Learn R Programming

⚠️There's a newer version (5.4.1) of this package.Take me there.

secr (version 2.9.2)

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

1,565

Version

2.9.2

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

November 26th, 2014

Functions in secr (2.9.2)

Exchange data with SPACECAP package

Orongorongo Valley Brushtail Possums

Profile Likelihood Confidence Intervals

Covariates Attribute

Dissect Spatial Capture History Object

predictDsurface

Predict Density Surface

Probability Density of Home Range Centre

Convert Data To Or From BUGS Format

Mask Buffer Diagnostic Plot (internal)

Smoothed Resource Surface

Empirical Variance of H-T Density Estimate

First or Last Part of an Object

Coefficient of Variation

Spatial Capture History Object

Plot likelihood surface

Plot popn Object

Telemetry Fixes in Polygons

Initial Parameter Values for SECR

Compare SECR Models

Detector Clustering

Fit Multiple SECR Models

Net Detection Probability

Summarise Detector Array

Likelihood Ratio Test

Population Object

Plot traps Object

House mouse live trapping data

Confidence Ellipses

Expected Number of Individuals

Home Range Statistics

Contour Detection Probability

make.systematic

Construct Systematic Detector Design

Hybrid Mixture Model

Spatially Explicit Capture--Recapture by Inverse Prediction

Averaging of SECR Models Using Akaike's Information Criterion

Print secr Object

Density Surfaces

pointsInPolygon

Points Inside Polygon

Convert Data to RMark Input Format

Coefficients of secr Object

Closed population estimates

Mask Buffer Diagnostic Plot

Construct Density Design Data

Build Detector Array on Triangular or Hexagonal Grid

Multi-core Processing

Subset traps Object

Multinomial Coefficient of SECR Likelihood

Combine capthist Objects

Simulate Detection Histories

Flat-tailed Horned Lizard Dataset

Mask Diagnostics

Combine or Split Sessions of capthist Object

Detail Specification for secr.fit

Ovenbird Mist-netting Dataset

Print Detections

Read Habitat Mask From File

Plot Detection Functions

Combine Columns

Drop Unwanted List Components

Random Landscape

Add Covariates to Mask or Traps

Import or export data

Frequently Asked Questions, And Others

SECR Model Predictions

SECR Models Fitted to Demonstration Data

Time-varying Detector Covariates

Combine popn Objects

Reformat Signal Data

Deermouse Live-trapping Datasets

secr.model.detection

Models for Detection Parameters

Goodness-of-Fit Test

Construct Detection Model Design Matrices and Lookups

Detector Attributes

Complex Detector Layouts

rectangularMask

Rectangular Mask

Import Radio Fixes

secr.model.density

subset.capthist

Subset or Split capthist Object

Population Size

Detector or Mask Spacing

Variance - Covariance Matrix of SECR Parameters

secr.make.newdata

Create Default Design Data

Colour Strip Legend

Deviance of fitted secr model and residual degrees of freedom

Plot Detection Histories

Simulate 2-D Population

Sort Rows of capthist Object

Goodness-of-fit Test Results

Detection Functions

Circular Probability

Summarise Habitat Mask

Smooth Terms in SECR Models

Multi-session Objects

Derived Parameters of Fitted SECR Model

Construct capthist Object

Build Detector Array

Combine traps Objects

Score Test for SECR Models

Read Detector Data From File

Slice Transect Into Shorter Sections

Area of Polygon(s)

Simulate From Fitted secr Model

Subset popn Object

Write Data to Text File

transformations

Transform Point Array

Non-Euclidean Distances

Skink Pitfall Data

Print Detectors

reduce.capthist

Combine Occasions Or Detectors

Check SECR Data

Distance To Nearest Detector

Ovenbird Acoustic Dataset

Subset Mask Object

Troubleshooting

Problems in Fitting SECR Models

Spatially Explicit Capture--Recapture

Utility Functions

Spatially Explicit Capture--Recapture Models

Combine Telemetry and Detection Data

Activity Centres of Detected and Undetected Animals

Build Habitat Mask

Plot Habitat Mask, Density or Resource Surface

summary.capthist

Summarise Detections

Mask Buffer Width

Logit Transformation

Spatially Explicit Capture--Recapture Models

Brushtail Possum Trapping Dataset