Package: secr 5.1.0
Murray Efford
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:
secr_5.1.0.tar.gz
secr_5.1.0.tar.gz(r-4.5-noble)secr_5.1.0.tar.gz(r-4.4-noble)
secr_5.1.0.tgz(r-4.4-emscripten)secr_5.1.0.tgz(r-4.3-emscripten)
secr.pdf |secr.html✨
secr/json (API)
NEWS
| # Install 'secr' in R: |
| install.packages('secr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/murrayefford/secr/issues
- 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
Last updated 17 days agofrom:4a1abb2223. Checks:OK: 1 WARNING: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 05 2024 |
Exports:addCovariatesaddSightingsaddTelemetryadjustVarDAICcompatiblealivealongtransectanimalIDappend.capthistARLas.maskas.popnattenuationplotautoinibias.DbinCovariateboundarytoSFbuffer.contourbufferContourcentroidschat.nkcircular.pcircular.rclip.hexcloneclosedNclosure.testcluster.centrescluster.countsclusterIDclusterID<-clustertrapclustertrap<-collatecountscovariatescovariates<-CVCVaCVa0CVpdotD.designdatadbardeleteMaskPointsderivedderivedClusterderivedExternalderivedMashderivednjderivedSessiondetectfnplotdetectordetector<-detectparDfn2discretizedistancetotrapedistellipse.bvnellipse.secrEnkesaesa.plotesaPlotexpected.nextractMovesFletcher.chatflipfx.totalfxifxi.contourfxi.modefxi.secrfxiContourfxiModefxTotalgetMeanSDgridCellsinsertdimintervalsintervals<-invlogitip.secrjoinkfnlist.secr.fitLLsurfacelogitlogmultinomLR.testmake.capthistmake.circlemake.gridmake.laceworkmake.lookupmake.maskmake.polymake.spcosamake.systematicmake.telemetrymake.transectmake.trimakeNewDatamakeStartmarkoccmarkocc<-mashmask.checkmaskareamasklengthmasksizeMCgofMMDMmodel.averagemodelAveragemovesmsMS.capthistnearesttrapnedistnknoisenoise<-nontargetnontarget<-occasionoccasionKeyORLpar.derivedpar.region.Npar.secr.fitpdotpdot.contourpdotContourPGplotMaskEdgeplotMCPpmixProfileLLpointsInPolygonpolyareapolyIDpolyID<-predictDlambdapredictDsurfacerandomDensityrandomHabitatrastrasterread.capthistread.DAread.maskread.telemetryread.trapsrectangularMaskreduceregion.NrlnormCVRMarkInputrotateRPSVRSERsurfacescore.tablescore.testsearchareasecr.design.MSsecr.fitsecr.testsecrlistsessionsession<-sessionlabelssessionlabels<-setNumThreadsshareFactorLevelsshiftsightingsightingPlotsignalsignal<-signalframesignalframe<-signalmatrixsim.capthistsim.detectsim.popnsim.resightsim.secrsnipspacingspacing<-spotHeightstrip.legendsuggest.buffertelemeteredtelemetrytypetelemetrytype<-telemetryxytelemetryxy<-tiletimevaryingcovtimevaryingcov<-TmTm<-TnTn<-transectIDtransectID<-transectlengthtraptrap.buildertrapstraps<-trapsPerAnimaltrimTuTu<-unjoinunRMarkInputupdateCHusageusage<-usagePlotverifywrite.capthistwrite.captureswrite.DAwrite.maskwrite.trapswriteGPSxyxy<-xy2CH
Dependencies:abindBHclassclassIntcliDBIe1071glueKernSmoothlatticelifecyclemagrittrMASSMatrixmgcvmvtnormnlmeproxyrasterRcppRcppEigenRcppNumericalRcppParallelrlangs2sfspstringistringrterraunitsvctrswk
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 |
