Spatially Explicit Capture-Recapture

Documentation for package ‘secr’ version 5.2.4

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

Spatially Explicit Capture-Recapture Models

-- A --

addCovariates	Add Covariates to Mask or Traps
addSightings	Mark-resight Data
addTelemetry	Combine Telemetry and Detection Data
adjustVarD	Overdispersion of Activity Centres
AIC.secr	Compare SECR Models
AIC.secrlist	Compare SECR Models
AICcompatible	Model Compatibility
AICcompatible.secr	Model Compatibility
AICcompatible.secrlist	Model Compatibility
alive	Dissect Spatial Capture History Object
alongtransect	Dissect Spatial Capture History Object
animalID	Dissect Spatial Capture History Object
append.capthist	Combine capthist Objects
ARL	Home Range Statistics
as.array	Coerce capthist to Data Frame or Array
as.array.capthist	Coerce capthist to Data Frame or Array
as.data.frame	Coerce capthist to Data Frame or Array
as.data.frame.capthist	Coerce capthist to Data Frame or Array
as.data.frame.traps	Coerce capthist to Data Frame or Array
as.mask	Coerce traps object to mask
as.popn	Coerce ppp object to popn
attenuationplot	Plot Detection Functions
autoini	Initial Parameter Values for SECR

-- B --

bias.D	Mask Buffer Width
binCovariate	Add Binned Covariate
blackbear	Black Bear Hair Snag Dataset
blackbear.0	Black Bear Hair Snag Dataset
blackbear.h2bk	Black Bear Hair Snag Dataset
blackbearCH	Black Bear Hair Snag Dataset
boundarytoSF	Internal Functions
buffer.contour	Deprecated Functions in Package 'secr'
bufferContour	Contour Detection Probability

-- C --

capped	Detector Type
captdata	SECR Models Fitted to Demonstration Data
capthist	Spatial Capture History Object
captXY	SECR Models Fitted to Demonstration Data
centroids	Home Range Statistics
chat.nj	Overdispersion of Activity Centres
chat.nk	Number per detector
circular.p	Circular Probability
circular.r	Circular Probability
clip.hex	Build Detector Array on Triangular or Hexagonal Grid
clone	Replicate Rows
clone.capthist	Replicate Rows
clone.default	Replicate Rows
clone.popn	Replicate Rows
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	Array of Parameter Estimates
collate.ipsecr	Array of Parameter Estimates
collate.secr	Array of Parameter Estimates
collate.secrlist	Array of Parameter Estimates
confint.secr	Profile Likelihood Confidence Intervals
Coulombe	House mouse live trapping data
count	Detector Type
counts	Summarise Detections
covariates	Covariates Attribute
covariates<-	Covariates Attribute
CV	Coefficient of Variation
CVa	Coefficient of Variation
CVa0	Coefficient of Variation
CVpdot	Net Detection Probability

-- 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
defunct	Defunct Functions in Package 'secr'
deleteMaskPoints	Edit Mask Points
derived	Derived Parameters of Fitted SECR Model
derived.secr	Derived Parameters of Fitted SECR Model
derived.secrlist	Derived Parameters of Fitted SECR Model
derivedCluster	Empirical Variance of H-T Density Estimate
derivedDcoef	Derived Absolute Density
derivedDsurface	Derived Absolute Density
derivedExternal	Empirical Variance of H-T Density Estimate
derivedMash	Empirical Variance of H-T Density Estimate
derivednj	Empirical Variance of H-T Density Estimate
derivedSession	Empirical Variance of H-T Density Estimate
derivedSystematic	Defunct Functions in Package 'secr'
details	Detail Specification for secr.fit
detectfn	Detection Functions
detectfnplot	Plot Detection Functions
Detection functions	Detection Functions
detector	Detector Type
detector<-	Detector Type
detectpar	SECR Model Predictions
detectpar.secr	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
Dfn2	Internal Functions
discretize	Rasterize Area Search or Transect Data
distancetotrap	Distance To Nearest Detector
Dsurface	Density Surfaces
Dsurface-class	Density Surfaces

