secr: Spatially Explicit Capture-Recapture
Version 3.0.1

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 publication2017-05-03 16:22:09 UTC
MaintainerMurray Efford <murray.efford@otago.ac.nz>
LicenseGPL (>= 2)
Version3.0.1
URL http://www.otago.ac.nz/density
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("secr")

Getting started

Package overview
Data input for **secr**"
**secr** 3.0 - spatially explicit capture--recapture in R'

Popular man pages

addCovariates: Add Covariates to Mask or Traps
closure: Closure tests
hcov: Hybrid Mixture Model
homerange: Home Range Statistics
occasionKey: Key to Petal Plot
OVpossum: Orongorongo Valley Brushtail Possums
pointsInPolygon: Points Inside Polygon
See all...

All man pages Function index File listing

Man pages

addCovariates: Add Covariates to Mask or Traps
addSightings: Mark-resight Data
addTelemetry: Combine Telemetry and Detection Data
AIC.secr: Compare SECR Models
as.mask: Coerce traps object to mask
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
occasionKey: Key to Petal Plot
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 Telemetry 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
sharefactorlevels: Fix Inconsistent Covariates
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
updateCH: Update Old capthist Format
usage: Detector Usage
usagePlot: Plot usage, detections or sightings.
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

Functions

AIC.secr Man page Source code
AIC.secrlist Man page Source code
ANN Source code
ARL Man page Source code
BSS Source code
CG Source code
CHN Source code
CLN Source code
CLdensity Source code
CLgradient Source code
CLmeanesa Source code
CN Source code
CV Man page Source code
CVa Man page Source code
CVa0 Man page Source code
Coulombe Man page
D.designdata Man page Source code
Detection functions Man page
Dsurface Man page
Dsurface-class Man page
Dsurface.as.data.frame Source code
ESG.0 Man page
ESG.b Man page
ESG.h2 Man page
ESG.t Man page
EX Source code
FAQ Man page
HAN Source code
HCG Source code
HEX Source code
HHN Source code
HHR Source code
HN Source code
HR Source code
LLonly Man page
LLsurface.secr Man page Source code
LN.interval Source code
LR.test Man page Source code
LStraps Man page
M0 Source code
MATA Source code
MMDM Man page Source code
MRtraps Source code
MS.capthist Man page Source code
Mb Source code
Mh Source code
Mh2.est Source code
Mhbeta.est Source code
Mtnegloglik Source code
Multi-core processing Man page
N.Mt Source code
OLD.rbind.capthist Source code
OVpossum Man page
OVpossumCH Man page
PG Man page Source code
Parallel Man page
RMarkInput Man page Source code
RPSV Man page Source code
RPSVxy Source code
Rsurface Man page Source code
Rsurface.as.data.frame Source code
SN Source code
SNS Source code
SS Source code
SSS Source code
Speed tips Man page
Tm Man page Source code
Tm.default Source code
Tm<- Man page
Tn Man page Source code
Tn.default Source code
Tn<- Man page
Troubleshooting Man page
Tu Man page Source code
Tu.default Source code
Tu<- Man page
UN Source code
WEX Source code
WSG.0 Man page
WSG.b Man page
WSG.h2 Man page
WSG.t Man page
Xtransform Source code
Xuntransform Source code
[.secrlist Man page
add.cl Source code
addCovariates Man page Source code
addSightings Man page Source code
addTelemetry Man page Source code
addzeroCH Source code
addzerodf Source code
alive Man page Source code
allzero Source code
alongtransect Man page Source code
animalID Man page Source code
as.mask Man page Source code
attenuationplot Man page Source code
autoini Man page Source code
badsmooths Source code
bias.D Man page Source code
binomN Man page
bisect Source code
boundarytoSP Source code
boundarytoSPDF Source code
bubble.legend Source code
buffer.contour Man page Source code
