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secr (version 4.5.3)

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

4.5.3

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

February 13th, 2022

Functions in secr (4.5.3)

Telemetry Fixes in Polygons

RSE from Fitted Model

Smoothed Resource Surface

Likelihood Ratio Test

Plot Likelihood Surface

Add Covariates to Mask or Traps

Density Surfaces

Frequently Asked Questions, And Others

Contour Detection Probability

Detector Clustering

Profile Likelihood Confidence Intervals

Coefficients of secr Object

Coerce traps object to mask

Initial Parameter Values for SECR

Derived Parameters of Fitted SECR Model

Dissect Spatial Capture History Object

Mark-resight Data

Spatial Capture History Object

Detection Functions

Circular Probability

Convert Data To Or From BUGS Format

Import or export data

Multi-core Processing

deleteMaskPoints

Edit Mask Points

Deermouse Live-trapping Datasets

Convert Data to RMark Input Format

Mask Buffer Diagnostic Plot (internal)

Flat-tailed Horned Lizard Dataset

Expected Number of Individuals

Rasterize Area Search or Transect Data

Detail Specification for secr.fit

Deviance of fitted secr model and residual degrees of freedom

Spatially Explicit Capture--Recapture by Inverse Prediction

Home Range Statistics

Simulated Movements

Multi-session Objects

First or Last Part of an Object

Averaging of SECR Models Using Akaike's Information Criterion

Activity Centres of Detected and Undetected Animals

Plot Detection Functions

Mask Diagnostics

Plot traps Object

Combine popn Objects

Empirical Variance of H-T Density Estimate

Multinomial Coefficient of SECR Likelihood

Ovenbird Acoustic Dataset

pointsInPolygon

Points Inside Polygon

Fit Multiple SECR Models

Plot Habitat Mask, Density or Resource Surface

Defunct Functions in Package secr

Coefficient of Variation

Internal Functions

secr-deprecated

Deprecated Functions in Package secr

Area of Polygon(s)

Population Object

Combine traps Objects

Construct capthist Object

Construct Density Design Data

Plot Population Object

Read Habitat Mask From File

Brushtail Possum Trapping Dataset

Import Telemetry Fixes

Subset, Split or Combine Mask Objects

Combine Columns

Construct Lacework Detector Design

subset.capthist

Subset or Split capthist Object

Goodness-of-fit Test Results

Non-Euclidean Distances

Combine Telemetry and Detection Data

Sighting Attributes

Spatially Explicit Capture--Recapture Models

Number of Threads

reduce.capthist

Combine Occasions Or Detectors

shareFactorLevels

Fix Inconsistent Covariates

Summarise Habitat Mask

Simulate 2-D Population

Simulate From Fitted secr Model

Specifying a Dynamic Population

Slice Transect Into Shorter Sections

Hybrid Mixture Model

Mask Buffer Diagnostic Plot

Summarise Simulated Population

Coerce capthist to Data Frame

Probability Density of Home Range Centre

Utility Functions

make.systematic

Construct Systematic Detector Design

Closed population estimates

Variance - Covariance Matrix of SECR Parameters

Update Old capthist Format

Check SECR Data

Print Detections

Build Detector Array

House mouse live trapping data

Distance To Nearest Detector

Plot Detection Histories

Covariates Attribute

Net Detection Probability

Print or Summarise secr Object

Build Habitat Mask

Key to Petal Plot

Work with Open Population data

Outline Around Mask Cells

Ovenbird Mist-netting Dataset

Combine or Split Sessions of capthist Object

Build Detector Array on Triangular or Hexagonal Grid

Logit Transformation

Confidence Ellipses

Sort Rows of capthist or mask Object

Print Detectors

SECR Model Predictions

Random Landscape

SECR Models Fitted to Demonstration Data

Smooth Terms in SECR Models

Skink Pitfall Data

Random Number Seed

Detector Attributes

predictDsurface

Predict Density Surface

Read Detector Data From File

Combine capthist Objects

Mixture Model Check

rectangularMask

Rectangular Mask

Population Size

Create a RasterLayer Or SpatRaster Object from Mask or Dsurface

Construct Detection Model Design Matrices and Lookups

Spatially Explicit Capture--Recapture

Score Test for SECR Models

Detector or Mask Spacing

Goodness-of-Fit Test

Subset popn Object

Create Default Design Data

Reformat Signal Data

Subset traps Object

Summarise Detector Array

Drop Unwanted List Components

Colour Strip Legend

Mask Buffer Width

Simulate Detection Histories

transformations

Transform Point Array

summary.capthist

Summarise Detections

Time-varying Covariates

Troubleshooting

Problems in Fitting SECR Models

Complex Detector Layouts

Plot usage, detections or sightings.

Write Data to Text File

Compare SECR Models

Model Compatibility

Orongorongo Valley Brushtail Possums