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.

AuthorMurray Efford
Date of publication2016-12-04 14:52:42
MaintainerMurray Efford <murray.efford@otago.ac.nz>
LicenseGPL (>= 2)
Version2.10.4
http://www.otago.ac.nz/density

View on CRAN

Man pages

addCovariates: Add Covariates to Mask or Traps

addSightings: Mark-resight Data

addTelemetry: Combine Telemetry and Detection Data

AIC.secr: Compare SECR Models

autoini: Initial Parameter Values for SECR

capthist: Spatial Capture History Object

capthistfn: Dissect Spatial Capture History Object

circular: Circular Probability

clone: Replicate Rows

closedN: Closed population estimates

closure: Closure tests

cluster: Detector Clustering

coef.secr: Coefficients of secr Object

confint.secr: Profile Likelihood Confidence Intervals

contour: Contour Detection Probability

coulombe: House mouse live trapping data

covariates: Covariates Attribute

CV: Coefficient of Variation

DA: Convert Data To Or From BUGS Format

D.designdata: Construct Density Design Data

deermouse: Deermouse Live-trapping Datasets

deletemaskpoints: Edit Mask Points

DENSITY: Import or export data

derivedMS: Derived Parameters of Fitted SECR Model

details: Detail Specification for secr.fit

detectfn: Detection Functions

detector: Detector Type

deviance.secr: Deviance of fitted secr model and residual degrees of freedom

discretize: Rasterize Area Search or Transect Data

distancetotrap: Distance To Nearest Detector

Dsurface: Density Surfaces

ellipse.secr: Confidence Ellipses

empirical: Empirical Variance of H-T Density Estimate

esaplot: Mask Buffer Diagnostic Plot

esaplotsecr: Mask Buffer Diagnostic Plot (internal)

expected.n: Expected Number of Individuals

FAQ: Frequently Asked Questions, And Others

fxi: Probability Density of Home Range Centre

fx.total: Activity Centres of Detected and Undetected Animals

hcov: Hybrid Mixture Model

head: First or Last Part of an Object

homerange: Home Range Statistics

hornedlizard: Flat-tailed Horned Lizard Dataset

ip.secr: Spatially Explicit Capture-Recapture by Inverse Prediction

join: Combine or Split Sessions of capthist Object

LLsurface: Plot likelihood surface

logit: Logit Transformation

logmultinom: Multinomial Coefficient of SECR Likelihood

LRtest: Likelihood Ratio Test

make.capthist: Construct capthist Object

make.mask: Build Habitat Mask

make.systematic: Construct Systematic Detector Design

make.traps: Build Detector Array

make.tri: Build Detector Array on Triangular or Hexagonal Grid

mask: Mask Object

mask.check: Mask Diagnostics

model.average: Averaging of SECR Models Using Akaike's Information Criterion

ms: Multi-session Objects

ovenbird: Ovenbird Mist-netting Dataset

ovensong: Ovenbird Acoustic Dataset

OVpossum: Orongorongo Valley Brushtail Possums

Parallel: Multi-core Processing

par.secr.fit: Fit Multiple SECR Models

pdot: Net Detection Probability

PG: Telemetry Fixes in Polygons

plot.capthist: Plot Detection Histories

plot.mask: Plot Habitat Mask, Density or Resource Surface

plotmaskedge: Outline Around Mask Cells

plot.popn: Plot popn Object

plot.secr: Plot Detection Functions

plot.traps: Plot traps Object

pmixProfileLL: Mixture Model Check

pointsInPolygon: Points Inside Polygon

polyarea: Area of Polygon(s)