bufferbiascheck Source code
c.secrlist Source code
captXY Man page
captdata Man page
capthist Man page
cellPointsInPolygon Source code
chao.est Source code
chao.th1.est Source code
chao.th2.est Source code
chaomod.est Source code
check3D Source code
checkcovariatelevels Source code
circular.p Man page Source code
circular.r Man page Source code
clean.mlogit Source code
clip.hex Man page Source code
clone Man page Source code
clone.capthist Man page Source code
clone.default Man page Source code
clone.popn Man page Source code
closedN Man page Source code
closure.test Man page Source code
cluster Man page
cluster.centres Man page Source code
cluster.counts Man page Source code
clusterID Man page Source code Source code
clusterID.default Source code
clusterID<- Man page
clustertrap Man page Source code Source code
clustertrap.default Source code
clustertrap<- Man page
coef.secr Man page Source code
collapseocc Source code
collate Man page Source code
complete.beta Source code
complete.beta.vcv Source code
confint.secr Man page Source code
count Man page
counts Man page Source code
covariates Man page Source code
covariates.default Source code
covariates<- Man page
darr.est.c Source code
dbar Man page Source code
deermouse Man page
deermouse.ESG Man page
deermouse.WSG Man page
deleteMaskPoints Man page Source code
derived Man page Source code
derived.cluster Man page Source code
derived.external Man page Source code
derived.mash Man page Source code
derived.nj Man page Source code
derived.session Man page Source code
derived.stratified Source code
designmatrix Source code
details Man page
detectfn Man page
detectfnplot Man page Source code
detectionfunctionname Source code
detectionfunctionnumber Source code
detectionindex Source code
detector Man page Source code
detector.default Source code
detector<- Man page
detectorcode Source code
detectpar Man page Source code
detectpar.default Source code
detectpar.secr Man page Source code
deviance Man page
deviance.secr Man page Source code
df.residual Man page
df.residual.secr Man page Source code
discreteN Source code
discretize Man page Source code
disinteraction Source code
distances Source code
distancetotrap Man page Source code
edist Man page Source code
effort Man page
ellipse.bvn Man page Source code
ellipse.secr Man page Source code
empirical.varD Man page
esa Man page Source code
esa.plot Man page Source code
esa.plot.secr Man page Source code
esagradient Source code
expandbinomN Source code
expanddet Source code
expands Source code
expandsk Source code
expected.n Man page Source code
extract.estimates Source code
fixed.string Source code
fixedbeta Man page
fixpmix Source code
flatten Source code
flip Man page Source code
flip.default Source code
flip.popn Man page Source code
flip.traps Man page Source code
fullbeta Source code
fx.total Man page Source code
fxi Man page
fxi.contour Man page Source code
fxi.mode Man page Source code
fxi.secr Man page Source code
fxi2SPDF Source code
gamsetup Source code
general.model.matrix Source code
get.nmix Source code
getCentres Source code
getD Source code
getDensityArray Source code
getMeanSD Man page Source code
getbinomN Source code
getcellsize Source code
getcoord Source code
getdfn Source code
getgrpnum Source code
getknownclass Source code
getnmix Source code
getuserdistnames Source code
gradient Source code
group.factor Source code
group.levels Source code
h.levels Source code
hcov Man page
hdot Source code
head.Dsurface Man page Source code
head.capthist Man page Source code
head.mask Man page Source code
head.traps Man page Source code
hexagon Source code
hornedlizard Man page
hornedlizardCH Man page
housemouse Man page
housemouse.0 Man page
housemouse.ampm Man page
housemouse.ampmh2h2 Man page
