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secr (version 5.2.4)

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

1,551

Version

5.2.4

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

June 13th, 2025

Functions in secr (5.2.4)

Model Compatibility

Convert Data To Or From BUGS Format

Construct Density Design Data

Plot Likelihood Surface

Coefficient of Variation

Density Surfaces

Import or export data

Methods for MCgof Objects

Add Covariates to Mask or Traps

RSE from Fitted Model

Orongorongo Valley Brushtail Possums

Smoothed Resource Surface

Likelihood Ratio Test

Monte Carlo Goodness-of-fit for SECR Models

Convert Data to RMark Input Format

Multi-core Processing

Telemetry Fixes in Polygons

Spatial Capture History Object

Coerce ppp object to popn

Coerce capthist to Data Frame or Array

Coerce traps object to mask

Mark-resight Data

Combine Telemetry and Detection Data

Dissect Spatial Capture History Object

Initial Parameter Values for SECR

Coefficients of secr Object

Array of Parameter Estimates

Detector Clustering

Profile Likelihood Confidence Intervals

Overdispersion of Activity Centres

Closed population estimates

Number per detector

Circular Probability

Add Binned Covariate

Black Bear Hair Snag Dataset

Covariates Attribute

deleteMaskPoints

Edit Mask Points

Contour Detection Probability

Deermouse Live-trapping Datasets

Detection Functions

Detail Specification for secr.fit

Derived Parameters of Fitted SECR Model

House mouse live trapping data

derivedDsurface

Derived Absolute Density

Distance To Nearest Detector

Expected Number of Individuals

Activity Centres of Detected and Undetected Animals

Confidence Ellipses

Empirical Variance of H-T Density Estimate

Rasterize Area Search or Transect Data

Deviance of fitted secr model and residual degrees of freedom

Simulated Movements

Probability Density of Activity Centre

Mask Buffer Diagnostic Plot

Logit Transformation

Fit Multiple SECR Models

Construct Grid Cells

Combine or Split Sessions of capthist Object

Home Range Statistics

First or Last Part of an Object

Multinomial Coefficient of SECR Likelihood

Flat-tailed Horned Lizard Dataset

Hybrid Mixture Model

Work with Open Population data

Construct capthist Object

Initial Parameter Values

Construct Lacework Detector Design

Create Default Design Data

Build Detector Array on Triangular or Hexagonal Grid

Build Habitat Mask

Construct Spatial Coverage Design

make.systematic

Construct Systematic Detector Design

Build Detector Array

Averaging of SECR Models Using Akaike's Information Criterion

Multi-session Objects

Ovenbird Mist-netting Dataset

Ovenbird Acoustic Dataset

Mask Diagnostics

Net Detection Probability

Plot Detection Histories

Plot Detection Functions

Plot traps Object

Outline Around Mask Cells

Mixture Model Check

Non-target Data

Key to Petal Plot

Population Object

Brushtail Possum Trapping Dataset

Plot Population Object

Plot Habitat Mask, Density or Resource Surface

Combine traps Objects

Combine popn Objects

Print Detectors

Random Landscape

SECR Model Predictions

predictDsurface

Predict Density Surface

Print or Summarise secr Object

Population Size

Defunct Functions in Package secr

Read Habitat Mask From File

Print Detections

Import Telemetry Fixes

Read Detector Data From File

rectangularMask

Rectangular Mask

Score Test for SECR Models

Create a RasterLayer Object from Mask or Dsurface

pointsInPolygon

Points Inside Polygon

Area of Polygon(s)

reduce.capthist

Combine Occasions Or Detectors

Combine Columns

Combine capthist Objects

secr-deprecated

Deprecated Functions in Package secr

Changes in secr 5.0

Internal Functions

Repeat or Resume Model Fit

Spatially Explicit Capture--Recapture Models

Spatially Explicit Capture--Recapture

Construct Detection Model Design Matrices and Lookups

Random Number Seed

Goodness-of-Fit Test

SECR Models Fitted to Demonstration Data

Goodness-of-fit Test Results

Simulate From Fitted secr Model

Simulate 2-D Population

Sighting Attributes

shareFactorLevels

Fix Inconsistent Covariates

Simulate Detection Histories

Number of Threads

Skink Pitfall Data

Reformat Signal Data

Colour Strip Legend

Smooth Terms in SECR Models

Subset, Split or Combine Mask Objects

subset.capthist

Subset or Split capthist Object

Slice Transect Into Shorter Sections

Sort Rows of capthist or mask Object

Detector or Mask Spacing

Subset popn Object

Time-varying Covariates

summary.capthist

Summarise Detections

Complex Detector Layouts

Subset traps Object

Summarise Simulated Population

Mask Buffer Width

Summarise Detector Array

Summarise Habitat Mask

transformations

Transform Point Array

Detector Attributes

Plot usage, detections or sightings.

Utility Functions

Non-Euclidean Distances

Drop Unwanted List Components

Write Data to Text File

Variance - Covariance Matrix of SECR Parameters

Check SECR Data

Troubleshooting

Problems in Fitting SECR Models

Specifying a Dynamic Population

Update Old capthist Format

Compare SECR Models

Frequently Asked Questions, And Others

Estimate overdispersion