Spatially explicit capture-recapture


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Documentation for package ‘secr’ version 2.4.0

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A B C D E F H I J L M N O P R S T U V W X

secr-package Spatially Explicit Capture-Recapture Models

-- A --

addCovariates Add Covariates to Mask or Traps
addTelemetry Combine Telemetry and Detection Data
AIC.secr Compare SECR Models
AIC.secrlist Compare SECR Models
alive Dissect Spatial Capture History Object
alongtransect Dissect Spatial Capture History Object
animalID Dissect Spatial Capture History Object
ARL Home Range Statistics
attenuationplot Plot Detection Functions
autoini Initial Parameter Values for SECR

-- B --

bias.D Mask Buffer Width
binomN Spatially Explicit Capture-Recapture
buffer.contour Contour Detection Probability

-- C --

captdata SECR Models Fitted to Demonstration Data
capthist Spatial Capture History Object
captXY SECR Models Fitted to Demonstration Data
circular.p Circular Probability
circular.r Circular Probability
clip.hex Build Detector Array on Triangular or Hexagonal Grid
closedN Closed population estimates
closure.test Closure tests
cluster Detector Clustering
cluster.centres Complex Detector Layouts
cluster.counts Complex Detector Layouts
clusterID Detector Clustering
clusterID<- Detector Clustering
clustertrap Detector Clustering
clustertrap<- Detector Clustering
coef.secr Coefficients of secr Object
collate Model averaging for SECR Models
confint.secr Profile Likelihood Confidence Intervals
Coulombe House mouse live trapping data
count Detector Type
counts Summarise Detections
covariates Covariates Attribute
covariates<- Covariates Attribute

-- D --

D.designdata Construct Density Design Data
dbar Home Range Statistics
deermouse Deermouse Live-trapping Datasets
deermouse.ESG Deermouse Live-trapping Datasets
deermouse.WSG Deermouse Live-trapping Datasets
derived Derived Parameters of Fitted SECR Model
derived.cluster Empirical Variance of H-T Density Estimate
derived.external Empirical Variance of H-T Density Estimate
derived.mash Empirical Variance of H-T Density Estimate
derived.nj Empirical Variance of H-T Density Estimate
derived.session Empirical Variance of H-T Density Estimate
detectfn Detection Functions
detectfnplot Plot Detection Functions
detection functions Detection Functions
detector Detector Type
detector<- Detector Type
detectpar SECR Model Predictions
deviance Deviance of fitted secr model and residual degrees of freedom
deviance.secr Deviance of fitted secr model and residual degrees of freedom
df.residual Deviance of fitted secr model and residual degrees of freedom
df.residual.secr Deviance of fitted secr model and residual degrees of freedom
distancetotrap Distance To Nearest Detector
Dsurface Density Surfaces

-- E --

ellipse.secr Confidence ellipse
empirical.varD Empirical Variance of H-T Density Estimate
esa Derived Parameters of Fitted SECR Model
esa.plot Mask Buffer Diagnostic Plot
esa.plot.secr Mask Buffer Diagnostic Plot (internal)
ESG.0 Deermouse Live-trapping Datasets
ESG.b Deermouse Live-trapping Datasets
ESG.h2 Deermouse Live-trapping Datasets
ESG.t Deermouse Live-trapping Datasets
expected.n Expected Number of Individuals

-- F --

FAQ Frequently Asked Questions, And Others
flip Transform Point Array
flip.popn Transform Point Array
flip.traps Transform Point Array
fxi Probability Density of Home Range Centre
fxi.contour Probability Density of Home Range Centre
fxi.mode Probability Density of Home Range Centre
fxi.secr Probability Density of Home Range Centre

-- H --

head.capthist First or Last Part of an Object
head.Dsurface First or Last Part of an Object
head.mask First or Last Part of an Object
head.traps First or Last Part of an Object
hornedlizard Flat-tailed Horned Lizard Dataset
hornedlizardCH Flat-tailed Horned Lizard Dataset
housemouse House mouse live trapping data
housemouse.0 House mouse live trapping data
housemouse.ampm House mouse live trapping data
housemouse.ampmh2h2 House mouse live trapping data

-- I --

infraCH Skink Pitfall Data
invlogit Logit Transformation
ip.secr Spatially Explicit Capture-Recapture by Inverse Prediction

