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secr (version 2.9.4)

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

1,551

Version

2.9.4

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

March 24th, 2015

Functions in secr (2.9.4)

Detection Functions

Convert Data to RMark Input Format

Circular Probability

Dissect Spatial Capture History Object

Detector Attributes

Detail Specification for secr.fit

Confidence Ellipses

Spatially Explicit Capture--Recapture by Inverse Prediction

Density Surfaces

Mask Buffer Diagnostic Plot (internal)

Ovenbird Mist-netting Dataset

Activity Centres of Detected and Undetected Animals

Simulate 2-D Population

Population Object

Import or export data

Empirical Variance of H-T Density Estimate

Coefficients of secr Object

make.systematic

Construct Systematic Detector Design

Telemetry Fixes in Polygons

Averaging of SECR Models Using Akaike's Information Criterion

Plot Detection Histories

Exchange data with SPACECAP package

Coefficient of Variation

Construct Density Design Data

Spatially Explicit Capture--Recapture

Initial Parameter Values for SECR

Convert Data To Or From BUGS Format

Orongorongo Valley Brushtail Possums

deleteMaskPoints

Edit Mask Points

House mouse live trapping data

Combine Telemetry and Detection Data

predictDsurface

Predict Density Surface

Combine Columns

Plot Detection Functions

Derived Parameters of Fitted SECR Model

Closed population estimates

Flat-tailed Horned Lizard Dataset

Spatial Capture History Object

Read Habitat Mask From File

Logit Transformation

Mask Buffer Diagnostic Plot

Profile Likelihood Confidence Intervals

Home Range Statistics

Expected Number of Individuals

Population Size

Plot popn Object

secr.model.density

Probability Density of Home Range Centre

Sort Rows of capthist Object

Mask Diagnostics

Spatially Explicit Capture--Recapture Models

Contour Detection Probability

Goodness-of-fit Test Results

Subset traps Object

Simulate Detection Histories

Subset Mask Object

Ovenbird Acoustic Dataset

Build Habitat Mask

Print Detectors

Construct capthist Object

Area of Polygon(s)

secr.model.detection

Models for Detection Parameters

pointsInPolygon

Points Inside Polygon

Likelihood Ratio Test

Subset popn Object

Plot Habitat Mask, Density or Resource Surface

Multi-core Processing

Multi-session Objects

Utility Functions

secr.make.newdata

Create Default Design Data

Time-varying Detector Covariates

Summarise Detector Array

First or Last Part of an Object

Net Detection Probability

Import Radio Fixes

Spatially Explicit Capture--Recapture Models

Combine capthist Objects

Troubleshooting

Problems in Fitting SECR Models

Add Covariates to Mask or Traps

Goodness-of-Fit Test

Deermouse Live-trapping Datasets

Drop Unwanted List Components

sim.popn details

Specifying a Dynamic Population

Skink Pitfall Data

Summarise Habitat Mask

SECR Models Fitted to Demonstration Data

Combine popn Objects

Detector or Mask Spacing

Combine traps Objects

SECR Model Predictions

reduce.capthist

Combine Occasions Or Detectors

Print secr Object

Construct Detection Model Design Matrices and Lookups

subset.capthist

Subset or Split capthist Object

Mask Buffer Width

Complex Detector Layouts

Hybrid Mixture Model

transformations

Transform Point Array

summary.capthist

Summarise Detections

Plot likelihood surface

Detector Clustering

Build Detector Array

Distance To Nearest Detector

Build Detector Array on Triangular or Hexagonal Grid

Multinomial Coefficient of SECR Likelihood

Print Detections

Read Detector Data From File

Score Test for SECR Models

rectangularMask

Rectangular Mask

Simulate From Fitted secr Model

Variance - Covariance Matrix of SECR Parameters

Write Data to Text File

Check SECR Data

Frequently Asked Questions, And Others

Compare SECR Models

Smoothed Resource Surface

Covariates Attribute

Deviance of fitted secr model and residual degrees of freedom

Combine or Split Sessions of capthist Object

Fit Multiple SECR Models

Plot traps Object

Random Landscape

Colour Strip Legend

Slice Transect Into Shorter Sections

Smooth Terms in SECR Models

Non-Euclidean Distances

Reformat Signal Data

Brushtail Possum Trapping Dataset