived Parameters of Fitted SECR Model
predictDsurface

Predict Density Surface
homerange

Home Range Statistics
popn

Population Object
model.average

Model averaging for SECR Models
plot.secr

Plot Detection Functions
capthist

Spatial Capture History Object
circular

Circular Probability
covariates

Covariates Attribute
region.N

Population Size
ellipse.secr

Confidence ellipse
predict.secr

SECR Model Predictions
empirical.varD

Empirical Variance of H-T Density Estimate
autoini

Initial Parameter Values for SECR
confint.secr

Profile Likelihood Confidence Intervals
expected.n

Expected Number of Individuals
cluster

Detector Clustering
AIC.secr

Compare SECR Models
Dsurface

Density Surfaces
housemouse

House mouse live trapping data
detector

Detector Type
capthist.parts

Dissect Spatial Capture History Object
LR.test

Likelihood Ratio Test
pointsInPolygon

Points Inside Polygon
polyarea

Area of Polygon(s)
make.systematic

Construct Systematic Detector Design
mask.check

Mask Diagnostics
join

Combine or Split Sessions of capthist Object
read.mask

Read Habitat Mask From File
make.tri

Build Detector Array on Triangular or Hexagonal Grid
mask

Mask Object
plot.capthist

Plot Detection Histories
read.traps

Read Detector Data From File
reduce.capthist

Combine Occasions Or Detectors
sim.secr

Simulate From Fitted secr Model
plot.traps

Plot traps Object
sim.capthist

Simulate Detection Histories
logit

Logit Transformation
make.capthist

Construct capthist Object
secrdemo

SECR Models Fitted to Demonstration Data
make.traps

Build Detector Array
ms

Multi-session Objects
ovensong

Ovenbird Acoustic Dataset
trap.builder

Complex Detector Layouts
timevaryingcov

Time-varying Detector Covariates
verify

Check SECR Data
secr.design.MS

Construct Detection Model Design Matrices and Lookups
secr.model

Spatially Explicit Capture--Recapture Models
usagePlot

Plot Usage
subset.capthist

Subset or Split capthist Object
print.secr

Print secr Object
troubleshooting

Problems in Fitting SECR Models
skink

Skink Pitfall Data
rectangularMask

Rectangular Mask
stoatDNA

Stoat DNA Data
subset.popn

Subset popn Object
trim

Drop Unwanted List Components
score.test

Score Test for SECR Models
secr.model.detection

Models for Detection Parameters
usage

Detector Usage
snip

Slice Transect Into Shorter Sections
summary.mask

Summarise Habitat Mask
write.captures

Write Data to Text File
vcov.secr

Variance - Covariance Matrix of SECR Parameters
deermouse

Deermouse Live-trapping Datasets
traps

Detector Array
writeGPS

Upload to GPS
traps.info

Detector Attributes
read.capthist

Import or export data
LLsurface.secr

Plot likelihood surface
deviance

Deviance of fitted secr model and residual degrees of freedom
fxi

Probability Density of Home Range Centre
print.traps

Print Detectors
print.capthist

Print Detections
rbind.popn

Combine popn Objects
suggest.buffer

Mask Buffer Width
subset.traps

Subset traps Object
RMarkInput

Convert Data to RMark Input Format
addTelemetry

Combine Telemetry and Detection Data
detectfn

Detection Functions
make.mask

Build Habitat Mask
plot.popn

Plot popn Object
rbind.capthist

Combine capthist Objects
secr.model.density

Density Models
session

Session Vector
logmultinom

Multinomial Coefficient of SECR Likelihood
BUGS

Convert Data To Or From BUGS Format
Parallel

Multi-core Processing
coef.secr

Coefficients of secr Object
pdot

Net Detection Probability
distancetotrap

Distance To Nearest Detector
SPACECAP

Exchange data with SPACECAP package
plot.mask

Plot Habitat Mask or Density Surface
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
secr.fit

Spatially Explicit Capture--Recapture
spacing

Detector or Mask Spacing
FAQ

Frequently Asked Questions, And Others
randomHabitat

Random Landscape
contour

Contour Detection Probability
rbind.traps

Combine traps Objects
possum

Brushtail Possum Trapping Dataset
secr-package

Spatially Explicit Capture--Recapture Models
secr.make.newdata

Create Default Design Data
signalmatrix

Reformat Signal Data
sim.popn

Simulate 2-D Population
transformations

Transform Point Array
summary.traps

Summarise Detector Array
subset.mask

Subset Mask Object
summary.capthist

Summarise Detections