popn: Population Object

possum: Brushtail Possum Trapping Dataset

predictDsurface: Predict Density Surface

predict.secr: SECR Model Predictions

print.capthist: Print Detections

print.secr: Print secr Object

print.traps: Print Detectors

randomHabitat: Random Landscape

raster2: Create a RasterLayer Object from Mask or Dsurface

rbind.capthist: Combine capthist Objects

rbind.popn: Combine popn Objects

rbind.traps: Combine traps Objects

read.mask: Read Habitat Mask From File

read.telemetry: Import Radio Fixes

read.traps: Read Detector Data From File

rectangularMask: Rectangular Mask

reduce: Combine Columns

reduce.capthist: Combine Occasions Or Detectors

region.N: Population Size

RMarkInput: Convert Data to RMark Input Format

Rsurface: Smoothed Resource Surface

score.test: Score Test for SECR Models

secrdemo: SECR Models Fitted to Demonstration Data

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.density: Density Models

secr.model.detection: Models for Detection Parameters

secr.models: Spatially Explicit Capture-Recapture Models

secr-package: Spatially Explicit Capture-Recapture Models

secrtest: Goodness-of-fit Test Results

secr.test: Goodness-of-Fit Test

session: Session Vector

sighting: Sighting Attributes

signal: Signal Fields

signalmatrix: Reformat Signal Data

sim.capthist: Simulate Detection Histories

sim.popn: Simulate 2-D Population

simpopndetails: Specifying a Dynamic Population

sim.secr: Simulate From Fitted secr Model

skink: Skink Pitfall Data

smooths: Smooth Terms in SECR Models

snip: Slice Transect Into Shorter Sections

sort: Sort Rows of capthist or mask Object

SPACECAP: Exchange data with SPACECAP package

spacing: Detector or Mask Spacing

speed: Speed Tips

stoatDNA: Stoat DNA Data

strip.legend: Colour Strip Legend

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.mask: Summarise Habitat Mask

