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 <>
LicenseGPL (>= 2)

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

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 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 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 Construct Detection Model Design Matrices and Lookups 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


addCovariates Man page
addSightings Man page
addTelemetry Man page
AIC.secr Man page
AIC.secrlist Man page
alive Man page
alongtransect Man page
animalID Man page
ARL Man page
attenuationplot Man page
autoini Man page
bias.D Man page
binomN Man page
buffer.contour Man page
captdata Man page
capthist Man page
captXY Man page
circular.p Man page
circular.r Man page
clip.hex Man page
clone Man page
clone.capthist Man page
clone.default Man page
clone.popn Man page
closedN Man page
closure.test Man page
cluster Man page
cluster.centres Man page
cluster.counts Man page
clusterID Man page
clusterID<- Man page
clustertrap Man page
clustertrap<- Man page
coef.secr Man page
collate Man page
confint.secr Man page
Coulombe Man page
count Man page
counts Man page
covariates Man page
covariates<- Man page
CV Man page
CVa Man page
CVa0 Man page
dbar Man page
D.designdata Man page
deermouse Man page
deermouse.ESG Man page
deermouse.WSG Man page
deleteMaskPoints Man page
derived Man page
derived.cluster Man page
derived.external Man page
derived.mash Man page
derived.nj Man page
derived.session Man page
details Man page
detectfn Man page
detectfnplot Man page
Detection functions Man page
detector Man page
detector<- Man page
detectpar Man page
detectpar.secr Man page
deviance Man page
deviance.secr Man page
df.residual Man page
df.residual.secr Man page
discretize Man page
distancetotrap Man page
Dsurface Man page
Dsurface-class Man page
edist Man page
effort Man page
ellipse.bvn Man page
ellipse.secr Man page
empirical.varD Man page
esa Man page
esa.plot Man page
esa.plot.secr Man page
ESG.0 Man page
ESG.b Man page
ESG.h2 Man page
ESG.t Man page
expected.n Man page
FAQ Man page
fixedbeta Man page
flip Man page
flip.popn Man page
flip.traps Man page
fxi Man page
fxi.contour Man page
fxi.mode Man page
fxi.secr Man page Man page
getMeanSD Man page
hcov Man page
head.capthist Man page
head.Dsurface Man page
head.mask Man page
head.traps Man page
hornedlizard Man page
hornedlizardCH Man page
housemouse Man page
housemouse.0 Man page
housemouse.ampm Man page
housemouse.ampmh2h2 Man page
infraCH Man page
invlogit Man page
ip.secr Man page
join Man page
lineoCH Man page
LLonly Man page
LLsurface.secr Man page
logit Man page
logLik.secr Man page
logmultinom Man page
LR.test Man page
LStraps Man page
make.capthist Man page Man page
make.grid Man page
make.hex Man page
make.lookup Man page
make.mask Man page
make.poly Man page
make.systematic Man page
make.telemetry Man page
make.transect Man page
make.tri Man page
markocc Man page
markocc<- Man page
mash Man page
mask Man page
maskarea Man page
mask.check Man page
mask-class Man page
masklength Man page
miscparm Man page
MMDM Man page
model.average Man page
morning.0 Man page
morning.0h2 Man page
morning.b Man page
morning.h2 Man page
morning.h2h2 Man page
morning.t Man page
moves Man page
ms Man page
MS.capthist Man page
ms.default Man page
ms.mask Man page
ms.secr Man page
multi Man page
Multi-core processing Man page
ncores Man page
nearesttrap Man page
nedist Man page
noise Man page
noise<- Man page
noise.capthist Man page
noneuc Man page
occasion Man page
ovenbird Man page
ovenbird.model.1 Man page
ovenbird.model.1b Man page
ovenbird.model.1T Man page
ovenbird.model.D Man page
ovenbird.model.h2 Man page
ovenCH Man page
ovenmask Man page
ovensong Man page
ovensong.model.1 Man page
ovensong.model.2 Man page
OVpossum Man page
OVpossumCH Man page
Parallel Man page
param Man page
par.derived Man page
par.region.N Man page Man page
pdot Man page
pdot.contour Man page
pfn Man page
PG Man page
plot.capthist Man page
plot.Dsurface Man page
plot.mask Man page
plotMaskEdge Man page
plotMCP Man page
plot.popn Man page
plot.Rsurface Man page
plot.secr Man page
plot.secrlist Man page
plot.secrtest Man page
plot.traps Man page
pmixProfileLL Man page
pointsInPolygon Man page
polyarea Man page
polygon Man page
polygonX Man page
polyID Man page
polyID<- Man page
