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secr (version 2.9.1)

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

2.9.1

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

November 18th, 2014

Functions in secr (2.9.1)

Convert Data To Or From BUGS Format

Detector Clustering

Area of Polygon(s)

Net Detection Probability

Telemetry Fixes in Polygons

Detail Specification for secr.fit

Convert Data to RMark Input Format

Population Object

Deviance of fitted secr model and residual degrees of freedom

predictDsurface

Predict Density Surface

secr.make.newdata

Create Default Design Data

Activity Centres of Detected and Undetected Animals

Likelihood Ratio Test

Exchange data with SPACECAP package

Spatial Capture History Object

Closed population estimates

Distance To Nearest Detector

Dissect Spatial Capture History Object

Plot likelihood surface

Multi-session Objects

Initial Parameter Values for SECR

Mask Buffer Diagnostic Plot

Profile Likelihood Confidence Intervals

Fit Multiple SECR Models

Plot Detection Functions

Spatially Explicit Capture--Recapture Models

Combine capthist Objects

Variance - Covariance Matrix of SECR Parameters

Coefficients of secr Object

Read Detector Data From File

Combine or Split Sessions of capthist Object

secr.model.density

Population Size

Summarise Detector Array

Detection Functions

Mask Buffer Diagnostic Plot (internal)

Combine popn Objects

Print secr Object

Expected Number of Individuals

Spatially Explicit Capture--Recapture Models

Random Landscape

Coefficient of Variation

Construct capthist Object

Logit Transformation

Spatially Explicit Capture--Recapture

Combine Columns

Averaging of SECR Models Using Akaike's Information Criterion

Contour Detection Probability

Goodness-of-Fit Test

make.systematic

Construct Systematic Detector Design

First or Last Part of an Object

Circular Probability

Colour Strip Legend

Multinomial Coefficient of SECR Likelihood

Import Radio Fixes

Covariates Attribute

Mask Buffer Width

Spatially Explicit Capture--Recapture by Inverse Prediction

Deermouse Live-trapping Datasets

Construct Density Design Data

Orongorongo Valley Brushtail Possums

Ovenbird Mist-netting Dataset

SECR Model Predictions

Build Detector Array on Triangular or Hexagonal Grid

SECR Models Fitted to Demonstration Data

Plot traps Object

Density Surfaces

Add Covariates to Mask or Traps

Plot Habitat Mask, Density or Resource Surface

Smoothed Resource Surface

summary.capthist

Summarise Detections

Ovenbird Acoustic Dataset

Read Habitat Mask From File

Time-varying Detector Covariates

Empirical Variance of H-T Density Estimate

Smooth Terms in SECR Models

Summarise Habitat Mask

Score Test for SECR Models

Subset traps Object

transformations

Transform Point Array

Complex Detector Layouts

Slice Transect Into Shorter Sections

Simulate Detection Histories

Drop Unwanted List Components

Detector Attributes

Troubleshooting

Problems in Fitting SECR Models

secr.model.detection

Models for Detection Parameters

Build Habitat Mask

Write Data to Text File

Hybrid Mixture Model

Subset popn Object

Plot Detection Histories

Combine traps Objects

Goodness-of-fit Test Results

Construct Detection Model Design Matrices and Lookups

Reformat Signal Data

reduce.capthist

Combine Occasions Or Detectors

Subset Mask Object

Utility Functions

Non-Euclidean Distances

Skink Pitfall Data

Compare SECR Models

House mouse live trapping data

Derived Parameters of Fitted SECR Model

Home Range Statistics

Probability Density of Home Range Centre

Confidence Ellipses

Print Detections

pointsInPolygon

Points Inside Polygon

Print Detectors

Simulate From Fitted secr Model

Detector or Mask Spacing

Check SECR Data

Import or export data

Simulate 2-D Population

Multi-core Processing

Combine Telemetry and Detection Data

Frequently Asked Questions, And Others

Mask Diagnostics

Build Detector Array

Plot popn Object

rectangularMask

Rectangular Mask

Flat-tailed Horned Lizard Dataset

Sort Rows of capthist Object

subset.capthist

Subset or Split capthist Object

Brushtail Possum Trapping Dataset