Package: secr 5.1.1

secr: Spatially Explicit Capture-Recapture

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.

Authors:Murray Efford [aut, cre], Philipp Jund [ctb], David Fletcher [ctb], Yan Ru Choo [ctb]

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secr.pdf |secr.html✨
secr/json (API)
NEWS

# Install 'secr' in R:

install.packages('secr', repos = c('https://murrayefford.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/murrayefford/secr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

GSM - Black Bear Hair Snag Dataset
LStraps - Skink Pitfall Data
OVpossumCH - Orongorongo Valley Brushtail Possums
blackbear.0 - Black Bear Hair Snag Dataset
blackbear.h2bk - Black Bear Hair Snag Dataset
blackbearCH - Black Bear Hair Snag Dataset
captXY - SECR Models Fitted to Demonstration Data
captdata - SECR Models Fitted to Demonstration Data
deermouse.ESG - Deermouse Live-trapping Datasets
deermouse.WSG - Deermouse Live-trapping Datasets
hornedlizardCH - Flat-tailed Horned Lizard Dataset
housemouse - House mouse live trapping data
infraCH - Skink Pitfall Data
lineoCH - Skink Pitfall Data
ovenCH - Ovenbird Mist-netting Dataset
ovenCHp - Ovenbird Mist-netting Dataset
ovenbird.model.1 - Ovenbird Mist-netting Dataset
ovenbird.model.D - Ovenbird Mist-netting Dataset
ovenmask - Ovenbird Mist-netting Dataset
ovensong.model.1 - Ovenbird Acoustic Dataset
ovensong.model.2 - Ovenbird Acoustic Dataset
possum.model.0 - Brushtail Possum Trapping Dataset
possum.model.Ds - Brushtail Possum Trapping Dataset
possumCH - Brushtail Possum Trapping Dataset
possumarea - Brushtail Possum Trapping Dataset
possummask - Brushtail Possum Trapping Dataset
possumremovalarea - Brushtail Possum Trapping Dataset
secrdemo.0 - SECR Models Fitted to Demonstration Data
secrdemo.CL - SECR Models Fitted to Demonstration Data
secrdemo.b - SECR Models Fitted to Demonstration Data
signalCH - Ovenbird Acoustic Dataset
stoat.model.EX - Stoat DNA Data
stoat.model.HN - Stoat DNA Data
stoatCH - Stoat DNA Data
trapXY - SECR Models Fitted to Demonstration Data

On CRAN:

9.98 score 3 stars 5 packages 394 scripts 2.0k downloads 33 mentions 233 exports 33 dependencies

Last updated 14 days agofrom:3b7e33db07. Checks:OK: 3 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 07 2024
R-4.5-win-x86_64	OK	Nov 07 2024
R-4.5-linux-x86_64	OK	Nov 07 2024
R-4.4-win-x86_64	NOTE	Nov 07 2024
R-4.4-mac-x86_64	NOTE	Nov 07 2024
R-4.4-mac-aarch64	NOTE	Nov 07 2024
R-4.3-win-x86_64	NOTE	Nov 07 2024
R-4.3-mac-x86_64	NOTE	Nov 07 2024
R-4.3-mac-aarch64	NOTE	Nov 07 2024

