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secr (version 4.3.1)

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

1,407

Version

4.3.1

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

September 1st, 2020

Functions in secr (4.3.1)

CV

Coefficient of Variation
LLsurface

Plot Likelihood Surface
capthist

Spatial Capture History Object
OVpossum

Orongorongo Valley Brushtail Possums
Dsurface

Density Surfaces
LR.test

Likelihood Ratio Test
D.designdata

Construct Density Design Data
PG

Telemetry Fixes in Polygons
capthist.parts

Dissect Spatial Capture History Object
read.capthist

Import or export data
BUGS

Convert Data To Or From BUGS Format
addCovariates

Add Covariates to Mask or Traps
Rsurface

Smoothed Resource Surface
closure.test

Closure tests
RSE

RSE from Fitted Model
covariates

Covariates Attribute
closedN

Closed population estimates
deermouse

Deermouse Live-trapping Datasets
as.mask

Coerce traps object to mask
housemouse

House mouse live trapping data
autoini

Initial Parameter Values for SECR
coef.secr

Coefficients of secr Object
addSightings

Mark-resight Data
cluster

Detector Clustering
confint.secr

Profile Likelihood Confidence Intervals
contour

Contour Detection Probability
deleteMaskPoints

Edit Mask Points
circular

Circular Probability
as.data.frame

Coerce capthist to Data Frame
addTelemetry

Combine Telemetry and Detection Data
clone

Replicate Rows
distancetotrap

Distance To Nearest Detector
esa.plot

Mask Buffer Diagnostic Plot
ellipse.secr

Confidence Ellipses
details

Detail Specification for secr.fit
empirical.varD

Empirical Variance of H-T Density Estimate
derived

Derived Parameters of Fitted SECR Model
hcov

Hybrid Mixture Model
join

Combine or Split Sessions of capthist Object
fx.total

Activity Centres of Detected and Undetected Animals
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
FAQ

Frequently Asked Questions, And Others
fxi

Probability Density of Home Range Centre
logit

Logit Transformation
expected.n

Expected Number of Individuals
intervals

Work with Open Population data
esa.plot.secr

Mask Buffer Diagnostic Plot (internal)
make.capthist

Construct capthist Object
make.mask

Build Habitat Mask
make.lacework

Construct Lacework Detector Design
mask

Mask Object
make.traps

Build Detector Array
plot.traps

Plot traps Object
make.tri

Build Detector Array on Triangular or Hexagonal Grid
plot.secr

Plot Detection Functions
plot.popn

Plot Population Object
make.systematic

Construct Systematic Detector Design
plotMaskEdge

Outline Around Mask Cells
logmultinom

Multinomial Coefficient of SECR Likelihood
par.secr.fit

Fit Multiple SECR Models
pdot

Net Detection Probability
head

First or Last Part of an Object
mask.check

Mask Diagnostics
predict.secr

SECR Model Predictions
possum

Brushtail Possum Trapping Dataset
print.secr

Print or Summarise secr Object
print.traps

Print Detectors
pointsInPolygon

Points Inside Polygon
pmixProfileLL

Mixture Model Check
discretize

Rasterize Area Search or Transect Data
detector

Detector Type
RMarkInput

Convert Data to RMark Input Format
Parallel

Multi-core Processing
rectangularMask

Rectangular Mask
hornedlizard

Flat-tailed Horned Lizard Dataset
deviance

Deviance of fitted secr model and residual degrees of freedom
homerange

Home Range Statistics
detectfn

Detection Functions
ms

Multi-session Objects
predictDsurface

Predict Density Surface
model.average

Averaging of SECR Models Using Akaike's Information Criterion
ovensong

Ovenbird Acoustic Dataset
ovenbird

Ovenbird Mist-netting Dataset
occasionKey

Key to Petal Plot
read.traps

Read Detector Data From File
read.telemetry

Import Telemetry Fixes
plot.capthist

Plot Detection Histories
plot.mask

Plot Habitat Mask, Density or Resource Surface
popn

Population Object
polyarea

Area of Polygon(s)
randomHabitat

Random Landscape
raster

Create a RasterLayer Object from Mask or Dsurface
reduce.capthist

Combine Occasions Or Detectors
rbind.traps

Combine traps Objects
score.test

Score Test for SECR Models
print.capthist

Print Detections
secr-package

Spatially Explicit Capture--Recapture Models
read.mask

Read Habitat Mask From File
secrRNG

Random Number Seed
rbind.popn

Combine popn Objects
rbind.capthist

Combine capthist Objects
secrtest

Goodness-of-fit Test Results
secr.make.newdata

Create Default Design Data
region.N

Population Size
sim.popn

Simulate 2-D Population
snip

Slice Transect Into Shorter Sections
session

Session Vector
sim.secr

Simulate From Fitted secr Model
stoatDNA

Stoat DNA Data
subset.capthist

Subset or Split capthist Object
strip.legend

Colour Strip Legend
subset.mask

Subset, Split or Combine Mask Objects
sort.capthist

Sort Rows of capthist or mask Object
secr.test

Goodness-of-Fit Test
secrdemo

SECR Models Fitted to Demonstration Data
signalmatrix

Reformat Signal Data
sim.capthist

Simulate Detection Histories
sighting

Sighting Attributes
suggest.buffer

Mask Buffer Width
summary.capthist

Summarise Detections
reduce

Combine Columns
signal

Signal Fields
transformations

Transform Point Array
secr.design.MS

Construct Detection Model Design Matrices and Lookups
secr.fit

Spatially Explicit Capture--Recapture
skink

Skink Pitfall Data
summary.popn

Summarise Simulated Population
summary.mask

Summarise Habitat Mask
setNumThreads

Number of Threads
spacing

Detector or Mask Spacing
shareFactorLevels

Fix Inconsistent Covariates
speed

Speed Tips
trim

Drop Unwanted List Components
traps

Detector Array
summary.traps

Summarise Detector Array
timevaryingcov

Time-varying Covariates
userdist

Non-Euclidean Distances
traps.info

Detector Attributes
usage

Detector Usage
utility

Utility Functions
write.captures

Write Data to Text File
updateCH

Update Old capthist Format
trap.builder

Complex Detector Layouts
turnover

Specifying a Dynamic Population
Troubleshooting

Problems in Fitting SECR Models
usagePlot

Plot usage, detections or sightings.
subset.popn

Subset popn Object
smooths

Smooth Terms in SECR Models
subset.traps

Subset traps Object
writeGPS

Upload to GPS
verify

Check SECR Data
vcov.secr

Variance - Covariance Matrix of SECR Parameters
AIC.secr

Compare SECR Models
AICcompatible

Model Compatibility