inflate Source code
inflatechull Source code
infraCH Man page
insertdim Source code
invlogit Man page Source code
invodds Source code
invsine Source code
ip.secr Man page Source code
is.wholenumber Source code
jack.est Source code
jackknife.est Source code
join Man page Source code
leadingzero Source code
lineoCH Man page
lnbinomial Source code
localvar Source code
logLik.secr Man page Source code
logit Man page Source code
logmultinom Man page Source code
make.capthist Man page Source code
make.circle Man page Source code
make.grid Man page Source code
make.hex Man page Source code
make.lookup Man page Source code
make.mask Man page Source code
make.poly Man page Source code
make.systematic Man page Source code
make.telemetry Man page Source code
make.transect Man page Source code
make.tri Man page Source code
makerealparameters Source code
mapbeta Source code
markocc Man page Source code
markocc.default Source code
markocc<- Man page
markresight Source code
mash Man page Source code
mask Man page
mask-class Man page
mask.check Man page Source code
maskarea Man page Source code
masklength Man page Source code
memo Source code
merge.capthist Source code
mindistfromedge Source code
miscparm Man page
mlogit Source code
mlogit.untransform Source code
model.average Man page Source code
model.string Source code
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 Source code
ms Man page Source code
ms.default Man page Source code
ms.mask Man page Source code
ms.secr Man page Source code
ms.secrtest Source code
multi Man page
n.occasion Source code
naivesigma Source code
nclusters Source code
ncores Man page
ndetector Source code
ndetectpar Source code
nearesttrap Man page Source code
nedist Man page Source code
negloglikM0 Source code
negloglikMb Source code
new.param Source code
newstr Source code
noise Man page Source code
noise.capthist Man page Source code
noise.default Source code
noise<- Man page
noneuc Man page
nparameters Source code
null.est.c Source code
occasion Man page Source code
occasionKey Man page Source code
odds Source code
onAttach Source code
oneline.secr Source code
outsidemask Source code
ovenCH Man page
ovenCHp Man page
ovenbird Man page
ovenbird.model.1 Man page
ovenbird.model.1T Man page
ovenbird.model.1b Man page
ovenbird.model.D Man page
ovenbird.model.h2 Man page
ovenmask Man page
ovensong Man page
ovensong.model.1 Man page
ovensong.model.2 Man page
overlapcells Source code
overlappoly Source code
pad1 Source code
padarray Source code
par.derived Man page Source code
par.region.N Man page Source code
par.secr.fit Man page Source code
param Man page
parnames Source code
pdot Man page Source code
pdot.contour Man page Source code
pfn Man page Source code
pfnold Source code
plot.Dsurface Man page Source code
plot.Rsurface Man page Source code
plot.capthist Man page Source code
plot.mask Man page Source code
plot.popn Man page Source code
plot.secr Man page Source code
plot.secrlist Man page Source code
plot.secrtest Man page Source code
plot.traps Man page Source code
plotMCP Man page Source code
plotMaskEdge Man page Source code
plotMaskEdgeOld Source code
pmixProfileLL Man page Source code
pointsInPolygon Man page Source code
poly2point Source code
polyID Man page Source code
polyID<- Man page
polyarea Man page Source code
polygon Man page
polygonX Man page
polys Source code
popn Man page
population size Man page
possum Man page
possum.model.0 Man page
possum.model.D Man page
possum.model.Ds Man page
possum.model.b Man page
possum.model.h2 Man page
possumCH Man page
possumarea Man page
possummask Man page
possumremovalarea Man page
predict.secr Man page Source code
predict.secrlist Man page Source code
predictD Source code
predictDsurface Man page Source code
prepare Source code
