Learn R Programming

⚠️There's a newer version (5.2.4) of this package.Take me there.

secr (version 4.5.10)

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.

Copy Link

Version

Install

install.packages('secr')

Monthly Downloads

1,470

Version

4.5.10

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 10th, 2023

Functions in secr (4.5.10)

Plot Likelihood Surface

Frequently Asked Questions, And Others

Coefficient of Variation

Likelihood Ratio Test

Model Compatibility

Construct Density Design Data

Import or export data

Coerce capthist to Data Frame

Multi-core Processing

Add Covariates to Mask or Traps

Telemetry Fixes in Polygons

Smoothed Resource Surface

Orongorongo Valley Brushtail Possums

Convert Data to RMark Input Format

RSE from Fitted Model

Mark-resight Data

Combine Telemetry and Detection Data

Overdispersion of Activity Centres

Dissect Spatial Capture History Object

Spatial Capture History Object

Circular Probability

Closed population estimates

Initial Parameter Values for SECR

Coerce traps object to mask

Detector Clustering

deleteMaskPoints

Edit Mask Points

Detection Functions

Covariates Attribute

Coefficients of secr Object

Profile Likelihood Confidence Intervals

House mouse live trapping data

Deermouse Live-trapping Datasets

Contour Detection Probability

Detail Specification for secr.fit

Derived Parameters of Fitted SECR Model

Simulated Movements

Rasterize Area Search or Transect Data

Mask Buffer Diagnostic Plot (internal)

Deviance of fitted secr model and residual degrees of freedom

Mask Buffer Diagnostic Plot

Distance To Nearest Detector

Expected Number of Individuals

Confidence Ellipses

Empirical Variance of H-T Density Estimate

First or Last Part of an Object

Construct Grid Cells

Probability Density of Home Range Centre

Logit Transformation

Multinomial Coefficient of SECR Likelihood

Home Range Statistics

Combine or Split Sessions of capthist Object

Hybrid Mixture Model

Activity Centres of Detected and Undetected Animals

Flat-tailed Horned Lizard Dataset

Mask Diagnostics

Initial Parameter Values

make.systematic

Construct Systematic Detector Design

Build Detector Array on Triangular or Hexagonal Grid

Build Detector Array

Work with Open Population data

Build Habitat Mask

Construct capthist Object

Construct Lacework Detector Design

Multi-session Objects

Non-target Data

model.average-deprecated

Old Model Average Function

Net Detection Probability

Ovenbird Acoustic Dataset

Plot Detection Histories

Ovenbird Mist-netting Dataset

Fit Multiple SECR Models

Key to Petal Plot

Brushtail Possum Trapping Dataset

pointsInPolygon

Points Inside Polygon

Plot Population Object

Population Object

Mixture Model Check

Outline Around Mask Cells

Area of Polygon(s)

Plot Habitat Mask, Density or Resource Surface

Plot traps Object

Plot Detection Functions

Averaging of SECR Models Using Akaike's Information Criterion

Create a RasterLayer Object from Mask or Dsurface

Random Landscape

Print or Summarise secr Object

Combine capthist Objects

Print Detections

Print Detectors

Combine traps Objects

SECR Model Predictions

Combine popn Objects

predictDsurface

Predict Density Surface

Defunct Functions in Package secr

Read Habitat Mask From File

rectangularMask

Rectangular Mask

Population Size

Combine Columns

secr-deprecated

Deprecated Functions in Package secr

reduce.capthist

Combine Occasions Or Detectors

Score Test for SECR Models

Read Detector Data From File

Import Telemetry Fixes

Construct Detection Model Design Matrices and Lookups

Random Number Seed

Goodness-of-fit Test Results

Create Default Design Data

SECR Models Fitted to Demonstration Data

Goodness-of-Fit Test

Spatially Explicit Capture--Recapture Models

Internal Functions

Spatially Explicit Capture--Recapture

Simulate From Fitted secr Model

Number of Threads

Smooth Terms in SECR Models

Reformat Signal Data

Skink Pitfall Data

Simulate Detection Histories

Simulate 2-D Population

Sighting Attributes

shareFactorLevels

Fix Inconsistent Covariates

Slice Transect Into Shorter Sections

Subset traps Object

Subset, Split or Combine Mask Objects

subset.capthist

Subset or Split capthist Object

Colour Strip Legend

Sort Rows of capthist or mask Object

Detector or Mask Spacing

Subset popn Object

Mask Buffer Width

transformations

Transform Point Array

Summarise Habitat Mask

Summarise Simulated Population

Summarise Detector Array

Complex Detector Layouts

Detector Attributes

Time-varying Covariates

summary.capthist

Summarise Detections

Variance - Covariance Matrix of SECR Parameters

Check SECR Data

Troubleshooting

Problems in Fitting SECR Models

Plot usage, detections or sightings.

Non-Euclidean Distances

Specifying a Dynamic Population

Utility Functions

Drop Unwanted List Components

Update Old capthist Format

Write Data to Text File

Convert Data To Or From BUGS Format

Compare SECR Models

Density Surfaces