-- E --

edist	Utility Functions
effort	Detector Usage
ellipse.bvn	Confidence Ellipses
ellipse.secr	Confidence Ellipses
empirical.varD	Empirical Variance of H-T Density Estimate
Enk	Number per detector
esa	Derived Parameters of Fitted SECR Model
esa.plot	Deprecated Functions in Package 'secr'
esa.secr	Derived Parameters of Fitted SECR Model
esaPlot	Mask Buffer Diagnostic Plot
expected.n	Expected Number of Individuals
extractMoves	Simulated Movements

-- F --

FAQ	Frequently Asked Questions, And Others
fixedbeta	Detail Specification for secr.fit
Fletcher.chat	Estimate overdispersion
flip	Transform Point Array
flip.popn	Transform Point Array
flip.traps	Transform Point Array
fx.total	Deprecated Functions in Package 'secr'
fxi	Probability Density of Activity Centre
fxi.contour	Deprecated Functions in Package 'secr'
fxi.mode	Deprecated Functions in Package 'secr'
fxi.secr	Probability Density of Activity Centre
fxiContour	Probability Density of Activity Centre
fxiMode	Probability Density of Activity Centre
fxTotal	Activity Centres of Detected and Undetected Animals
fxTotal.secr	Activity Centres of Detected and Undetected Animals

-- G --

getMeanSD	Utility Functions
gridCells	Construct Grid Cells
GSM	Black Bear Hair Snag Dataset

-- H --

hcov	Hybrid Mixture Model
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
hist.MCgof	Methods for MCgof Objects
hornedlizard	Flat-tailed Horned Lizard Dataset
hornedlizardCH	Flat-tailed Horned Lizard Dataset
housemouse	House mouse live trapping data

-- I --

infraCH	Skink Pitfall Data
insertdim	Construct Detection Model Design Matrices and Lookups
interference	Non-target Data
intervals	Work with Open Population data
intervals<-	Work with Open Population data
invlogit	Logit Transformation
ip.secr	Defunct Functions in Package 'secr'

-- J --

join	Combine or Split Sessions of capthist Object

-- K --

kfn	Overlap Index

-- L --

lineoCH	Skink Pitfall Data
list.secr.fit	Fit Multiple SECR Models
LLonly	Detail Specification for secr.fit
LLsurface	Plot Likelihood Surface
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.lacework	Construct Lacework Detector Design
make.lookup	Construct Detection Model Design Matrices and Lookups
make.mask	Build Habitat Mask
make.newdata	Defunct Functions in Package 'secr'
make.poly	Build Detector Array
make.spcosa	Construct Spatial Coverage Design
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
makeNewData	Create Default Design Data
makeNewData.default	Create Default Design Data
makeNewData.secr	Create Default Design Data
makeStart	Initial Parameter Values
markocc	Sighting Attributes
markocc<-	Sighting Attributes
mash	Complex Detector Layouts
mask	Mask Object
mask-class	Mask Object
mask.check	Mask Diagnostics
maskarea	Utility Functions
masklength	Utility Functions
masksize	Utility Functions
maxdistance	Detail Specification for secr.fit
MCgof	Monte Carlo Goodness-of-fit for SECR Models
MCgof.secr	Monte Carlo Goodness-of-fit for SECR Models
MCgof.secrlist	Monte Carlo Goodness-of-fit for SECR Models
miscparm	Detail Specification for secr.fit
MMDM	Home Range Statistics
model.average	Defunct Functions in Package 'secr'
modelAverage	Averaging of SECR Models Using Akaike's Information Criterion
modelAverage.secr	Averaging of SECR Models Using Akaike's Information Criterion
modelAverage.secrlist	Averaging of SECR Models Using Akaike's Information Criterion
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
nedist	Utility Functions
newdata	Create Default Design Data
nk	Number per detector
noise	Signal Fields
noise.capthist	Signal Fields
noise<-	Signal Fields
noneuc	Non-Euclidean Distances
nontarget	Non-target Data
nontarget<-	Non-target Data