print.Dsurface Man page Source code
print.Rsurface Source code
print.capthist Man page Source code
print.secr Man page Source code
print.secrdata Source code
print.secrlist Source code
print.secrtest Man page Source code
print.summary.capthist Man page Source code
print.summary.mask Man page Source code
print.summary.traps Man page Source code
print.traps Man page Source code
proximity Man page
randomHabitat Man page Source code
raster Man page
raster,Dsurface-method Man page
raster,mask-method Man page
rbind.capthist Man page Source code
rbind.mask Man page Source code
rbind.popn Man page Source code
rbind.traps Man page Source code
read.DA Man page Source code
read.SPACECAP Man page Source code
read.capthist Man page Source code
read.mask Man page Source code
read.telemetry Man page Source code
read.traps Man page Source code
rectangularMask Man page Source code
reduce Man page Source code
reduce.capthist Man page Source code
reduce.default Man page Source code
reduce.traps Man page Source code
refreshMCP Source code
region.N Man page Source code
renamepolyrows Source code
rep.capthist Source code
reparameterize Source code
reparameterize.a0 Source code
reparameterize.esa Source code
reparameterize.sigmak Source code
replacedefaults Source code
ringID Source code
rotate Man page Source code
rotate.default Source code
rotate.popn Man page Source code
rotate.traps Man page Source code
score.table Man page Source code
score.test Man page Source code
se.Xtransform Source code
se.Xuntransform Source code
se.untransform Source code
searcharea Man page Source code
searcharea<- Man page
secr Man page
secr density models Man page
secr detection models Man page
secr models Man page
secr-package Man page
secr.design.MS Man page Source code
secr.fit Man page Source code
secr.loglikfn Source code
secr.lpredictor Source code
secr.make.newdata Man page Source code
secr.model Man page
secr.model.density Man page
secr.model.detection Man page
secr.test Man page Source code
secrdemo Man page
secrdemo.0 Man page
secrdemo.CL Man page
secrdemo.b Man page
secrlist Man page Source code
secrtest Man page
session Man page Source code
session.default Source code
session<- Man page
shareFactorLevels Man page Source code
shift Man page Source code
shift.default Source code
shift.mask Man page Source code
shift.popn Man page Source code
shift.traps Man page Source code
sighting Man page Source code
sighting.chat Source code
sightingPlot Man page Source code
sightings Man page
signal Man page Man page Source code
signal.capthist Man page Source code
signal.default Source code
signal<- Man page
signalCH Man page
signalframe Man page Source code
signalframe<- Man page
signalmatrix Man page Source code
sim.capthist Man page Source code
sim.detect Man page Source code
sim.popn Man page Source code
sim.resight Man page Source code
sim.secr Man page Source code
simulate Man page
simulate.secr Man page Source code
sine Source code
single Man page
skink Man page
slice Source code
smooths Man page Source code
snip Man page Source code
sort.capthist Man page Source code
sort.mask Man page Source code
spacing Man page Source code
spacing.default Source code
spacing.mask Man page Source code
spacing.traps Man page Source code
spacing<- Man page
spatialscale Source code
speed Man page
split.by Source code
split.capthist Man page Source code
split.traps Man page Source code
spotHeight Man page Source code
stdform Source code
stoat.model.EX Man page
stoat.model.HN Man page
stoat.model.HZ Man page
stoatCH Man page
stoatDNA Man page
strip.legend Man page Source code
subset.capthist Man page Source code
subset.mask Man page Source code
subset.popn Man page Source code
subset.traps Man page Source code
suggest.buffer Man page Source code
sumDpdot Source code
