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secr (version 4.6.4)

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

1,470

Version

4.6.4

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

October 17th, 2023

Functions in secr (4.6.4)

Coefficient of Variation

Model Compatibility

Estimate overdispersion

Construct Density Design Data

Density Surfaces

Frequently Asked Questions, And Others

Telemetry Fixes in Polygons

Convert Data to RMark Input Format

Smoothed Resource Surface

Add Covariates to Mask or Traps

Multi-core Processing

Overdispersion of Activity Centres

Plot Likelihood Surface

Closed population estimates

RSE from Fitted Model

Circular Probability

Likelihood Ratio Test

Mark-resight Data

Coerce capthist to Data Frame

Import or export data

Orongorongo Valley Brushtail Possums

Spatial Capture History Object

Empirical Variance of H-T Density Estimate

Coerce traps object to mask

Mask Buffer Diagnostic Plot

Coerce ppp object to popn

Probability Density of Home Range Centre

Initial Parameter Values for SECR

Profile Likelihood Confidence Intervals

Construct Grid Cells

Dissect Spatial Capture History Object

House mouse live trapping data

Contour Detection Probability

Construct Lacework Detector Design

Construct capthist Object

Derived Parameters of Fitted SECR Model

Detail Specification for secr.fit

Covariates Attribute

Coefficients of secr Object

Deviance of fitted secr model and residual degrees of freedom

Mask Buffer Diagnostic Plot (internal)

Rasterize Area Search or Transect Data

Detector Clustering

Array of Parameter Estimates

Averaging of SECR Models Using Akaike's Information Criterion

Expected Number of Individuals

Combine Telemetry and Detection Data

Deermouse Live-trapping Datasets

Build Habitat Mask

Multi-session Objects

make.systematic

Construct Systematic Detector Design

Combine or Split Sessions of capthist Object

Detection Functions

deleteMaskPoints

Edit Mask Points

Hybrid Mixture Model

Simulated Movements

Plot Population Object

Distance To Nearest Detector

First or Last Part of an Object

Ovenbird Mist-netting Dataset

Activity Centres of Detected and Undetected Animals

Build Detector Array

Non-target Data

Build Detector Array on Triangular or Hexagonal Grid

Confidence Ellipses

Plot Detection Functions

Brushtail Possum Trapping Dataset

Home Range Statistics

Ovenbird Acoustic Dataset

Initial Parameter Values

Key to Petal Plot

Mask Diagnostics

Flat-tailed Horned Lizard Dataset

Fit Multiple SECR Models

SECR Model Predictions

Mixture Model Check

Work with Open Population data

Logit Transformation

Combine traps Objects

Read Habitat Mask From File

Net Detection Probability

Area of Polygon(s)

Population Object

reduce.capthist

Combine Occasions Or Detectors

Random Landscape

Multinomial Coefficient of SECR Likelihood

Plot Detection Histories

pointsInPolygon

Points Inside Polygon

Plot traps Object

Create a RasterLayer Object from Mask or Dsurface

Plot Habitat Mask, Density or Resource Surface

Combine capthist Objects

Combine popn Objects

Population Size

secr-deprecated

Deprecated Functions in Package secr

Print or Summarise secr Object

Score Test for SECR Models

Defunct Functions in Package secr

Outline Around Mask Cells

rectangularMask

Rectangular Mask

predictDsurface

Predict Density Surface

Print Detections

Internal Functions

Goodness-of-Fit Test

Simulate Detection Histories

shareFactorLevels

Fix Inconsistent Covariates

Random Number Seed

Sort Rows of capthist or mask Object

Print Detectors

Detector or Mask Spacing

Simulate 2-D Population

Import Telemetry Fixes

Read Detector Data From File

Subset traps Object

Reformat Signal Data

Combine Columns

Spatially Explicit Capture--Recapture Models

Mask Buffer Width

Spatially Explicit Capture--Recapture

Simulate From Fitted secr Model

Construct Detection Model Design Matrices and Lookups

Complex Detector Layouts

Skink Pitfall Data

Sighting Attributes

Number of Threads

Subset, Split or Combine Mask Objects

Drop Unwanted List Components

Subset popn Object

Troubleshooting

Problems in Fitting SECR Models

Create Default Design Data

Colour Strip Legend

SECR Models Fitted to Demonstration Data

Goodness-of-fit Test Results

Summarise Simulated Population

Variance - Covariance Matrix of SECR Parameters

subset.capthist

Subset or Split capthist Object

Smooth Terms in SECR Models

Slice Transect Into Shorter Sections

summary.capthist

Summarise Detections

Non-Euclidean Distances

Summarise Detector Array

Summarise Habitat Mask

Time-varying Covariates

Utility Functions

Specifying a Dynamic Population

transformations

Transform Point Array

Update Old capthist Format

Plot usage, detections or sightings.

Check SECR Data

Write Data to Text File

Detector Attributes

Compare SECR Models

Convert Data To Or From BUGS Format