Exports:addCovariates addSightings addTelemetry adjustVarD AICcompatible alive alongtransect animalID append.capthist ARL as.mask as.popn attenuationplot autoini bias.D binCovariate boundarytoSF buffer.contour bufferContour centroids chat.nk circular.p circular.r clip.hex clone closedN closure.test cluster.centres cluster.counts clusterID clusterID<-clustertrap clustertrap<-collate counts covariates covariates<-CV CVa CVa0 CVpdot D.designdata dbar deleteMaskPoints derived derivedCluster derivedExternal derivedMash derivednj derivedSession detectfnplot detector detector<-detectpar Dfn2 discretize distancetotrap edist ellipse.bvn ellipse.secr Enk esa esa.plot esaPlot expected.n extractMoves Fletcher.chat flip fx.total fxi fxi.contour fxi.mode fxi.secr fxiContour fxiMode fxTotal getMeanSD gridCells insertdim intervals intervals<-invlogit ip.secr join kfn list.secr.fit LLsurface logit logmultinom LR.test make.capthist make.circle make.grid make.lacework make.lookup make.mask make.poly make.spcosa make.systematic make.telemetry make.transect make.tri makeNewData makeStart markocc markocc<-mash mask.check maskarea masklength masksize MCgof MMDM model.average modelAverage moves ms MS.capthist nearesttrap nedist nk noise noise<-nontarget nontarget<-occasion occasionKey ORL par.derived par.region.N par.secr.fit pdot pdot.contour pdotContour PG plotMaskEdge plotMCP pmixProfileLL pointsInPolygon polyarea polyID polyID<-predictDlambda predictDsurface randomDensity randomHabitat rast raster read.capthist read.DA read.mask read.telemetry read.traps rectangularMask reduce region.N rlnormCV RMarkInput rotate RPSV RSE Rsurface score.table score.test searcharea secr.design.MS secr.fit secr.test secrlist session session<-sessionlabels sessionlabels<-setNumThreads shareFactorLevels shift sighting sightingPlot signal signal<-signalframe signalframe<-signalmatrix sim.capthist sim.detect sim.popn sim.resight sim.secr snip spacing spacing<-spotHeight strip.legend suggest.buffer telemetered telemetrytype telemetrytype<-telemetryxy telemetryxy<-tile timevaryingcov timevaryingcov<-Tm Tm<-Tn Tn<-transectID transectID<-transectlength trap trap.builder traps traps<-trapsPerAnimal trim Tu Tu<-unjoin unRMarkInput updateCH usage usage<-usagePlot verify write.capthist write.captures write.DA write.mask write.traps writeGPS xy xy<-xy2CH

Dependencies:abind BH class classInt cli DBI e1071 glue KernSmooth lattice lifecycle magrittr MASS Matrix mgcv mvtnorm nlme proxy raster Rcpp RcppEigen RcppNumerical RcppParallel rlang s2 sf sp stringi stringr terra units vctrs wk

Data input for secr

Murray Efford

Rendered fromsecr-datainput.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2022-04-22
Started: 2022-04-22

