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secr (version 4.5.8)

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

1,427

Version

4.5.8

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

November 29th, 2022

Functions in secr (4.5.8)

Plot Likelihood Surface

Coefficient of Variation

Construct Density Design Data

Compare SECR Models

Convert Data To Or From BUGS Format

Likelihood Ratio Test

Density Surfaces

Frequently Asked Questions, And Others

Add Covariates to Mask or Traps

Mark-resight Data

Multi-core Processing

Model Compatibility

RSE from Fitted Model

Import or export data

Convert Data to RMark Input Format

Smoothed Resource Surface

Coerce traps object to mask

Combine Telemetry and Detection Data

Overdispersion of Activity Centres

Orongorongo Valley Brushtail Possums

Coerce capthist to Data Frame

Spatial Capture History Object

Initial Parameter Values for SECR

Detector Clustering

Circular Probability

Dissect Spatial Capture History Object

deleteMaskPoints

Edit Mask Points

Detail Specification for secr.fit

Closed population estimates

Telemetry Fixes in Polygons

Derived Parameters of Fitted SECR Model

Contour Detection Probability

Rasterize Area Search or Transect Data

Distance To Nearest Detector

Coefficients of secr Object

Covariates Attribute

Detection Functions

Deermouse Live-trapping Datasets

Profile Likelihood Confidence Intervals

Flat-tailed Horned Lizard Dataset

Mask Buffer Diagnostic Plot

Expected Number of Individuals

House mouse live trapping data

Mask Buffer Diagnostic Plot (internal)

Simulated Movements

Confidence Ellipses

Empirical Variance of H-T Density Estimate

ip.secr-deprecated

Deprecated Functions

Activity Centres of Detected and Undetected Animals

Probability Density of Home Range Centre

Logit Transformation

Combine or Split Sessions of capthist Object

Build Detector Array on Triangular or Hexagonal Grid

Construct Lacework Detector Design

Deviance of fitted secr model and residual degrees of freedom

Initial Parameter Values

First or Last Part of an Object

Home Range Statistics

Construct Grid Cells

Work with Open Population data

Averaging of SECR Models Using Akaike's Information Criterion

Non-target Data

Multi-session Objects

Plot Detection Histories

Build Habitat Mask

Key to Petal Plot

Hybrid Mixture Model

Multinomial Coefficient of SECR Likelihood

Construct capthist Object

Fit Multiple SECR Models

Import Telemetry Fixes

Mask Diagnostics

Ovenbird Mist-netting Dataset

Plot Habitat Mask, Density or Resource Surface

model.average-deprecated

Old Model Average Function

make.systematic

Construct Systematic Detector Design

Ovenbird Acoustic Dataset

Read Detector Data From File

Build Detector Array

Spatially Explicit Capture--Recapture

Plot traps Object

Create Default Design Data

predictDsurface

Predict Density Surface

Score Test for SECR Models

Print Detections

Net Detection Probability

shareFactorLevels

Fix Inconsistent Covariates

Mixture Model Check

Outline Around Mask Cells

Defunct Functions in Package secr

Area of Polygon(s)

pointsInPolygon

Points Inside Polygon

Sighting Attributes

Subset, Split or Combine Mask Objects

Population Object

Subset popn Object

Plot Population Object

Combine capthist Objects

Combine popn Objects

Random Landscape

secr-deprecated

Deprecated Functions in Package secr

Detector Attributes

Create a RasterLayer Object from Mask or Dsurface

reduce.capthist

Combine Occasions Or Detectors

Brushtail Possum Trapping Dataset

SECR Models Fitted to Demonstration Data

Plot Detection Functions

SECR Model Predictions

Print or Summarise secr Object

Population Size

Spatially Explicit Capture--Recapture Models

Drop Unwanted List Components

Goodness-of-fit Test Results

Simulate Detection Histories

Internal Functions

Construct Detection Model Design Matrices and Lookups

Simulate 2-D Population

rectangularMask

Rectangular Mask

Summarise Simulated Population

Summarise Detector Array

Print Detectors

Combine Columns

Check SECR Data

Update Old capthist Format

Goodness-of-Fit Test

Random Number Seed

Colour Strip Legend

Reformat Signal Data

subset.capthist

Subset or Split capthist Object

Sort Rows of capthist or mask Object

Write Data to Text File

summary.capthist

Summarise Detections

Combine traps Objects

Summarise Habitat Mask

Utility Functions

Read Habitat Mask From File

Number of Threads

Variance - Covariance Matrix of SECR Parameters

Detector or Mask Spacing

Smooth Terms in SECR Models

Simulate From Fitted secr Model

Skink Pitfall Data

Time-varying Covariates

transformations

Transform Point Array

Troubleshooting

Problems in Fitting SECR Models

Complex Detector Layouts

Plot usage, detections or sightings.

Non-Euclidean Distances

Specifying a Dynamic Population

Slice Transect Into Shorter Sections

Subset traps Object

Mask Buffer Width