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secr (version 2.7.0)

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

2.7.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

October 30th, 2013

Functions in secr (2.7.0)

capthist

Spatial Capture History Object
circular

Circular Probability
print.secr

Print secr Object
AIC.secr

Compare SECR Models
cluster

Detector Clustering
Parallel

Multi-core Processing
detectfn

Detection Functions
hornedlizard

Flat-tailed Horned Lizard Dataset
confint.secr

Profile Likelihood Confidence Intervals
polyarea

Area of Polygon(s)
make.systematic

Construct Systematic Detector Design
contour

Contour Detection Probability
read.capthist

Import or export data
empirical.varD

Empirical Variance of H-T Density Estimate
coef.secr

Coefficients of secr Object
ms

Multi-session Objects
signal

Signal Fields
plot.secr

Plot Detection Functions
pointsInPolygon

Points Inside Polygon
closure.test

Closure tests
homerange

Home Range Statistics
housemouse

House mouse live trapping data
deermouse

Deermouse Live-trapping Datasets
distancetotrap

Distance To Nearest Detector
ovenbird

Ovenbird Mist-netting Dataset
hcov

Hybrid Mixture Model
plot.mask

Plot Habitat Mask or Density Surface
expected.n

Expected Number of Individuals
predictDsurface

Predict Density Surface
rbind.capthist

Combine capthist Objects
plot.popn

Plot popn Object
read.mask

Read Habitat Mask From File
plot.traps

Plot traps Object
summary.capthist

Summarise Detections
secr.model.density

Density Models
mask.check

Mask Diagnostics
rbind.traps

Combine traps Objects
ovensong

Ovenbird Acoustic Dataset
secr.design.MS

Construct Detection Model Design Matrices and Lookups
join

Combine or Split Sessions of capthist Object
LLsurface.secr

Plot likelihood surface
randomHabitat

Random Landscape
BUGS

Convert Data To Or From BUGS Format
D.designdata

Construct Density Design Data
score.test

Score Test for SECR Models
print.capthist

Print Detections
stoatDNA

Stoat DNA Data
autoini

Initial Parameter Values for SECR
SPACECAP

Exchange data with SPACECAP package
addCovariates

Add Covariates to Mask or Traps
sort.capthist

Sort Rows of capthist Object
signalmatrix

Reformat Signal Data
skink

Skink Pitfall Data
secrdemo

SECR Models Fitted to Demonstration Data
summary.mask

Summarise Habitat Mask
ellipse.secr

Confidence ellipse
rbind.popn

Combine popn Objects
summary.traps

Summarise Detector Array
derived

Derived Parameters of Fitted SECR Model
sim.secr

Simulate From Fitted secr Model
head

First or Last Part of an Object
FAQ

Frequently Asked Questions, And Others
transformations

Transform Point Array
logit

Logit Transformation
write.captures

Write Data to Text File
RMarkInput

Convert Data to RMark Input Format
mask

Mask Object
closedN

Closed population estimates
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
reduce

Combine Columns
read.traps

Read Detector Data From File
LR.test

Likelihood Ratio Test
make.mask

Build Habitat Mask
sim.capthist

Simulate Detection Histories
logmultinom

Multinomial Coefficient of SECR Likelihood
make.capthist

Construct capthist Object
addTelemetry

Combine Telemetry and Detection Data
esa.plot

Mask Buffer Diagnostic Plot
timevaryingcov

Time-varying Detector Covariates
verify

Check SECR Data
suggest.buffer

Mask Buffer Width
pdot

Net Detection Probability
plot.capthist

Plot Detection Histories
vcov.secr

Variance - Covariance Matrix of SECR Parameters
deviance

Deviance of fitted secr model and residual degrees of freedom
capthist.parts

Dissect Spatial Capture History Object
model.average

Averaging of SECR Models Using Akaike's Information Criterion
possum

Brushtail Possum Trapping Dataset
trim

Drop Unwanted List Components
secr.fit

Spatially Explicit Capture--Recapture
region.N

Population Size
Troubleshooting

Problems in Fitting SECR Models
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
secr-package

Spatially Explicit Capture--Recapture Models
secr.model

Spatially Explicit Capture--Recapture Models
traps

Detector Array
secr.model.detection

Models for Detection Parameters
make.tri

Build Detector Array on Triangular or Hexagonal Grid
secr.make.newdata

Create Default Design Data
print.traps

Print Detectors
read.telemetry

Import Radio Fixes
predict.secr

SECR Model Predictions
subset.mask

Subset Mask Object
detector

Detector Type
subset.capthist

Subset or Split capthist Object
fxi

Probability Density of Home Range Centre
snip

Slice Transect Into Shorter Sections
spacing

Detector or Mask Spacing
make.traps

Build Detector Array
subset.popn

Subset popn Object
reduce.capthist

Combine Occasions Or Detectors
sim.popn

Simulate 2-D Population
subset.traps

Subset traps Object
covariates

Covariates Attribute
traps.info

Detector Attributes
trap.builder

Complex Detector Layouts
writeGPS

Upload to GPS
usagePlot

Plot Usage
usage

Detector Usage
popn

Population Object
Dsurface

Density Surfaces
details

Detail Specification for secr.fit
rectangularMask

Rectangular Mask
session

Session Vector
speed

Speed Tips