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secr (version 2.8.0)

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

1,429

Version

2.8.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

March 31st, 2014

Functions in secr (2.8.0)

Dsurface

Density Surfaces
autoini

Initial Parameter Values for SECR
housemouse

House mouse live trapping data
deviance

Deviance of fitted secr model and residual degrees of freedom
homerange

Home Range Statistics
contour

Contour Detection Probability
detectfn

Detection Functions
ellipse.secr

Confidence Ellipses
LLsurface.secr

Plot likelihood surface
pdot

Net Detection Probability
rbind.capthist

Combine capthist Objects
plot.capthist

Plot Detection Histories
secr.make.newdata

Create Default Design Data
make.mask

Build Habitat Mask
expected.n

Expected Number of Individuals
addCovariates

Add Covariates to Mask or Traps
hornedlizard

Flat-tailed Horned Lizard Dataset
print.capthist

Print Detections
LR.test

Likelihood Ratio Test
plot.secr

Plot Detection Functions
print.secr

Print secr Object
coef.secr

Coefficients of secr Object
polyarea

Area of Polygon(s)
read.capthist

Import or export data
RMarkInput

Convert Data to RMark Input Format
capthist

Spatial Capture History Object
summary.mask

Summarise Habitat Mask
predict.secr

SECR Model Predictions
head

First or Last Part of an Object
mask.check

Mask Diagnostics
model.average

Averaging of SECR Models Using Akaike's Information Criterion
BUGS

Convert Data To Or From BUGS Format
clone

Replicate Rows
derived

Derived Parameters of Fitted SECR Model
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
traps

Detector Array
print.traps

Print Detectors
write.captures

Write Data to Text File
summary.capthist

Summarise Detections
randomHabitat

Random Landscape
rbind.popn

Combine popn Objects
logmultinom

Multinomial Coefficient of SECR Likelihood
cluster

Detector Clustering
esa.plot

Mask Buffer Diagnostic Plot
ovensong

Ovenbird Acoustic Dataset
pointsInPolygon

Points Inside Polygon
ovenbird

Ovenbird Mist-netting Dataset
secr.model.density

Density Models
rbind.traps

Combine traps Objects
read.mask

Read Habitat Mask From File
region.N

Population Size
secr.fit

Spatially Explicit Capture--Recapture
secr.model.detection

Models for Detection Parameters
vcov.secr

Variance - Covariance Matrix of SECR Parameters
skink

Skink Pitfall Data
capthist.parts

Dissect Spatial Capture History Object
secr.design.MS

Construct Detection Model Design Matrices and Lookups
suggest.buffer

Mask Buffer Width
closure.test

Closure tests
usagePlot

Plot Usage
confint.secr

Profile Likelihood Confidence Intervals
subset.traps

Subset traps Object
Troubleshooting

Problems in Fitting SECR Models
writeGPS

Upload to GPS
sim.capthist

Simulate Detection Histories
plot.traps

Plot traps Object
usage

Detector Usage
secrdemo

SECR Models Fitted to Demonstration Data
sim.secr

Simulate From Fitted secr Model
empirical.varD

Empirical Variance of H-T Density Estimate
popn

Population Object
sort.capthist

Sort Rows of capthist Object
signal

Signal Fields
subset.mask

Subset Mask Object
fxi

Probability Density of Home Range Centre
join

Combine or Split Sessions of capthist Object
reduce.capthist

Combine Occasions Or Detectors
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
score.test

Score Test for SECR Models
stoatDNA

Stoat DNA Data
subset.capthist

Subset or Split capthist Object
spacing

Detector or Mask Spacing
summary.traps

Summarise Detector Array
addTelemetry

Combine Telemetry and Detection Data
closedN

Closed population estimates
deermouse

Deermouse Live-trapping Datasets
details

Detail Specification for secr.fit
possum

Brushtail Possum Trapping Dataset
CV

Coefficient of Variation
FAQ

Frequently Asked Questions, And Others
detector

Detector Type
make.capthist

Construct capthist Object
make.systematic

Construct Systematic Detector Design
hcov

Hybrid Mixture Model
read.telemetry

Import Radio Fixes
mask

Mask Object
predictDsurface

Predict Density Surface
rectangularMask

Rectangular Mask
signalmatrix

Reformat Signal Data
read.traps

Read Detector Data From File
snip

Slice Transect Into Shorter Sections
session

Session Vector
transformations

Transform Point Array
secr-package

Spatially Explicit Capture--Recapture Models
trim

Drop Unwanted List Components
D.designdata

Construct Density Design Data
AIC.secr

Compare SECR Models
Rsurface

Smoothed Resource Surface
Parallel

Multi-core Processing
SPACECAP

Exchange data with SPACECAP package
PG

Telemetry Fixes in Polygons
circular

Circular Probability
covariates

Covariates Attribute
distancetotrap

Distance To Nearest Detector
logit

Logit Transformation
par.secr.fit

Fit Multiple SECR Models
ms

Multi-session Objects
make.traps

Build Detector Array
plot.mask

Plot Habitat Mask, Density or Resource Surface
reduce

Combine Columns
plot.popn

Plot popn Object
subset.popn

Subset popn Object
make.tri

Build Detector Array on Triangular or Hexagonal Grid
secr.model

Spatially Explicit Capture--Recapture Models
speed

Speed Tips
sim.popn

Simulate 2-D Population
timevaryingcov

Time-varying Detector Covariates
traps.info

Detector Attributes
verify

Check SECR Data
trap.builder

Complex Detector Layouts