summary.traps: Summarise Detector Array

timevaryingcov: Time-varying Detector Covariates

transformations: Transform Point Array

trap.builder: Complex Detector Layouts

traps: Detector Array

trapsfn: Detector Attributes

trim: Drop Unwanted List Components

troubleshooting: Problems in Fitting SECR Models

usage: Detector Usage

usagePlot: Plot Usage

userdist: Non-Euclidean Distances

utility: Utility Functions

vcov.secr: Variance - Covariance Matrix of SECR Parameters

verify: Check SECR Data

write: Write Data to Text File

writeGPS: Upload to GPS

Files in this package

secr
secr/inst
secr/inst/CITATION
secr/inst/extdata
secr/inst/extdata/OVforest.shp
secr/inst/extdata/possumarea.shx
secr/inst/extdata/lizarddata.R
secr/inst/extdata/possumarea.shp
secr/inst/extdata/stoatcapt.txt
secr/inst/extdata/OVforest.shx
secr/inst/extdata/stoattrap.txt
secr/inst/extdata/capt.txt
secr/inst/extdata/OVforest.dbf
secr/inst/extdata/possumarea.dbf
secr/inst/extdata/trap.txt
secr/inst/extdata/leftbank.txt
secr/inst/extdata/possumarea.txt
secr/inst/doc
secr/inst/doc/index.html
secr/inst/doc/secr-datainput.Rmd
secr/inst/doc/secr-overview.R
secr/inst/doc/secr-manual.pdf
secr/inst/doc/secr-overview.pdf
secr/inst/doc/secr-datainput.R
secr/inst/doc/secr-overview.Rmd
secr/inst/doc/secr-datainput.pdf
secr/src
secr/src/sighting.c
secr/src/detectfn.c
secr/src/trapping.c
secr/src/utils.c
secr/src/secr.c
secr/src/secr.h
secr/src/unmarked.c
secr/src/polygon.c
secr/src/simsecr.c
secr/NAMESPACE
secr/NEWS
secr/data
secr/data/secrdemo.RData
secr/data/OVpossum.RData
secr/data/hornedlizard.RData
secr/data/deermouse.RData
secr/data/stoatDNA.RData
secr/data/skink.RData
secr/data/possum.RData
secr/data/housemouse.RData
secr/data/ovensong.RData
secr/data/ovenbird.RData
secr/R
secr/R/mash.r
secr/R/DENSITY.R secr/R/write.captures.R secr/R/secr.make.newdata.R secr/R/addCovariates.R secr/R/head.R secr/R/writeGPS.R secr/R/par.secr.fit.R secr/R/PG.R secr/R/D.designdata.R
secr/R/plot.mask.r
secr/R/confint.secr.R secr/R/clone.R secr/R/onAttach.R secr/R/trap.builder.R secr/R/usagePlot.R secr/R/make.grid.R secr/R/sim.popn.R secr/R/secr.design.MS.R secr/R/closure.R secr/R/addSightings.R secr/R/secrloglik.R secr/R/reduce.R secr/R/make.mask.R
secr/R/plot.capthist.r
secr/R/sim.secr.R secr/R/sim.capthist.R secr/R/model.average.R secr/R/fxi.R secr/R/telemetry.R secr/R/methods.R secr/R/score.test.R secr/R/suggest.buffer.R secr/R/utility.R secr/R/snip.R secr/R/split.traps.R secr/R/ellipse.secr.R secr/R/derivedMS.R secr/R/secr.fit.R secr/R/mask.check.R secr/R/secr.test.R secr/R/SPACECAP.R secr/R/raster.R secr/R/make.tri.R secr/R/empirical.R secr/R/rbind.capthist.R secr/R/esa.R secr/R/verify.R secr/R/join.R secr/R/predict.secr.R secr/R/CV.R secr/R/read.traps.R secr/R/randomHabitat.R secr/R/deviance.R secr/R/sighting.chat.R secr/R/pdot.R secr/R/homerange.R secr/R/plot.secr.R secr/R/autoini.R secr/R/make.capthist.R secr/R/logmultinom.R secr/R/Dsurface.R secr/R/Rsurface.R secr/R/DA.R secr/R/write.traps.R secr/R/discretize.R secr/R/plotMaskEdge.R secr/R/circular.R secr/R/split.capthist.R secr/R/LLsurface.secr.R secr/R/ClosedN.R secr/R/ip.secr.R secr/R/pmixProfileLL.R secr/R/LRtest.R secr/R/regionN.R
secr/vignettes
secr/vignettes/secr-datainput.Rmd
secr/vignettes/secr-overview_files
secr/vignettes/secr-overview_files/figure-latex
secr/vignettes/secr-overview_files/figure-latex/unnamed-chunk-3-1.pdf
secr/vignettes/detectionfn.png
secr/vignettes/secr-overview_cache
secr/vignettes/secr-overview_cache/latex
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.rdx
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.rdx
secr/vignettes/secr-overview_cache/latex/__packages
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.rdx
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.rdb
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.rdb
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.rdb
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.rdb
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.RData
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-12_e5fd389165f44ff0d2f73d2392aa3393.RData
