A B C D E F H I J L M N O P R S T U V W X
secr-package | Spatially Explicit Capture-Recapture Models |
addCovariates | Add Covariates to Mask or Traps |
addTelemetry | Combine Telemetry and Detection Data |
AIC.secr | Compare SECR Models |
AIC.secrlist | Compare SECR Models |
alive | Dissect Spatial Capture History Object |
alongtransect | Dissect Spatial Capture History Object |
animalID | Dissect Spatial Capture History Object |
ARL | Home Range Statistics |
attenuationplot | Plot Detection Functions |
autoini | Initial Parameter Values for SECR |
bias.D | Mask Buffer Width |
binomN | Spatially Explicit Capture-Recapture |
buffer.contour | Contour Detection Probability |
captdata | SECR Models Fitted to Demonstration Data |
capthist | Spatial Capture History Object |
captXY | SECR Models Fitted to Demonstration Data |
circular.p | Circular Probability |
circular.r | Circular Probability |
clip.hex | Build Detector Array on Triangular or Hexagonal Grid |
closedN | Closed population estimates |
closure.test | Closure tests |
cluster | Detector Clustering |
cluster.centres | Complex Detector Layouts |
cluster.counts | Complex Detector Layouts |
clusterID | Detector Clustering |
clusterID<- | Detector Clustering |
clustertrap | Detector Clustering |
clustertrap<- | Detector Clustering |
coef.secr | Coefficients of secr Object |
collate | Averaging of SECR Models Using Akaike's Information Criterion |
confint.secr | Profile Likelihood Confidence Intervals |
Coulombe | House mouse live trapping data |
count | Detector Type |
counts | Summarise Detections |
covariates | Covariates Attribute |
covariates<- | Covariates Attribute |
D.designdata | Construct Density Design Data |
dbar | Home Range Statistics |
deermouse | Deermouse Live-trapping Datasets |
deermouse.ESG | Deermouse Live-trapping Datasets |
deermouse.WSG | Deermouse Live-trapping Datasets |
derived | Derived Parameters of Fitted SECR Model |
derived.cluster | Empirical Variance of H-T Density Estimate |
derived.external | Empirical Variance of H-T Density Estimate |
derived.mash | Empirical Variance of H-T Density Estimate |
derived.nj | Empirical Variance of H-T Density Estimate |
derived.session | Empirical Variance of H-T Density Estimate |
details | Detail Specification for secr.fit |
detectfn | Detection Functions |
detectfnplot | Plot Detection Functions |
Detection functions | Detection Functions |
detector | Detector Type |
detector<- | Detector Type |
detectpar | SECR Model Predictions |
deviance | Deviance of fitted secr model and residual degrees of freedom |
deviance.secr | Deviance of fitted secr model and residual degrees of freedom |
df.residual | Deviance of fitted secr model and residual degrees of freedom |
df.residual.secr | Deviance of fitted secr model and residual degrees of freedom |
distancetotrap | Distance To Nearest Detector |
Dsurface | Density Surfaces |
effort | Detector Usage |
ellipse.secr | Confidence ellipse |
empirical.varD | Empirical Variance of H-T Density Estimate |
esa | Derived Parameters of Fitted SECR Model |
esa.plot | Mask Buffer Diagnostic Plot |
esa.plot.secr | Mask Buffer Diagnostic Plot (internal) |
ESG.0 | Deermouse Live-trapping Datasets |
ESG.b | Deermouse Live-trapping Datasets |
ESG.h2 | Deermouse Live-trapping Datasets |
ESG.t | Deermouse Live-trapping Datasets |
expected.n | Expected Number of Individuals |
FAQ | Frequently Asked Questions, And Others |
flip | Transform Point Array |
flip.popn | Transform Point Array |
flip.traps | Transform Point Array |
fxi | Probability Density of Home Range Centre |
fxi.contour | Probability Density of Home Range Centre |
fxi.mode | Probability Density of Home Range Centre |