-- O --

occasion	Dissect Spatial Capture History Object
occasionKey	Key to Petal Plot
ORL	Home Range Statistics
ovenbird	Ovenbird Mist-netting Dataset
ovenbird.model.1	Ovenbird Mist-netting Dataset
ovenbird.model.D	Ovenbird Mist-netting Dataset
ovenCH	Ovenbird Mist-netting Dataset
ovenCHp	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
OVpossum	Orongorongo Valley Brushtail Possums
OVpossumCH	Orongorongo Valley Brushtail Possums

-- P --

par.derived	Deprecated Functions in Package 'secr'
par.region.N	Deprecated Functions in Package 'secr'
par.secr.fit	Deprecated Functions in Package 'secr'
Parallel	Multi-core Processing
param	Detail Specification for secr.fit
pdot	Net Detection Probability
pdot.contour	Deprecated Functions in Package 'secr'
pdotContour	Contour Detection Probability
pfn	Defunct Functions in Package 'secr'
PG	Telemetry Fixes in Polygons
plot.capthist	Plot Detection Histories
plot.Dsurface	Plot Habitat Mask, Density or Resource Surface
plot.mask	Plot Habitat Mask, Density or Resource Surface
plot.MCgof	Methods for MCgof Objects
plot.popn	Plot Population Object
plot.Rsurface	Plot Habitat Mask, Density or Resource Surface
plot.secr	Plot Detection Functions
plot.secrlist	Plot Detection Functions
plot.secrtest	Goodness-of-fit Test Results
plot.traps	Plot traps Object
plotMaskEdge	Outline Around Mask Cells
plotMCP	Plot Detection Histories
pmixProfileLL	Mixture Model Check
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.Ds	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
predictDlambda	Density Trend
predictDsurface	Predict Density Surface
print.capthist	Print Detections
print.Dsurface	Density Surfaces
print.MCgof	Methods for MCgof Objects
print.secr	Print or Summarise secr Object
print.secrtest	Goodness-of-fit Test Results
print.summary.capthist	Summarise Detections
print.summary.mask	Summarise Habitat Mask
print.summary.popn	Summarise Simulated Population
print.summary.traps	Summarise Detector Array
print.traps	Print Detectors
proximity	Detector Type

-- R --

random numbers	Random Number Seed
randomDensity	Random Landscape
randomHabitat	Random Landscape
rast	Create a RasterLayer Object from Mask or Dsurface
rast-method	Create a RasterLayer Object from Mask or Dsurface
raster	Create a RasterLayer Object from Mask or Dsurface
raster-method	Create a RasterLayer Object from Mask or Dsurface
rbind.capthist	Combine capthist Objects
rbind.mask	Subset, Split or Combine Mask Objects
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	Defunct Functions in Package 'secr'
read.telemetry	Import Telemetry Fixes
read.traps	Read Detector Data From File
rectangularMask	Rectangular Mask
reduce	Combine Columns
reduce.capthist	Combine Occasions Or Detectors
reduce.default	Combine Columns
reduce.traps	Combine Occasions Or Detectors
region.N	Population Size
region.N.secr	Population Size
region.N.secrlist	Population Size
rlnormCV	Utility Functions
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
RSE	RSE from Fitted Model
Rsurface	Smoothed Resource Surface

