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secr (version 2.8.1)

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

2.8.1

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

April 3rd, 2014

Functions in secr (2.8.1)

rbind.capthist

Combine capthist Objects
Rsurface

Smoothed Resource Surface
Parallel

Multi-core Processing
fxi

Probability Density of Home Range Centre
par.secr.fit

Fit Multiple SECR Models
ellipse.secr

Confidence Ellipses
mask.check

Mask Diagnostics
closure.test

Closure tests
AIC.secr

Compare SECR Models
make.traps

Build Detector Array
pdot

Net Detection Probability
capthist.parts

Dissect Spatial Capture History Object
ms

Multi-session Objects
deviance

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

Plot Habitat Mask, Density or Resource Surface
rbind.popn

Combine popn Objects
capthist

Spatial Capture History Object
hcov

Hybrid Mixture Model
addTelemetry

Combine Telemetry and Detection Data
rectangularMask

Rectangular Mask
print.secr

Print secr Object
ip.secr

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

Build Habitat Mask
mask

Mask Object
usage

Detector Usage
clone

Replicate Rows
addCovariates

Add Covariates to Mask or Traps
reduce

Combine Columns
housemouse

House mouse live trapping data
make.capthist

Construct capthist Object
covariates

Covariates Attribute
secr.model

Spatially Explicit Capture--Recapture Models
region.N

Population Size
summary.capthist

Summarise Detections
secr.fit

Spatially Explicit Capture--Recapture
details

Detail Specification for secr.fit
deermouse

Deermouse Live-trapping Datasets
contour

Contour Detection Probability
model.average

Averaging of SECR Models Using Akaike's Information Criterion
sim.secr

Simulate From Fitted secr Model
read.capthist

Import or export data
read.traps

Read Detector Data From File
snip

Slice Transect Into Shorter Sections
SPACECAP

Exchange data with SPACECAP package
head

First or Last Part of an Object
autoini

Initial Parameter Values for SECR
print.traps

Print Detectors
make.systematic

Construct Systematic Detector Design
homerange

Home Range Statistics
speed

Speed Tips
predictDsurface

Predict Density Surface
secrdemo

SECR Models Fitted to Demonstration Data
subset.popn

Subset popn Object
plot.traps

Plot traps Object
spacing

Detector or Mask Spacing
score.test

Score Test for SECR Models
Dsurface

Density Surfaces
BUGS

Convert Data To Or From BUGS Format
plot.capthist

Plot Detection Histories
LLsurface.secr

Plot likelihood surface
coef.secr

Coefficients of secr Object
derived

Derived Parameters of Fitted SECR Model
polyarea

Area of Polygon(s)
plot.secr

Plot Detection Functions
possum

Brushtail Possum Trapping Dataset
sort.capthist

Sort Rows of capthist Object
session

Session Vector
expected.n

Expected Number of Individuals
summary.traps

Summarise Detector Array
stoatDNA

Stoat DNA Data
verify

Check SECR Data
subset.traps

Subset traps Object
summary.mask

Summarise Habitat Mask
reduce.capthist

Combine Occasions Or Detectors
trap.builder

Complex Detector Layouts
vcov.secr

Variance - Covariance Matrix of SECR Parameters
transformations

Transform Point Array
subset.mask

Subset Mask Object
trim

Drop Unwanted List Components
suggest.buffer

Mask Buffer Width
ovenbird

Ovenbird Mist-netting Dataset
secr.model.detection

Models for Detection Parameters
secr.design.MS

Construct Detection Model Design Matrices and Lookups
subset.capthist

Subset or Split capthist Object
skink

Skink Pitfall Data
write.captures

Write Data to Text File
usagePlot

Plot Usage
secr-package

Spatially Explicit Capture--Recapture Models
D.designdata

Construct Density Design Data
detectfn

Detection Functions
esa.plot

Mask Buffer Diagnostic Plot
join

Combine or Split Sessions of capthist Object
pointsInPolygon

Points Inside Polygon
popn

Population Object
plot.popn

Plot popn Object
read.telemetry

Import Radio Fixes
read.mask

Read Habitat Mask From File
secr.make.newdata

Create Default Design Data
signalmatrix

Reformat Signal Data
sim.popn

Simulate 2-D Population
closedN

Closed population estimates
FAQ

Frequently Asked Questions, And Others
LR.test

Likelihood Ratio Test
RMarkInput

Convert Data to RMark Input Format
confint.secr

Profile Likelihood Confidence Intervals
cluster

Detector Clustering
detector

Detector Type
distancetotrap

Distance To Nearest Detector
empirical.varD

Empirical Variance of H-T Density Estimate
logit

Logit Transformation
logmultinom

Multinomial Coefficient of SECR Likelihood
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
ovensong

Ovenbird Acoustic Dataset
predict.secr

SECR Model Predictions
print.capthist

Print Detections
secr.model.density

Density Models
signal

Signal Fields
sim.capthist

Simulate Detection Histories
traps.info

Detector Attributes
Troubleshooting

Problems in Fitting SECR Models
writeGPS

Upload to GPS
timevaryingcov

Time-varying Detector Covariates
traps

Detector Array
circular

Circular Probability
CV

Coefficient of Variation
PG

Telemetry Fixes in Polygons
hornedlizard

Flat-tailed Horned Lizard Dataset
make.tri

Build Detector Array on Triangular or Hexagonal Grid
randomHabitat

Random Landscape
rbind.traps

Combine traps Objects