summary.Dsurface Man page Source code
summary.capthist Man page Source code
summary.mask Man page Source code
summary.traps Man page Source code
tail.Dsurface Man page Source code
tail.capthist Man page Source code
tail.mask Man page Source code
tail.traps Man page Source code
telemetered Man page Source code
telemetry.LC Source code
telemetry.LCmask Source code
telemetry.LT Source code
telemetrytype Man page Source code
telemetrytype.default Source code
telemetrytype<- Man page
telemetryxy Man page Source code
telemetryxy<- Man page
tile Man page Source code
timevaryingcov Man page Source code
timevaryingcov.default Source code
timevaryingcov<- Man page
toroidal.wrap Source code
transect Man page
transect2point Source code
transectID Man page Source code
transectID<- Man page
transectX Man page
transectlength Man page Source code
transform Source code
transformations Man page
trap Man page Source code
trap.builder Man page Source code
trapXY Man page
trapmerge Source code
traps Man page Source code
traps object Man page
traps.default Source code
traps<- Man page
trim Man page Source code
trim.default Man page Source code
trim.secr Man page Source code
turnover Man page
unRMarkInput Man page Source code
unjoin Man page Source code
untransform Source code
updateCH Man page Source code
updatemodel Source code
usage Man page Source code
usage.default Source code
usage<- Man page
usagePlot Man page Source code
userD Source code
userdist Man page
valid.detectfn Source code
valid.detectpar Source code
valid.model Source code
valid.pnames Source code
valid.userdist Source code
validpoly Source code
var.in.model Source code
vcov.secr Man page Source code
verify Man page Source code
verify.capthist Man page Source code
verify.default Man page Source code
verify.mask Man page Source code
verify.traps Man page Source code
write.DA Man page Source code
write.SPACECAP Man page Source code
write.capthist Man page Source code
write.captures Man page Source code
write.traps Man page Source code
writeGPS Man page Source code
xy Man page Source code
xy2CH Man page Source code
xy<- Man page
xyinpoly Source code
xyontransect Source code
zip.est.c Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/OVforest.shp
inst/extdata/possumarea.shx
inst/extdata/lizarddata.R
inst/extdata/possumarea.shp
inst/extdata/stoatcapt.txt
inst/extdata/OVforest.shx
inst/extdata/stoattrap.txt
inst/extdata/capt.txt
inst/extdata/OVforest.dbf
inst/extdata/possumarea.dbf
inst/extdata/trap.txt
inst/extdata/leftbank.txt
inst/extdata/possumarea.txt
inst/doc
inst/doc/index.html
inst/doc/secr-datainput.Rmd
inst/doc/secr-overview.R
inst/doc/secr-manual.pdf
inst/doc/secr-overview.pdf
inst/doc/secr-datainput.R
inst/doc/secr-overview.Rmd
inst/doc/secr-datainput.pdf
src
src/sighting.c
src/detectfn.c
src/trapping.c
src/utils.c
src/secr.c
src/secr.h
src/unmarked.c
src/polygon.c
src/init.c
src/simsecr.c
NAMESPACE
NEWS
data
data/secrdemo.RData
data/OVpossum.RData
data/hornedlizard.RData
data/deermouse.RData
data/stoatDNA.RData
data/skink.RData
data/possum.RData
data/housemouse.RData
data/ovensong.RData
data/ovenbird.RData
R
R/mash.r
R/DENSITY.R
R/write.captures.R
R/secr.make.newdata.R
R/addCovariates.R
R/head.R
R/writeGPS.R
R/par.secr.fit.R
R/PG.R
R/D.designdata.R
R/plot.mask.r
R/confint.secr.R
R/clone.R
R/onAttach.R
R/trap.builder.R
R/usagePlot.R
R/plot.traps.R
R/make.grid.R
R/sim.popn.R
R/secr.design.MS.R
R/closure.R
R/addSightings.R
R/secrloglik.R
R/reduce.R
R/make.mask.R
R/plot.capthist.r
R/sim.secr.R
R/sim.capthist.R
R/model.average.R
R/fxi.R
R/telemetry.R
R/methods.R
R/score.test.R
R/suggest.buffer.R
R/utility.R
R/snip.R
R/split.traps.R
R/ellipse.secr.R
R/derivedMS.R
R/addTelemetry.R
R/secr.fit.R
R/mask.check.R
R/secr.test.R
R/SPACECAP.R
R/raster.R
