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secr (version 5.4.1)

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

2,704

Version

5.4.1

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

January 11th, 2026

Functions in secr (5.4.1)

Smoothed Resource Surface

Multi-core Processing

Methods for MCgof Objects

RSE from Fitted Model

Add Covariates to Mask or Traps

Likelihood Ratio Test

Convert Data to RMark Input Format

Monte Carlo Goodness-of-fit for SECR Models

Telemetry Fixes in Polygons

Orongorongo Valley Brushtail Possums

Dissect Spatial Capture History Object

Mark-resight Data

Coerce traps object to mask

Coerce capthist to Data Frame or Array

Add Binned Covariate

Combine Telemetry and Detection Data

Spatial Capture History Object

Coerce ppp object to popn

Black Bear Hair Snag Dataset

Initial Parameter Values for SECR

Detector Clustering

Closed population estimates

Overdispersion of Activity Centres

Array of Parameter Estimates

Circular Probability

Coefficients of secr Object

Profile Likelihood Confidence Intervals

Number per detector

Derived Parameters of Fitted SECR Model

Covariates Attribute

derivedDsurface

Derived Absolute Density

deleteMaskPoints

Edit Mask Points

Contour Detection Probability

Deermouse Live-trapping Datasets

House mouse live trapping data

Detail Specification for secr.fit

Detection Functions

Expected Number of Individuals

Distance To Nearest Detector

Probability Density of Activity Centre

Activity Centres of Detected and Undetected Animals

Mask Buffer Diagnostic Plot

Confidence Ellipses

Deviance of fitted secr model and residual degrees of freedom

Rasterize Area Search or Transect Data

Empirical Variance of H-T Density Estimate

Simulated Movements

Multinomial Coefficient of SECR Likelihood

First or Last Part of an Object

Hybrid Mixture Model

Combine or Split Sessions of capthist Object

Fit Multiple SECR Models

Home Range Statistics

Flat-tailed Horned Lizard Dataset

Construct Grid Cells

Logit Transformation

Work with Open Population data

Create Default Design Data

Construct capthist Object

make.systematic

Construct Systematic Detector Design

Initial Parameter Values

Build Detector Array

Build Detector Array on Triangular or Hexagonal Grid

Build Habitat Mask

Construct Spatial Coverage Design

Construct Lacework Detector Design

Multi-session Objects

Net Detection Probability

Plot Detection Histories

Averaging of SECR Models Using Akaike's Information Criterion

Mask Diagnostics

Non-target Data

Ovenbird Mist-netting Dataset

Ovenbird Acoustic Dataset

Key to Petal Plot

pointsInPolygon

Points Inside Polygon

Area of Polygon(s)

Plot traps Object

Plot Population Object

Population Object

Outline Around Mask Cells

Plot Habitat Mask, Density or Resource Surface

Brushtail Possum Trapping Dataset

Plot Detection Functions

Mixture Model Check

Create a RasterLayer Object from Mask or Dsurface

Combine popn Objects

Combine traps Objects

Print Detections

SECR Model Predictions

predictDsurface

Predict Density Surface

Combine capthist Objects

Print or Summarise secr Object

Print Detectors

Random Landscape

rectangularMask

Rectangular Mask

Defunct Functions in Package secr

Score Test for SECR Models

Import Telemetry Fixes

Population Size

Read Detector Data From File

Combine Columns

secr-deprecated

Deprecated Functions in Package secr

Read Habitat Mask From File

reduce.capthist

Combine Occasions Or Detectors

Goodness-of-fit Test Results

Construct Detection Model Design Matrices and Lookups

Internal Functions

Goodness-of-Fit Test

Spatially Explicit Capture--Recapture Models

Changes in secr 5.0

SECR Models Fitted to Demonstration Data

Random Number Seed

Repeat or Resume Model Fit

Spatially Explicit Capture--Recapture

shareFactorLevels

Fix Inconsistent Covariates

Sighting Attributes

Reformat Signal Data

Simulate Detections For Ornstein-Uhlenbeck Movement

Simulate From Fitted secr Model

Simulate Detection Histories

Number of Threads

Simulate 2-D Population

Colour Strip Legend

subset.capthist

Subset or Split capthist Object

Slice Transect Into Shorter Sections

Sort Rows of capthist or mask Object

Smooth Terms in SECR Models

Subset, Split or Combine Mask Objects

Detector or Mask Spacing

Skink Pitfall Data

Summarise Detector Array

Time-varying Covariates

summary.capthist

Summarise Detections

transformations

Transform Point Array

Mask Buffer Width

Complex Detector Layouts

Subset popn Object

Subset traps Object

Summarise Simulated Population

Summarise Habitat Mask

Detector Attributes

Non-Euclidean Distances

Plot usage, detections or sightings.

Drop Unwanted List Components

Update Old capthist Format

Troubleshooting

Problems in Fitting SECR Models

Specifying a Dynamic Population

Utility Functions

Variance - Covariance Matrix of SECR Parameters

Write Data to Text File

Check SECR Data

Frequently Asked Questions, And Others

Import or export data

Construct Density Design Data

Density Surfaces

Model Compatibility

Estimate overdispersion

Plot Likelihood Surface

Compare SECR Models

Convert Data To Or From BUGS Format

Coefficient of Variation