-- S --

saveprogress	Detail Specification for secr.fit
score.table	Score Test for SECR Models
score.test	Score Test for SECR Models
searcharea	Detector Attributes
secr	Spatially Explicit Capture-Recapture Models
secr-defunct	Defunct Functions in Package 'secr'
secr-deprecated	Deprecated Functions in Package 'secr'
secr-version5	Changes in 'secr' 5.0
secr.design.MS	Construct Detection Model Design Matrices and Lookups
secr.fit	Spatially Explicit Capture-Recapture
secr.make.newdata	Defunct Functions in Package 'secr'
secr.refit	Repeat or Resume Model Fit
secr.test	Goodness-of-Fit Test
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
secrlist	Compare SECR Models
secrRNG	Random Number Seed
secrtest	Goodness-of-fit Test Results
seed	Random Number Seed
session	Session Vector
session<-	Session Vector
sessionlabels	Work with Open Population data
sessionlabels<-	Work with Open Population data
setNumThreads	Number of Threads
shareFactorLevels	Fix Inconsistent Covariates
shift	Transform Point Array
shift.mask	Transform Point Array
shift.popn	Transform Point Array
shift.traps	Transform Point Array
sighting	Sighting Attributes
sightingPlot	Plot usage, detections or sightings.
sightings	Sighting Attributes
signal	Signal Fields
signal.capthist	Signal Fields
signal<-	Signal Fields
signalCH	Ovenbird Acoustic Dataset
signalframe	Signal Fields
signalframe<-	Signal Fields
signalmatrix	Reformat Signal Data
sim.capthist	Simulate Detection Histories
sim.detect	Simulate From Fitted secr Model
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
smooths	Smooth Terms in SECR Models
snip	Slice Transect Into Shorter Sections
sort.capthist	Sort Rows of capthist or mask Object
sort.mask	Sort Rows of capthist or mask Object
spacing	Detector or Mask Spacing
spacing.mask	Detector or Mask Spacing
spacing.traps	Detector or Mask Spacing
spacing<-	Detector or Mask Spacing
speed	Speed Tips
Speed tips	Speed Tips
split.capthist	Subset or Split capthist Object
split.mask	Subset, Split or Combine Mask Objects
split.traps	Subset traps Object
spotHeight	Plot Habitat Mask, Density or Resource Surface
stoat.model.EX	Stoat DNA Data
stoat.model.HN	Stoat DNA Data
stoatCH	Stoat DNA Data
stoatDNA	Stoat DNA Data
strip.legend	Colour Strip Legend
subset.capthist	Subset or Split capthist Object
subset.mask	Subset, Split or Combine Mask Objects
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.MCgof	Methods for MCgof Objects
summary.popn	Summarise Simulated Population
summary.secr	Print or Summarise secr Object
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
telemetered	Dissect Spatial Capture History Object
telemetrytype	Combine Telemetry and Detection Data
telemetrytype<-	Combine Telemetry and Detection Data
telemetryxy	Dissect Spatial Capture History Object
telemetryxy<-	Dissect Spatial Capture History Object
tile	Simulate 2-D Population
timevaryingcov	Time-varying Covariates
timevaryingcov<-	Time-varying Covariates
Tm	Sighting Attributes
Tm<-	Sighting Attributes
Tn	Sighting Attributes
Tn<-	Sighting Attributes
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
trapsPerAnimal	Home Range Statistics
trapXY	SECR Models Fitted to Demonstration Data
trim	Drop Unwanted List Components
trim.default	Drop Unwanted List Components
trim.secr	Drop Unwanted List Components
trim.secrlist	Drop Unwanted List Components
Troubleshooting	Problems in Fitting SECR Models
Tu	Sighting Attributes
Tu<-	Sighting Attributes
turnover	Specifying a Dynamic Population

-- U --

unjoin	Combine or Split Sessions of capthist Object
unRMarkInput	Convert Data to RMark Input Format
updateCH	Update Old capthist Format
usage	Detector Usage
usage.traps	Detector Usage
usage<-	Detector Usage
usagePlot	Plot usage, detections or sightings.
userdist	Non-Euclidean Distances

-- 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
version5	Changes in 'secr' 5.0

-- W --

write.capthist	Import or export data
write.captures	Write Data to Text File
write.DA	Convert Data To Or From BUGS Format
write.mask	Write Data to Text File
write.SPACECAP	Defunct Functions in Package 'secr'
write.traps	Write Data to Text File
writeGPS	Upload to GPS

-- X --

xy	Dissect Spatial Capture History Object
xy2CH	Combine Telemetry and Detection Data
xy<-	Dissect Spatial Capture History Object

-- misc --

[.secrlist

Compare SECR Models