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secr (version 4.6.9)

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

4.6.9

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Last Published

June 29th, 2024

Functions in secr (4.6.9)

Convert Data To Or From BUGS Format

Compare SECR Models

Likelihood Ratio Test

Model Compatibility

Orongorongo Valley Brushtail Possums

Import or export data

Convert Data to RMark Input Format

Construct Density Design Data

RSE from Fitted Model

Coefficient of Variation

Telemetry Fixes in Polygons

Multi-core Processing

Mark-resight Data

Smoothed Resource Surface

Add Binned Covariate

Deermouse Live-trapping Datasets

Circular Probability

Spatial Capture History Object

Covariates Attribute

Coerce ppp object to popn

Add Covariates to Mask or Traps

Combine Telemetry and Detection Data

Initial Parameter Values for SECR

Overdispersion of Activity Centres

Dissect Spatial Capture History Object

Coefficients of secr Object

Detector Clustering

deleteMaskPoints

Edit Mask Points

Array of Parameter Estimates

Coerce traps object to mask

Coerce capthist to Data Frame

Profile Likelihood Confidence Intervals

Confidence Ellipses

Derived Parameters of Fitted SECR Model

Hybrid Mixture Model

Empirical Variance of H-T Density Estimate

Construct Grid Cells

Mask Buffer Diagnostic Plot

Closed population estimates

Flat-tailed Horned Lizard Dataset

Mask Buffer Diagnostic Plot (internal)

Distance To Nearest Detector

Rasterize Area Search or Transect Data

Logit Transformation

Work with Open Population data

Combine or Split Sessions of capthist Object

Multinomial Coefficient of SECR Likelihood

Activity Centres of Detected and Undetected Animals

Probability Density of Home Range Centre

Contour Detection Probability

House mouse live trapping data

Plot Population Object

Deviance of fitted secr model and residual degrees of freedom

Plot Detection Functions

Area of Polygon(s)

Expected Number of Individuals

Detail Specification for secr.fit

Multi-session Objects

Construct capthist Object

Population Object

Initial Parameter Values

Construct Lacework Detector Design

Build Detector Array on Triangular or Hexagonal Grid

Simulated Movements

Detection Functions

Non-target Data

First or Last Part of an Object

Key to Petal Plot

Combine capthist Objects

Combine popn Objects

Fit Multiple SECR Models

Combine traps Objects

Read Habitat Mask From File

Construct Spatial Coverage Design

Build Habitat Mask

Home Range Statistics

Mask Diagnostics

Ovenbird Mist-netting Dataset

Population Size

Build Detector Array

make.systematic

Construct Systematic Detector Design

Averaging of SECR Models Using Akaike's Information Criterion

reduce.capthist

Combine Occasions Or Detectors

predictDsurface

Predict Density Surface

Net Detection Probability

Print Detections

Ovenbird Acoustic Dataset

Spatially Explicit Capture--Recapture Models

Reformat Signal Data

Construct Detection Model Design Matrices and Lookups

Goodness-of-fit Test Results

SECR Models Fitted to Demonstration Data

Brushtail Possum Trapping Dataset

Plot traps Object

Outline Around Mask Cells

Read Detector Data From File

Print Detectors

Print or Summarise secr Object

Import Telemetry Fixes

Detector or Mask Spacing

Defunct Functions in Package secr

Simulate From Fitted secr Model

Skink Pitfall Data

Score Test for SECR Models

Sort Rows of capthist or mask Object

shareFactorLevels

Fix Inconsistent Covariates

rectangularMask

Rectangular Mask

Plot Detection Histories

Summarise Simulated Population

SECR Model Predictions

Plot Habitat Mask, Density or Resource Surface

Mixture Model Check

pointsInPolygon

Points Inside Polygon

Summarise Detector Array

summary.capthist

Summarise Detections

Random Landscape

Subset, Split or Combine Mask Objects

Create a RasterLayer Object from Mask or Dsurface

Subset popn Object

transformations

Transform Point Array

Summarise Habitat Mask

Time-varying Covariates

Specifying a Dynamic Population

Smooth Terms in SECR Models

Goodness-of-Fit Test

Sighting Attributes

Slice Transect Into Shorter Sections

Internal Functions

secr-deprecated

Deprecated Functions in Package secr

Random Number Seed

Combine Columns

Update Old capthist Format

Write Data to Text File

Spatially Explicit Capture--Recapture

Complex Detector Layouts

Number of Threads

Colour Strip Legend

Create Default Design Data

subset.capthist

Subset or Split capthist Object

Detector Attributes

Variance - Covariance Matrix of SECR Parameters

Simulate Detection Histories

Simulate 2-D Population

Mask Buffer Width

Non-Euclidean Distances

Plot usage, detections or sightings.

Utility Functions

Check SECR Data

Drop Unwanted List Components

Troubleshooting

Problems in Fitting SECR Models

Subset traps Object

Frequently Asked Questions, And Others

Estimate overdispersion

Plot Likelihood Surface

Density Surfaces