popn Man page
population size Man page
possum Man page
possumarea Man page
possumCH Man page
possummask Man page
possum.model.0 Man page
possum.model.b Man page
possum.model.D Man page
possum.model.Ds Man page
possum.model.h2 Man page
possumremovalarea Man page
predictDsurface Man page
predict.secr Man page
predict.secrlist Man page
print.capthist Man page
print.Dsurface Man page
print.secr Man page
print.secrtest Man page
print.summary.capthist Man page
print.summary.mask Man page
print.summary.traps Man page
print.traps Man page
proximity Man page
randomHabitat Man page
raster Man page
raster,Dsurface-method Man page
raster,mask-method Man page
rbind.capthist Man page
rbind.mask Man page
rbind.popn Man page
rbind.traps Man page
read.capthist Man page
read.DA Man page
read.mask Man page
read.SPACECAP Man page
read.telemetry Man page
read.traps Man page
rectangularMask Man page
reduce Man page
reduce.capthist Man page
reduce.default Man page
reduce.traps Man page
region.N Man page
RMarkInput Man page
rotate Man page
rotate.popn Man page
rotate.traps Man page
RPSV Man page
Rsurface Man page
score.table Man page
score.test Man page
searcharea Man page
searcharea<- Man page
secr Man page
secrdemo Man page
secrdemo.0 Man page
secrdemo.b Man page
secrdemo.CL Man page
secr density models Man page Man page
secr detection models Man page Man page
secrlist Man page
[.secrlist Man page
secr.make.newdata Man page
secr.model Man page
secr.model.density Man page
secr.model.detection Man page
secr models Man page
secr-package Man page
secrtest Man page
secr.test Man page
session Man page
session<- Man page
shift Man page
shift.mask Man page
shift.popn Man page
shift.traps Man page
sighting Man page
signal Man page
signal Man page
signal<- Man page
signal.capthist Man page
signalCH Man page
signalframe Man page
signalframe<- Man page
signalmatrix Man page
sim.capthist Man page
sim.detect Man page
sim.popn Man page
sim.resight Man page
sim.secr Man page
simulate Man page
simulate.secr Man page
single Man page
skink Man page
smooths Man page
snip Man page
sort.capthist Man page
sort.mask Man page
spacing Man page
spacing<- Man page
spacing.mask Man page
spacing.traps Man page
speed Man page
Speed tips Man page
split.capthist Man page
split.traps Man page
spotHeight Man page
stoatCH Man page
stoatDNA Man page
stoat.model.EX Man page
stoat.model.HN Man page
stoat.model.HZ Man page
strip.legend Man page
subset.capthist Man page
subset.mask Man page
subset.popn Man page
subset.traps Man page
suggest.buffer Man page
summary.capthist Man page
summary.Dsurface Man page
summary.mask Man page
summary.traps Man page
tail.capthist Man page
tail.Dsurface Man page
tail.mask Man page
tail.traps Man page
telemetered Man page
telemetryxy Man page
tile Man page
timevaryingcov Man page
timevaryingcov<- Man page
Tm Man page
Tm<- Man page
transect Man page
transectID Man page
transectID<- Man page
transectlength Man page
transectX Man page
transformations Man page
trap Man page
trap.builder Man page
traps Man page
traps<- Man page
traps object Man page
trapXY Man page
trim Man page
trim.default Man page
trim.secr Man page
Troubleshooting Man page
Tu Man page
Tu<- Man page
turnover Man page
unjoin Man page
unRMarkInput Man page
usage Man page
usage<- Man page
usagePlot Man page
userdist Man page
vcov.secr Man page
verify Man page
verify.capthist Man page
verify.default Man page
verify.mask Man page
verify.traps Man page
write.capthist Man page
write.captures Man page
write.DA Man page
writeGPS Man page
write.SPACECAP Man page
write.traps Man page
WSG.0 Man page
WSG.b Man page
WSG.h2 Man page
WSG.t Man page
xy Man page
xy<- Man page
xy2CH Man page


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/ secr/R/PG.R secr/R/D.designdata.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/R/closure.R secr/R/addSightings.R secr/R/secrloglik.R secr/R/reduce.R secr/R/make.mask.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/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/ 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/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/ 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/ secr/man/ 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/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

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