R/make.tri.R
R/empirical.R
R/rbind.capthist.R
R/esa.R
R/verify.R
R/join.R
R/predict.secr.R
R/CV.R
R/read.traps.R
R/randomHabitat.R
R/deviance.R
R/sighting.chat.R
R/pdot.R
R/homerange.R
R/plot.secr.R
R/autoini.R
R/make.capthist.R
R/logmultinom.R
R/Dsurface.R
R/Rsurface.R
R/DA.R
R/write.traps.R
R/discretize.R
R/plotMaskEdge.R
R/circular.R
R/split.capthist.R
R/LLsurface.secr.R
R/ClosedN.R
R/ip.secr.R
R/rbind.traps.R
R/pmixProfileLL.R
R/LRtest.R
R/regionN.R
vignettes
vignettes/secr-datainput.Rmd
vignettes/secr-overview_files
vignettes/secr-overview_files/figure-latex
vignettes/secr-overview_files/figure-latex/unnamed-chunk-3-1.pdf
vignettes/secr-overview_cache
vignettes/secr-overview_cache/latex
vignettes/secr-overview_cache/latex/__packages
vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.rdx
vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.rdb
vignettes/secr-overview_cache/latex/unnamed-chunk-3_e17219e6059ea46c4fd3ae1634a8f221.RData
vignettes/capt.txt
vignettes/schematic3.png
vignettes/simpoly.png
vignettes/trap.txt
vignettes/secr-overview.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/LRtest.Rd
man/secr.models.Rd
man/read.mask.Rd
man/sim.popn.Rd
man/ip.secr.Rd
man/coef.secr.Rd
man/rbind.popn.Rd
man/plot.secr.Rd
man/trapsfn.Rd
man/head.Rd
man/signalmatrix.Rd
man/plotmaskedge.Rd
man/utility.Rd
man/make.capthist.Rd
man/SPACECAP.Rd
man/print.secr.Rd
man/D.designdata.Rd
man/summary.traps.Rd
man/DA.Rd
man/ellipse.secr.Rd
man/smooths.Rd
man/as.mask.Rd
man/skink.Rd
man/sharefactorlevels.Rd
man/plot.traps.Rd
man/secr.model.density.Rd
man/randomHabitat.Rd
man/Rsurface.Rd
man/secrdemo.Rd
man/polyarea.Rd
man/autoini.Rd
man/closure.Rd
man/plot.popn.Rd
man/esaplotsecr.Rd
man/CV.Rd
man/subset.traps.Rd
man/addSightings.Rd
man/cluster.Rd
man/plot.capthist.Rd
man/score.test.Rd
man/deviance.secr.Rd
man/pmixProfileLL.Rd
man/AIC.secr.Rd
man/raster2.Rd
man/popn.Rd
man/rectangularMask.Rd
man/LLsurface.Rd
man/addTelemetry.Rd
man/strip.legend.Rd
man/reduce.capthist.Rd
man/summary.capthist.Rd
man/suggest.buffer.Rd
man/secr.test.Rd
man/updateCH.Rd
man/speed.Rd
man/stoatDNA.Rd
man/DENSITY.Rd
man/sim.capthist.Rd
man/ovenbird.Rd
man/print.capthist.Rd
man/predictDsurface.Rd
man/subset.popn.Rd
man/subset.mask.Rd
man/write.Rd
man/OVpossum.Rd
man/discretize.Rd
man/region.N.Rd
man/hcov.Rd
man/timevaryingcov.Rd
man/make.tri.Rd
man/writeGPS.Rd
man/clone.Rd
man/PG.Rd
man/fxi.Rd
man/vcov.secr.Rd
man/session.Rd
man/ovensong.Rd
man/read.traps.Rd
man/make.traps.Rd
man/userdist.Rd
man/logit.Rd
man/capthistfn.Rd
man/occasionKey.Rd
man/esaplot.Rd
man/expected.n.Rd
man/addCovariates.Rd
man/secr-package.Rd
man/fx.total.Rd
man/spacing.Rd
man/sort.Rd
man/coulombe.Rd
man/plot.mask.Rd
man/mask.check.Rd
man/usagePlot.Rd
man/make.systematic.Rd
man/confint.secr.Rd
man/par.secr.fit.Rd
man/secr.fit.Rd
man/logmultinom.Rd
man/transformations.Rd
man/distancetotrap.Rd
man/join.Rd
man/possum.Rd
man/capthist.Rd
man/pdot.Rd
man/print.traps.Rd
man/trim.Rd
man/simpopndetails.Rd
man/rbind.capthist.Rd
man/contour.Rd
man/hornedlizard.Rd
man/make.mask.Rd
man/trap.builder.Rd
man/secr.model.detection.Rd
man/rbind.traps.Rd
man/subset.capthist.Rd
man/verify.Rd
man/RMarkInput.Rd
man/FAQ.Rd
man/mask.Rd
man/deermouse.Rd
man/closedN.Rd
man/predict.secr.Rd
man/ms.Rd
man/circular.Rd
man/reduce.Rd
man/read.telemetry.Rd
man/pointsInPolygon.Rd
man/derivedMS.Rd
man/snip.Rd
man/troubleshooting.Rd
man/detector.Rd
man/model.average.Rd
man/signal.Rd
man/traps.Rd
man/empirical.Rd
man/summary.mask.Rd
man/secr.design.MS.Rd
man/sim.secr.Rd
man/details.Rd
man/deletemaskpoints.Rd
man/covariates.Rd
man/usage.Rd
man/Dsurface.Rd
man/secrtest.Rd
man/secr.make.newdata.Rd
man/sighting.Rd
man/Parallel.Rd
man/homerange.Rd
man/detectfn.Rd
secr documentation built on May 19, 2017, 10:32 p.m.