secr 5.1 - spatially explicit capture--recapture in R

Murray Efford

Rendered fromsecr-overview.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2024-11-07
Started: 2022-04-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Spatially Explicit Capture-Recapture Models	secr-package secr
Add Covariates to Mask or Traps	addCovariates
Mark-resight Data	addSightings
Combine Telemetry and Detection Data	addTelemetry telemetrytype telemetrytype<- xy2CH
Compare SECR Models	AIC.secr AIC.secrlist logLik.secr secrlist [.secrlist
Model Compatibility	AICcompatible AICcompatible.secr AICcompatible.secrlist
Coerce capthist to Data Frame or Array	as.array as.array.capthist as.data.frame as.data.frame.capthist as.data.frame.traps
Coerce traps object to mask	as.mask
Coerce ppp object to popn	as.popn
Initial Parameter Values for SECR	autoini
Add Binned Covariate	binCovariate
Black Bear Hair Snag Dataset	blackbear blackbear.0 blackbear.h2bk blackbearCH GSM
Convert Data To Or From BUGS Format	read.DA write.DA
Spatial Capture History Object	capthist
Dissect Spatial Capture History Object	alive alongtransect animalID occasion telemetered telemetryxy telemetryxy<- trap xy xy<-
Overdispersion of Activity Centres	adjustVarD chat.nk Enk nk
Circular Probability	circular.p circular.r
Replicate Rows	clone clone.capthist clone.default clone.popn
Closed population estimates	closedN
Closure tests	closure.test
Detector Clustering	cluster clusterID clusterID<- clustertrap clustertrap<-
Coefficients of secr Object	coef.secr
Array of Parameter Estimates	collate collate.ipsecr collate.secr collate.secrlist
Profile Likelihood Confidence Intervals	confint.secr
Contour Detection Probability	bufferContour pdotContour
Covariates Attribute	covariates covariates<-
Coefficient of Variation	CV CVa CVa0
Construct Density Design Data	D.designdata
Deermouse Live-trapping Datasets	deermouse deermouse.ESG deermouse.WSG
Edit Mask Points	deleteMaskPoints
Derived Parameters of Fitted SECR Model	derived derived.secr derived.secrlist esa esa.secr
Detail Specification for secr.fit	details fixedbeta LLonly maxdistance miscparm param
Detection Functions	detectfn Detection functions
Detector Type	capped count detector detector<- multi polygon polygonX proximity single transect transectX
Deviance of fitted secr model and residual degrees of freedom	deviance deviance.secr df.residual df.residual.secr
Rasterize Area Search or Transect Data	discretize
Distance To Nearest Detector	distancetotrap nearesttrap
Density Surfaces	Dsurface Dsurface-class print.Dsurface summary.Dsurface
Confidence Ellipses	ellipse.bvn ellipse.secr
Empirical Variance of H-T Density Estimate	derivedCluster derivedExternal derivedMash derivednj derivedSession empirical.varD
Mask Buffer Diagnostic Plot	esaPlot
Expected Number of Individuals	expected.n
Simulated Movements	extractMoves
Frequently Asked Questions, And Others	FAQ
Estimate overdispersion	Fletcher.chat
Probability Density of Activity Centre	fxi fxi.secr fxiContour fxiMode
Activity Centres of Detected and Undetected Animals	fxTotal fxTotal.secr
Construct Grid Cells	gridCells
Hybrid Mixture Model	hcov
First or Last Part of an Object	head.capthist head.Dsurface head.mask head.traps tail.capthist tail.Dsurface tail.mask tail.traps
Home Range Statistics	ARL centroids dbar MMDM moves ORL RPSV trapsPerAnimal
Flat-tailed Horned Lizard Dataset	hornedlizard hornedlizardCH
House mouse live trapping data	Coulombe housemouse
Internal Functions	boundarytoSF Dfn2
Work with Open Population data	intervals intervals<- sessionlabels sessionlabels<-
Combine or Split Sessions of capthist Object	join unjoin
Overlap Index	kfn
Fit Multiple SECR Models	list.secr.fit
Plot Likelihood Surface	LLsurface LLsurface.secr
Logit Transformation	invlogit logit
Multinomial Coefficient of SECR Likelihood	logmultinom
Likelihood Ratio Test	LR.test
Construct capthist Object	make.capthist
Construct Lacework Detector Design	make.lacework
Build Habitat Mask	make.mask
Construct Spatial Coverage Design	make.spcosa
Construct Systematic Detector Design	make.systematic
Build Detector Array	make.circle make.grid make.poly make.telemetry make.transect
Build Detector Array on Triangular or Hexagonal Grid	clip.hex make.tri
Initial Parameter Values	makeStart
Mask Object	mask mask-class
Mask Diagnostics	mask.check
Monte Carlo Goodness-of-fit for SECR Models	MCgof MCgof.secr MCgof.secrlist
Averaging of SECR Models Using Akaike's Information Criterion	modelAverage modelAverage.secr modelAverage.secrlist
Multi-session Objects	ms ms.default ms.mask ms.secr
Create Default Design Data	makeNewData makeNewData.default makeNewData.secr newdata
Non-target Data	interference nontarget nontarget<-
Key to Petal Plot	occasionKey
Ovenbird Mist-netting Dataset	ovenbird ovenbird.model.1 ovenbird.model.D ovenCH ovenCHp ovenmask
Ovenbird Acoustic Dataset	ovensong ovensong.model.1 ovensong.model.2 signalCH
Orongorongo Valley Brushtail Possums	OVpossum OVpossumCH
Multi-core Processing	Multi-core processing ncores Parallel
