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secr (version 5.2.1)

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

2,295

Version

5.2.1

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/MurrayEfford/secr/

Homepage

https://www.otago.ac.nz/density/

Maintainer

Murray Efford

Last Published

March 18th, 2025

Functions in secr (5.2.1)

Compare SECR Models

Model Compatibility

Frequently Asked Questions, And Others

Plot Likelihood Surface

Estimate overdispersion

Density Surfaces

Convert Data To Or From BUGS Format

Coefficient of Variation

Construct Density Design Data

Import or export data

Telemetry Fixes in Polygons

Monte Carlo Goodness-of-fit for SECR Models

Smoothed Resource Surface

Multi-core Processing

Likelihood Ratio Test

Orongorongo Valley Brushtail Possums

Methods for MCgof Objects

Convert Data to RMark Input Format

RSE from Fitted Model

Add Covariates to Mask or Traps

Add Binned Covariate

Dissect Spatial Capture History Object

Coerce traps object to mask

Coerce capthist to Data Frame or Array

Spatial Capture History Object

Black Bear Hair Snag Dataset

Coerce ppp object to popn

Initial Parameter Values for SECR

Detector Clustering

Mark-resight Data

Combine Telemetry and Detection Data

Closed population estimates

Circular Probability

Overdispersion of Activity Centres

Coefficients of secr Object

Array of Parameter Estimates

Profile Likelihood Confidence Intervals

Contour Detection Probability

House mouse live trapping data

derivedDsurface

Derived Absolute Density

Derived Parameters of Fitted SECR Model

Covariates Attribute

Detail Specification for secr.fit

Detection Functions

Deviance of fitted secr model and residual degrees of freedom

Deermouse Live-trapping Datasets

deleteMaskPoints

Edit Mask Points

Mask Buffer Diagnostic Plot

Construct Grid Cells

Rasterize Area Search or Transect Data

Simulated Movements

Empirical Variance of H-T Density Estimate

Distance To Nearest Detector

Expected Number of Individuals

Activity Centres of Detected and Undetected Animals

Confidence Ellipses

Probability Density of Activity Centre

Fit Multiple SECR Models

Hybrid Mixture Model

Logit Transformation

Home Range Statistics

Multinomial Coefficient of SECR Likelihood

Construct capthist Object

First or Last Part of an Object

Flat-tailed Horned Lizard Dataset

Combine or Split Sessions of capthist Object

Work with Open Population data

Construct Spatial Coverage Design

Build Detector Array

Create Default Design Data

Build Habitat Mask

Construct Lacework Detector Design

make.systematic

Construct Systematic Detector Design

Initial Parameter Values

Build Detector Array on Triangular or Hexagonal Grid

Key to Petal Plot

Averaging of SECR Models Using Akaike's Information Criterion

Plot Detection Histories

Ovenbird Acoustic Dataset

Mask Diagnostics

Ovenbird Mist-netting Dataset

Non-target Data

Net Detection Probability

Multi-session Objects

Plot Habitat Mask, Density or Resource Surface

Mixture Model Check

Area of Polygon(s)

SECR Model Predictions

Brushtail Possum Trapping Dataset

Plot Population Object

Plot traps Object

Outline Around Mask Cells

Population Object

pointsInPolygon

Points Inside Polygon

Plot Detection Functions

Combine traps Objects

Print or Summarise secr Object

Random Landscape

predictDsurface

Predict Density Surface

Combine popn Objects

Combine capthist Objects

Print Detectors

Read Habitat Mask From File

Create a RasterLayer Object from Mask or Dsurface

Print Detections

Read Detector Data From File

Import Telemetry Fixes

Score Test for SECR Models

Defunct Functions in Package secr

rectangularMask

Rectangular Mask

Combine Columns

Internal Functions

secr-deprecated

Deprecated Functions in Package secr

reduce.capthist

Combine Occasions Or Detectors

Population Size

Goodness-of-fit Test Results

Repeat or Resume Model Fit

Construct Detection Model Design Matrices and Lookups

SECR Models Fitted to Demonstration Data

Random Number Seed

Spatially Explicit Capture--Recapture Models

Goodness-of-Fit Test

Changes in secr 5.0

Spatially Explicit Capture--Recapture

Simulate Detection Histories

shareFactorLevels

Fix Inconsistent Covariates

Number of Threads

Sighting Attributes

Reformat Signal Data

Smooth Terms in SECR Models

Skink Pitfall Data

Simulate 2-D Population

Simulate From Fitted secr Model

Slice Transect Into Shorter Sections

subset.capthist

Subset or Split capthist Object

Detector or Mask Spacing

Subset, Split or Combine Mask Objects

Subset popn Object

Subset traps Object

Colour Strip Legend

Sort Rows of capthist or mask Object

Summarise Detector Array

Summarise Habitat Mask

summary.capthist

Summarise Detections

Time-varying Covariates

Summarise Simulated Population

Mask Buffer Width

transformations

Transform Point Array

Complex Detector Layouts

Detector Attributes

Specifying a Dynamic Population

Utility Functions

Non-Euclidean Distances

Drop Unwanted List Components

Troubleshooting

Problems in Fitting SECR Models

Variance - Covariance Matrix of SECR Parameters

Plot usage, detections or sightings.

Update Old capthist Format

Write Data to Text File

Check SECR Data