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secr (version 2.6.0)

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

1,565

Version

2.6.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

June 12th, 2013

Functions in secr (2.6.0)

AIC.secr

Compare SECR Models
D.designdata

Construct Density Design Data
confint.secr

Profile Likelihood Confidence Intervals
LR.test

Likelihood Ratio Test
make.capthist

Construct capthist Object
derived

Derived Parameters of Fitted SECR Model
BUGS

Convert Data To Or From BUGS Format
rectangularMask

Rectangular Mask
Dsurface

Density Surfaces
covariates

Covariates Attribute
closedN

Closed population estimates
timevaryingcov

Time-varying Detector Covariates
SPACECAP

Exchange data with SPACECAP package
coef.secr

Coefficients of secr Object
Parallel

Multi-core Processing
housemouse

House mouse live trapping data
head

First or Last Part of an Object
expected.n

Expected Number of Individuals
FAQ

Frequently Asked Questions, And Others
mask.check

Mask Diagnostics
ovenbird

Ovenbird Mist-netting Dataset
Troubleshooting

Problems in Fitting SECR Models
sort.capthist

Sort Rows of capthist Object
write.captures

Write Data to Text File
deermouse

Deermouse Live-trapping Datasets
traps

Detector Array
ms

Multi-session Objects
make.systematic

Construct Systematic Detector Design
details

Detail Specification for secr.fit
possum

Brushtail Possum Trapping Dataset
make.traps

Build Detector Array
trap.builder

Complex Detector Layouts
esa.plot

Mask Buffer Diagnostic Plot
model.average

Averaging of SECR Models Using Akaike's Information Criterion
region.N

Population Size
plot.popn

Plot popn Object
secr.model.detection

Models for Detection Parameters
stoatDNA

Stoat DNA Data
sim.capthist

Simulate Detection Histories
polyarea

Area of Polygon(s)
trim

Drop Unwanted List Components
vcov.secr

Variance - Covariance Matrix of SECR Parameters
rbind.popn

Combine popn Objects
randomHabitat

Random Landscape
pointsInPolygon

Points Inside Polygon
sim.popn

Simulate 2-D Population
read.mask

Read Habitat Mask From File
summary.capthist

Summarise Detections
rbind.traps

Combine traps Objects
summary.traps

Summarise Detector Array
suggest.buffer

Mask Buffer Width
score.test

Score Test for SECR Models
summary.mask

Summarise Habitat Mask
pdot

Net Detection Probability
transformations

Transform Point Array
usagePlot

Plot Usage
writeGPS

Upload to GPS
subset.mask

Subset Mask Object
print.secr

Print secr Object
addCovariates

Add Covariates to Mask or Traps
capthist

Spatial Capture History Object
ellipse.secr

Confidence ellipse
empirical.varD

Empirical Variance of H-T Density Estimate
logmultinom

Multinomial Coefficient of SECR Likelihood
ovensong

Ovenbird Acoustic Dataset
plot.capthist

Plot Detection Histories
plot.mask

Plot Habitat Mask or Density Surface
popn

Population Object
predictDsurface

Predict Density Surface
read.capthist

Import or export data
traps.info

Detector Attributes
reduce.capthist

Combine Occasions Or Detectors
secr.fit

Spatially Explicit Capture--Recapture
subset.traps

Subset traps Object
subset.popn

Subset popn Object
verify

Check SECR Data
capthist.parts

Dissect Spatial Capture History Object
homerange

Home Range Statistics
closure.test

Closure tests
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
make.tri

Build Detector Array on Triangular or Hexagonal Grid
plot.secr

Plot Detection Functions
plot.traps

Plot traps Object
session

Session Vector
join

Combine or Split Sessions of capthist Object
RMarkInput

Convert Data to RMark Input Format
print.traps

Print Detectors
secr.make.newdata

Create Default Design Data
LLsurface.secr

Plot likelihood surface
cluster

Detector Clustering
detector

Detector Type
signalmatrix

Reformat Signal Data
distancetotrap

Distance To Nearest Detector
contour

Contour Detection Probability
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
logit

Logit Transformation
predict.secr

SECR Model Predictions
reduce

Combine Columns
snip

Slice Transect Into Shorter Sections
hornedlizard

Flat-tailed Horned Lizard Dataset
secr.design.MS

Construct Detection Model Design Matrices and Lookups
spacing

Detector or Mask Spacing
secr.model.density

Density Models
subset.capthist

Subset or Split capthist Object
sim.secr

Simulate From Fitted secr Model
secr.model

Spatially Explicit Capture--Recapture Models
mask

Mask Object
usage

Detector Usage
fxi

Probability Density of Home Range Centre
circular

Circular Probability
detectfn

Detection Functions
addTelemetry

Combine Telemetry and Detection Data
autoini

Initial Parameter Values for SECR
deviance

Deviance of fitted secr model and residual degrees of freedom
make.mask

Build Habitat Mask
print.capthist

Print Detections
read.traps

Read Detector Data From File
rbind.capthist

Combine capthist Objects
skink

Skink Pitfall Data
secrdemo

SECR Models Fitted to Demonstration Data
secr-package

Spatially Explicit Capture--Recapture Models
speed

Speed Tips