Net Detection Probability	CVpdot pdot
Telemetry Fixes in Polygons	PG
Plot Detection Histories	plot.capthist plotMCP
Plot Habitat Mask, Density or Resource Surface	plot.Dsurface plot.mask plot.Rsurface spotHeight
Methods for MCgof Objects	hist.MCgof plot.MCgof print.MCgof summary.MCgof
Plot Population Object	plot.popn
Plot Detection Functions	attenuationplot detectfnplot plot.secr plot.secrlist
Plot traps Object	plot.traps
Outline Around Mask Cells	plotMaskEdge
Mixture Model Check	pmixProfileLL
Points Inside Polygon	pointsInPolygon
Area of Polygon(s)	polyarea
Population Object	popn
Brushtail Possum Trapping Dataset	possum possum.model.0 possum.model.Ds possumarea possumCH possummask possumremovalarea
SECR Model Predictions	detectpar detectpar.secr predict.secr predict.secrlist
Predict Density Surface	predictDsurface
Print Detections	print.capthist
Print or Summarise secr Object	print.secr summary.secr
Print Detectors	print.traps
Random Landscape	randomDensity randomHabitat
Create a RasterLayer Object from Mask or Dsurface	rast rast,Dsurface-method rast,mask-method raster raster,Dsurface-method raster,mask-method
Combine capthist Objects	append.capthist MS.capthist rbind.capthist
Combine popn Objects	rbind.popn
Combine traps Objects	rbind.traps
Import or export data	read.capthist write.capthist
Read Habitat Mask From File	read.mask
Import Telemetry Fixes	read.telemetry
Read Detector Data From File	read.traps
Rectangular Mask	rectangularMask
Combine Columns	reduce reduce.default
Combine Occasions Or Detectors	reduce.capthist reduce.traps
Population Size	population size region.N region.N.secr region.N.secrlist
Convert Data to RMark Input Format	RMarkInput unRMarkInput
RSE from Fitted Model	RSE
Smoothed Resource Surface	Rsurface
Score Test for SECR Models	score.table score.test
Defunct Functions in Package 'secr'	defunct derivedSystematic ip.secr make.newdata model.average pfn read.SPACECAP secr-defunct secr.make.newdata write.SPACECAP
Deprecated Functions in Package 'secr'	buffer.contour esa.plot fx.total fxi.contour fxi.mode par.derived par.region.N par.secr.fit pdot.contour secr-deprecated
Changes in 'secr' 5.0	secr-version5 version5
Construct Detection Model Design Matrices and Lookups	insertdim make.lookup secr.design.MS
Spatially Explicit Capture-Recapture	secr.fit
Goodness-of-Fit Test	secr.test
SECR Models Fitted to Demonstration Data	captdata captXY secrdemo secrdemo.0 secrdemo.b secrdemo.CL trapXY
Random Number Seed	random numbers secrRNG seed
Goodness-of-fit Test Results	plot.secrtest print.secrtest secrtest
Session Vector	session session<-
Number of Threads	setNumThreads
Fix Inconsistent Covariates	shareFactorLevels
Sighting Attributes	markocc markocc<- sighting sightings Tm Tm<- Tn Tn<- Tu Tu<-
Signal Fields	noise noise.capthist noise<- signal signal.capthist signal<- signalframe signalframe<-
Reformat Signal Data	signalmatrix
Simulate Detection Histories	sim.capthist sim.resight
Simulate 2-D Population	sim.popn tile
Simulate From Fitted secr Model	sim.detect sim.secr simulate simulate.secr
Skink Pitfall Data	infraCH lineoCH LStraps skink
Smooth Terms in SECR Models	smooths
Slice Transect Into Shorter Sections	snip
Sort Rows of capthist or mask Object	sort.capthist sort.mask
Detector or Mask Spacing	spacing spacing.mask spacing.traps spacing<-
Speed Tips	speed Speed tips
Stoat DNA Data	stoat.model.EX stoat.model.HN stoatCH stoatDNA
Colour Strip Legend	strip.legend
Subset or Split capthist Object	split.capthist subset.capthist
Subset, Split or Combine Mask Objects	rbind.mask split.mask subset.mask
Subset popn Object	subset.popn
Subset traps Object	split.traps subset.traps
Mask Buffer Width	bias.D suggest.buffer
Summarise Detections	counts print.summary.capthist summary.capthist
Summarise Habitat Mask	print.summary.mask summary.mask
Summarise Simulated Population	print.summary.popn summary.popn
Summarise Detector Array	print.summary.traps summary.traps
Time-varying Covariates	timevaryingcov timevaryingcov<-
Transform Point Array	flip flip.popn flip.traps rotate rotate.popn rotate.traps shift shift.mask shift.popn shift.traps transformations
Complex Detector Layouts	cluster.centres cluster.counts mash trap.builder
Detector Array	traps traps object traps<-
Detector Attributes	polyID polyID<- searcharea transectID transectID<- transectlength
Density Trend	predictDlambda
Drop Unwanted List Components	trim trim.default trim.secr trim.secrlist
Problems in Fitting SECR Models	Troubleshooting
Specifying a Dynamic Population	turnover
Update Old capthist Format	updateCH
Detector Usage	effort usage usage.traps usage<-
Plot usage, detections or sightings.	sightingPlot usagePlot
Non-Euclidean Distances	noneuc userdist
Utility Functions	edist getMeanSD maskarea masklength masksize nedist rlnormCV
Variance - Covariance Matrix of SECR Parameters	vcov.secr
Check SECR Data	verify verify.capthist verify.default verify.mask verify.traps
Write Data to Text File	write.captures write.mask write.traps
Upload to GPS	writeGPS