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secr (version 2.1.0)

Spatially explicit capture-recapture

Description

Functions to estimate the density 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

1,565

Version

2.1.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

June 17th, 2011

Functions in secr (2.1.0)

Spatial Capture History Object

Dissect Spatial Capture History Object

Spatially Explicit Capture--Recapture by Inverse Prediction

Mask Buffer Diagnostic Plot

Probability Density of Home Range Centre

Closed population estimates

subset.capthist

Subset or Split capthist Object

Contour Detection Probability

Deviance of fitted secr model and residual degrees of freedom

Detection Functions

Convert Data To Or From BUGS Format

Initial Parameter Values for SECR

Confidence ellipse

Detector Clustering

Simulate 2-D Population

make.systematic

Construct Systematic Detector Design

Mask Diagnostics

Brushtail Possum Trapping Dataset

Plot Detection Histories

Multinomial Coefficient of SECR Likelihood

Deermouse Live-trapping Datasets

Construct Detection Model Design Matrices and Lookups

Area of Polygon(s)

Build Habitat Mask

Sort Rows of capthist Object

Spatially Explicit Capture--Recapture Models

Drop Unwanted List Components

Model averaging for SECR Models

secr.model.detection

Models for Detection Parameters

Import or export data

Detector or Mask Spacing

Read Detector Data From File

Logit Transformation

Build Detector Array

Combine popn Objects

Read Habitat Mask From File

Plot likelihood surface

Covariates Attribute

SECR Models Fitted to Demonstration Data

Check SECR Data

Plot Habitat Mask

Construct Density Design Data

Summarise Detector Array

Ovenbird Acoustic Dataset

Print Detectors

SECR Model Predictions

Construct capthist Object

Write Data to Text File

Spatially Explicit Capture--Recapture Models

Multi-session Objects

Net Detection Probability

Population Object

Build Detector Array on Triangular or Hexagonal Grid

Exchange data with SPACECAP package

Derived Parameters of Fitted SECR Model

Home Range Statistics

Plot popn Object

Combine Columns

Combine capthist Objects

Spatially Explicit Capture--Recapture

secr.make.newdata

Create Default Design Data

Simulate From Fitted secr Model

Subset traps Object

House mouse live trapping data

Circular Probability

Distance To Nearest Detector

secr.model.density

Combine traps Objects

Mask Buffer Width

Summarise Habitat Mask

Print secr Object

Score Test for SECR Models

Frequently Asked Questions, And Others

Empirical Variance of H-T Density Estimate

transformations

Transform Point Array

Simulate Detection Histories

summary.capthist

Summarise Detections

Variance - Covariance Matrix of SECR Parameters

Skink Pitfall Data

Detector Attributes

Coefficients of secr Object

Complex Detector Layouts

Expected Number of Individuals

Likelihood Ratio Test for SECR Models

Flat-tailed Horned Lizard Dataset

Mask Buffer Diagnostic Plot (internal)

Ovenbird Mist-netting Dataset

Plot traps Object

Print Detections

Subset Mask Object

Profile Likelihood Confidence Intervals

Plot Detection Functions

Population Size

reduce.capthist

Combine Occasions Or Convert Detector Types

Compare SECR Models