-- J --

join Combine or Split Sessions of capthist Object

-- L --

lineoCH Skink Pitfall Data
LLsurface.secr Plot likelihood surface
logit Logit Transformation
logLik.secr Compare SECR Models
logmultinom Multinomial Coefficient of SECR Likelihood
LR.test Likelihood Ratio Test
LStraps Skink Pitfall Data

-- M --

make.capthist Construct capthist Object
make.circle Build Detector Array
make.grid Build Detector Array
make.mask Build Habitat Mask
make.poly Build Detector Array
make.systematic Construct Systematic Detector Design
make.telemetry Build Detector Array
make.transect Build Detector Array
make.tri Build Detector Array on Triangular or Hexagonal Grid
mash Complex Detector Layouts
mask Mask Object
mask.check Mask Diagnostics
MMDM Home Range Statistics
model.average Model averaging for SECR Models
morning.0 House mouse live trapping data
morning.0h2 House mouse live trapping data
morning.b House mouse live trapping data
morning.h2 House mouse live trapping data
morning.h2h2 House mouse live trapping data
morning.t House mouse live trapping data
moves Home Range Statistics
ms Multi-session Objects
MS.capthist Combine capthist Objects
ms.default Multi-session Objects
ms.mask Multi-session Objects
ms.secr Multi-session Objects
multi Detector Type
Multi-core processing Multi-core Processing

-- N --

ncores Multi-core Processing
nearesttrap Distance To Nearest Detector
noise Dissect Spatial Capture History Object
noise<- Dissect Spatial Capture History Object

-- O --

occasion Dissect Spatial Capture History Object
ovenbird Ovenbird Mist-netting Dataset
ovenbird.model.1 Ovenbird Mist-netting Dataset
ovenbird.model.1b Ovenbird Mist-netting Dataset
ovenbird.model.1T Ovenbird Mist-netting Dataset
ovenbird.model.D Ovenbird Mist-netting Dataset
ovenbird.model.h2 Ovenbird Mist-netting Dataset
ovenCH Ovenbird Mist-netting Dataset
ovenmask Ovenbird Mist-netting Dataset
ovensong Ovenbird Acoustic Dataset
ovensong.model.1 Ovenbird Acoustic Dataset
ovensong.model.2 Ovenbird Acoustic Dataset

-- P --

Parallel Multi-core Processing
pdot Net Detection Probability
pdot.contour Contour Detection Probability
pfn Spatially Explicit Capture-Recapture by Inverse Prediction
plot.capthist Plot Detection Histories
plot.Dsurface Plot Habitat Mask or Density Surface
plot.mask Plot Habitat Mask or Density Surface
plot.popn Plot popn Object
plot.secr Plot Detection Functions
plot.secrlist Plot Detection Functions
plot.traps Plot traps Object
pointsInPolygon Points Inside Polygon
polyarea Area of Polygon(s)
polygon Detector Type
polygonX Detector Type
polyID Detector Attributes
polyID<- Detector Attributes
popn Population Object
population size Population Size
possum Brushtail Possum Trapping Dataset
possum.model.0 Brushtail Possum Trapping Dataset
possum.model.b Brushtail Possum Trapping Dataset
possum.model.Dh2 Brushtail Possum Trapping Dataset
possum.model.Dsh2 Brushtail Possum Trapping Dataset
possum.model.h2 Brushtail Possum Trapping Dataset
possumarea Brushtail Possum Trapping Dataset
possumCH Brushtail Possum Trapping Dataset
possummask Brushtail Possum Trapping Dataset
possumremovalarea Brushtail Possum Trapping Dataset
predict.secr SECR Model Predictions
predict.secrlist SECR Model Predictions
predictDsurface Predict Density Surface
print.capthist Print Detections
print.Dsurface Density Surfaces
print.secr Print secr Object
print.summary.capthist Summarise Detections
print.summary.mask Summarise Habitat Mask
print.summary.traps Summarise Detector Array
print.traps Print Detectors
proximity Detector Type

-- R --

randomHabitat Random Landscape
rbind.capthist Combine capthist Objects
rbind.mask Subset Mask Object
rbind.popn Combine popn Objects
rbind.traps Combine traps Objects
read.capthist Import or export data
read.DA Convert Data To Or From BUGS Format
read.mask Read Habitat Mask From File
read.SPACECAP Exchange data with SPACECAP package
read.traps Read Detector Data From File
rectangularMask Rectangular Mask
reduce Combine Columns
reduce.capthist Combine Occasions Or Convert Detector Types
region.N Population Size
RMarkInput Convert Data to RMark Input Format
rotate Transform Point Array
rotate.popn Transform Point Array
rotate.traps Transform Point Array
RPSV Home Range Statistics