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-10_62f08dd0b969e0e0b4e5bfaafbac6c44.rdx
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.rdx
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-3_4f126cc9f2fb01842f41c5c2867f8a61.RData
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-13_53bc27e3a02b41327d0dbb7dd9a3adc6.RData
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.rdb
secr/vignettes/secr-overview_cache/latex/unnamed-chunk-11_132901f704c3b5e5a4aa0c23de9a069f.RData
secr/vignettes/capt.txt
secr/vignettes/schematic3.png
secr/vignettes/simpoly.png
secr/vignettes/trap.txt
secr/vignettes/secr-overview.Rmd
secr/MD5
secr/build
secr/build/vignette.rds
secr/DESCRIPTION
secr/man
secr/man/LRtest.Rd secr/man/secr.models.Rd secr/man/read.mask.Rd secr/man/sim.popn.Rd secr/man/ip.secr.Rd secr/man/coef.secr.Rd secr/man/rbind.popn.Rd secr/man/plot.secr.Rd secr/man/trapsfn.Rd secr/man/head.Rd secr/man/signalmatrix.Rd secr/man/plotmaskedge.Rd secr/man/utility.Rd secr/man/make.capthist.Rd secr/man/SPACECAP.Rd secr/man/print.secr.Rd secr/man/D.designdata.Rd secr/man/summary.traps.Rd secr/man/DA.Rd secr/man/ellipse.secr.Rd secr/man/smooths.Rd secr/man/skink.Rd secr/man/plot.traps.Rd secr/man/secr.model.density.Rd secr/man/randomHabitat.Rd secr/man/Rsurface.Rd secr/man/secrdemo.Rd secr/man/polyarea.Rd secr/man/autoini.Rd secr/man/closure.Rd secr/man/plot.popn.Rd secr/man/esaplotsecr.Rd secr/man/CV.Rd secr/man/subset.traps.Rd secr/man/addSightings.Rd secr/man/cluster.Rd secr/man/plot.capthist.Rd secr/man/score.test.Rd secr/man/deviance.secr.Rd secr/man/pmixProfileLL.Rd secr/man/AIC.secr.Rd secr/man/raster2.Rd secr/man/popn.Rd secr/man/rectangularMask.Rd secr/man/LLsurface.Rd secr/man/addTelemetry.Rd secr/man/strip.legend.Rd secr/man/reduce.capthist.Rd secr/man/summary.capthist.Rd secr/man/suggest.buffer.Rd secr/man/secr.test.Rd secr/man/speed.Rd secr/man/stoatDNA.Rd secr/man/DENSITY.Rd secr/man/sim.capthist.Rd secr/man/ovenbird.Rd secr/man/print.capthist.Rd secr/man/predictDsurface.Rd secr/man/subset.popn.Rd secr/man/subset.mask.Rd secr/man/write.Rd secr/man/OVpossum.Rd secr/man/discretize.Rd secr/man/region.N.Rd secr/man/hcov.Rd secr/man/timevaryingcov.Rd secr/man/make.tri.Rd secr/man/writeGPS.Rd secr/man/clone.Rd secr/man/PG.Rd secr/man/fxi.Rd secr/man/vcov.secr.Rd secr/man/session.Rd secr/man/ovensong.Rd secr/man/read.traps.Rd secr/man/make.traps.Rd secr/man/userdist.Rd secr/man/logit.Rd secr/man/capthistfn.Rd secr/man/esaplot.Rd secr/man/expected.n.Rd secr/man/addCovariates.Rd secr/man/secr-package.Rd secr/man/fx.total.Rd secr/man/spacing.Rd secr/man/sort.Rd secr/man/coulombe.Rd secr/man/plot.mask.Rd secr/man/mask.check.Rd secr/man/usagePlot.Rd secr/man/make.systematic.Rd secr/man/confint.secr.Rd secr/man/par.secr.fit.Rd secr/man/secr.fit.Rd secr/man/logmultinom.Rd secr/man/transformations.Rd secr/man/distancetotrap.Rd secr/man/join.Rd secr/man/possum.Rd secr/man/capthist.Rd secr/man/pdot.Rd secr/man/print.traps.Rd secr/man/trim.Rd secr/man/simpopndetails.Rd secr/man/rbind.capthist.Rd secr/man/contour.Rd secr/man/hornedlizard.Rd secr/man/make.mask.Rd secr/man/trap.builder.Rd secr/man/secr.model.detection.Rd secr/man/rbind.traps.Rd secr/man/subset.capthist.Rd secr/man/verify.Rd secr/man/RMarkInput.Rd secr/man/FAQ.Rd secr/man/mask.Rd secr/man/deermouse.Rd secr/man/closedN.Rd secr/man/predict.secr.Rd secr/man/ms.Rd secr/man/circular.Rd secr/man/reduce.Rd secr/man/read.telemetry.Rd secr/man/pointsInPolygon.Rd secr/man/derivedMS.Rd secr/man/snip.Rd secr/man/troubleshooting.Rd secr/man/detector.Rd secr/man/model.average.Rd secr/man/signal.Rd secr/man/traps.Rd secr/man/empirical.Rd secr/man/summary.mask.Rd secr/man/secr.design.MS.Rd secr/man/sim.secr.Rd secr/man/details.Rd secr/man/deletemaskpoints.Rd secr/man/covariates.Rd secr/man/usage.Rd secr/man/Dsurface.Rd secr/man/secrtest.Rd secr/man/secr.make.newdata.Rd secr/man/sighting.Rd secr/man/Parallel.Rd secr/man/homerange.Rd secr/man/detectfn.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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