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.

Author
Murray Efford
Date of publication
2016-12-04 14:52:42
Maintainer
Murray Efford <murray.efford@otago.ac.nz>
License
GPL (>= 2)
Version
2.10.4
URLs

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