-- S --

score.table Score Test for SECR Models
score.test Score Test for SECR Models
searcharea Detector Attributes
secr Spatially Explicit Capture-Recapture Models
secr density models Density Models
secr detection models Models for Detection Parameters
secr models Spatially Explicit Capture-Recapture Models
secr.design.MS Construct Detection Model Design Matrices and Lookups
secr.fit Spatially Explicit Capture-Recapture
secr.make.newdata Create Default Design Data
secr.model Spatially Explicit Capture-Recapture Models
secr.model.density Density Models
secr.model.detection Models for Detection Parameters
secrdemo SECR Models Fitted to Demonstration Data
secrdemo.0 SECR Models Fitted to Demonstration Data
secrdemo.b SECR Models Fitted to Demonstration Data
secrdemo.CL SECR Models Fitted to Demonstration Data
session Session Vector
session<- Session Vector
shift Transform Point Array
shift.popn Transform Point Array
shift.traps Transform Point Array
signal Dissect Spatial Capture History Object
signal<- Dissect Spatial Capture History Object
signalCH Ovenbird Acoustic Dataset
signalframe Dissect Spatial Capture History Object
signalframe<- Dissect Spatial Capture History Object
signalmatrix Reformat Signal Data
sim.capthist Simulate Detection Histories
sim.popn Simulate 2-D Population
sim.resight Simulate Detection Histories
sim.secr Simulate From Fitted secr Model
simulate Simulate From Fitted secr Model
simulate.secr Simulate From Fitted secr Model
single Detector Type
skink Skink Pitfall Data
sort.capthist Sort Rows of capthist Object
spacing Detector or Mask Spacing
spacing.mask Detector or Mask Spacing
spacing.traps Detector or Mask Spacing
spacing<- Detector or Mask Spacing
split.capthist Subset or Split capthist Object
split.traps Subset traps Object
spotHeight Plot Habitat Mask or Density Surface
stoat.model.EX Stoat DNA Data
stoat.model.HN Stoat DNA Data
stoat.model.HZ Stoat DNA Data
stoatCH Stoat DNA Data
stoatDNA Stoat DNA Data
subset.capthist Subset or Split capthist Object
subset.mask Subset Mask Object
subset.popn Subset popn Object
subset.traps Subset traps Object
suggest.buffer Mask Buffer Width
summary.capthist Summarise Detections
summary.Dsurface Density Surfaces
summary.mask Summarise Habitat Mask
summary.traps Summarise Detector Array

-- T --

tail.capthist First or Last Part of an Object
tail.Dsurface First or Last Part of an Object
tail.mask First or Last Part of an Object
tail.traps First or Last Part of an Object
tile Simulate 2-D Population
timevaryingcov Time-varying Detector Covariates
timevaryingcov<- Time-varying Detector Covariates
transect Detector Type
transectID Detector Attributes
transectID<- Detector Attributes
transectlength Detector Attributes
transectX Detector Type
transformations Transform Point Array
trap Dissect Spatial Capture History Object
trap.builder Complex Detector Layouts
traps Detector Array
traps object Detector Array
traps<- Detector Array
trapXY SECR Models Fitted to Demonstration Data
trim Drop Unwanted List Components
trim.default Drop Unwanted List Components
trim.secr Drop Unwanted List Components
troubleshooting Problems in Fitting SECR Models

-- U --

unjoin Combine or Split Sessions of capthist Object
unRMarkInput Convert Data to RMark Input Format
usage Detector Usage
usage<- Detector Usage

-- V --

vcov.secr Variance - Covariance Matrix of SECR Parameters
verify Check SECR Data
verify.capthist Check SECR Data
verify.default Check SECR Data
verify.mask Check SECR Data
verify.traps Check SECR Data

-- W --

write.capthist Import or export data
write.captures Write Data to Text File
write.DA Convert Data To Or From BUGS Format
write.SPACECAP Exchange data with SPACECAP package
write.traps Write Data to Text File
writeGPS Upload to GPS
WSG.0 Deermouse Live-trapping Datasets
WSG.b Deermouse Live-trapping Datasets
WSG.h2 Deermouse Live-trapping Datasets
WSG.t Deermouse Live-trapping Datasets

-- X --

xy Dissect Spatial Capture History Object
xy<- Dissect Spatial Capture History Object