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secr (version 4.6.10)

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

2,124

Version

4.6.10

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Last Published

August 22nd, 2024

Functions in secr (4.6.10)

Frequently Asked Questions, And Others

Model Compatibility

Density Surfaces

Coefficient of Variation

Compare SECR Models

Add Covariates to Mask or Traps

Multi-core Processing

RSE from Fitted Model

Convert Data to RMark Input Format

Combine Telemetry and Detection Data

Telemetry Fixes in Polygons

Smoothed Resource Surface

Likelihood Ratio Test

Mark-resight Data

Orongorongo Valley Brushtail Possums

Add Binned Covariate

Coerce traps object to mask

Dissect Spatial Capture History Object

Initial Parameter Values for SECR

Overdispersion of Activity Centres

Circular Probability

Coerce capthist to Data Frame or Array

Spatial Capture History Object

Coerce ppp object to popn

Array of Parameter Estimates

Detector Clustering

Profile Likelihood Confidence Intervals

House mouse live trapping data

Covariates Attribute

Deermouse Live-trapping Datasets

Contour Detection Probability

Coefficients of secr Object

Closed population estimates

deleteMaskPoints

Edit Mask Points

Deviance of fitted secr model and residual degrees of freedom

Rasterize Area Search or Transect Data

Derived Parameters of Fitted SECR Model

Distance To Nearest Detector

Detail Specification for secr.fit

Confidence Ellipses

Detection Functions

Empirical Variance of H-T Density Estimate

First or Last Part of an Object

Simulated Movements

Activity Centres of Detected and Undetected Animals

Probability Density of Home Range Centre

Expected Number of Individuals

Home Range Statistics

Mask Buffer Diagnostic Plot

Construct Grid Cells

Mask Buffer Diagnostic Plot (internal)

Hybrid Mixture Model

Multinomial Coefficient of SECR Likelihood

Fit Multiple SECR Models

Logit Transformation

Combine or Split Sessions of capthist Object

Construct Lacework Detector Design

Flat-tailed Horned Lizard Dataset

Construct capthist Object

Construct Spatial Coverage Design

Build Habitat Mask

Build Detector Array on Triangular or Hexagonal Grid

Initial Parameter Values

Work with Open Population data

make.systematic

Construct Systematic Detector Design

Averaging of SECR Models Using Akaike's Information Criterion

Mask Diagnostics

Build Detector Array

Key to Petal Plot

Plot Population Object

Plot traps Object

Ovenbird Acoustic Dataset

Non-target Data

Multi-session Objects

Plot Detection Histories

Plot Habitat Mask, Density or Resource Surface

Plot Detection Functions

Outline Around Mask Cells

Mixture Model Check

pointsInPolygon

Points Inside Polygon

predictDsurface

Predict Density Surface

Area of Polygon(s)

Ovenbird Mist-netting Dataset

SECR Model Predictions

Print or Summarise secr Object

Print Detectors

Net Detection Probability

Brushtail Possum Trapping Dataset

Population Object

Create a RasterLayer Object from Mask or Dsurface

Random Landscape

Combine Columns

rectangularMask

Rectangular Mask

Import Telemetry Fixes

Print Detections

Read Detector Data From File

Combine capthist Objects

Combine popn Objects

Combine traps Objects

Read Habitat Mask From File

Defunct Functions in Package secr

Population Size

Spatially Explicit Capture--Recapture

Spatially Explicit Capture--Recapture Models

Create Default Design Data

Score Test for SECR Models

Construct Detection Model Design Matrices and Lookups

reduce.capthist

Combine Occasions Or Detectors

secr-deprecated

Deprecated Functions in Package secr

Internal Functions

Goodness-of-fit Test Results

Number of Threads

Random Number Seed

Sighting Attributes

Goodness-of-Fit Test

Reformat Signal Data

shareFactorLevels

Fix Inconsistent Covariates

SECR Models Fitted to Demonstration Data

Skink Pitfall Data

Sort Rows of capthist or mask Object

Slice Transect Into Shorter Sections

Smooth Terms in SECR Models

Detector or Mask Spacing

Simulate Detection Histories

Simulate From Fitted secr Model

subset.capthist

Subset or Split capthist Object

Summarise Simulated Population

Subset traps Object

Simulate 2-D Population

Summarise Habitat Mask

Subset, Split or Combine Mask Objects

Summarise Detector Array

Subset popn Object

Mask Buffer Width

summary.capthist

Summarise Detections

Colour Strip Legend

Detector Attributes

Update Old capthist Format

Specifying a Dynamic Population

Time-varying Covariates

Troubleshooting

Problems in Fitting SECR Models

Drop Unwanted List Components

transformations

Transform Point Array

Complex Detector Layouts

Utility Functions

Plot usage, detections or sightings.

Variance - Covariance Matrix of SECR Parameters

Non-Euclidean Distances

Write Data to Text File

Check SECR Data

Construct Density Design Data

Estimate overdispersion

Plot Likelihood Surface

Convert Data To Or From BUGS Format

Import or export data