fxi.secr | Probability Density of Home Range Centre |
head.capthist | First or Last Part of an Object |
head.Dsurface | First or Last Part of an Object |
head.mask | First or Last Part of an Object |
head.traps | First or Last Part of an Object |
hornedlizard | Flat-tailed Horned Lizard Dataset |
hornedlizardCH | Flat-tailed Horned Lizard Dataset |
housemouse | House mouse live trapping data |
housemouse.0 | House mouse live trapping data |
housemouse.ampm | House mouse live trapping data |
housemouse.ampmh2h2 | House mouse live trapping data |
infraCH | Skink Pitfall Data |
invlogit | Logit Transformation |
ip.secr | Spatially Explicit Capture-Recapture by Inverse Prediction |
join | Combine or Split Sessions of capthist Object |
lineoCH | Skink Pitfall Data |
LLsurface.secr | Plot likelihood surface |
logit | Logit Transformation |
logLik.secr | Compare SECR Models |
logmultinom | Multinomial Coefficient of SECR Likelihood |
LR.test | Likelihood Ratio Test |
LStraps | Skink Pitfall Data |
make.capthist | Construct capthist Object |
make.circle | Build Detector Array |
make.grid | Build Detector Array |
make.lookup | Construct Detection Model Design Matrices and Lookups |
make.mask | Build Habitat Mask |
make.poly | Build Detector Array |
make.systematic | Construct Systematic Detector Design |
make.telemetry | Build Detector Array |
make.transect | Build Detector Array |
make.tri | Build Detector Array on Triangular or Hexagonal Grid |
mash | Complex Detector Layouts |
mask | Mask Object |
mask.check | Mask Diagnostics |
MMDM | Home Range Statistics |
model.average | Averaging of SECR Models Using Akaike's Information Criterion |
morning.0 | House mouse live trapping data |
morning.0h2 | House mouse live trapping data |
morning.b | House mouse live trapping data |
morning.h2 | House mouse live trapping data |
morning.h2h2 | House mouse live trapping data |
morning.t | House mouse live trapping data |
moves | Home Range Statistics |
ms | Multi-session Objects |
MS.capthist | Combine capthist Objects |
ms.default | Multi-session Objects |
ms.mask | Multi-session Objects |
ms.secr | Multi-session Objects |
multi | Detector Type |
Multi-core processing | Multi-core Processing |
ncores | Multi-core Processing |
nearesttrap | Distance To Nearest Detector |
noise | Dissect Spatial Capture History Object |
noise<- | Dissect Spatial Capture History Object |
occasion | Dissect Spatial Capture History Object |
ovenbird | Ovenbird Mist-netting Dataset |
ovenbird.model.1 | Ovenbird Mist-netting Dataset |
ovenbird.model.1b | Ovenbird Mist-netting Dataset |
ovenbird.model.1T | Ovenbird Mist-netting Dataset |
ovenbird.model.D | Ovenbird Mist-netting Dataset |
ovenbird.model.h2 | Ovenbird Mist-netting Dataset |
ovenCH | Ovenbird Mist-netting Dataset |
ovenmask | Ovenbird Mist-netting Dataset |
ovensong | Ovenbird Acoustic Dataset |
ovensong.model.1 | Ovenbird Acoustic Dataset |
ovensong.model.2 | Ovenbird Acoustic Dataset |
Parallel | Multi-core Processing |
pdot | Net Detection Probability |
pdot.contour | Contour Detection Probability |
pfn | Spatially Explicit Capture-Recapture by Inverse Prediction |
plot.capthist | Plot Detection Histories |
plot.Dsurface | Plot Habitat Mask or Density Surface |
plot.mask | Plot Habitat Mask or Density Surface |
plot.popn | Plot popn Object |
plot.secr | Plot Detection Functions |
plot.secrlist | Plot Detection Functions |
plot.traps | Plot traps Object |
pointsInPolygon | Points Inside Polygon |
polyarea | Area of Polygon(s) |
polygon | Detector Type |
polygonX | Detector Type |
polyID | Detector Attributes |
polyID<- | Detector Attributes |
popn | Population Object |
population size | Population Size |
possum | Brushtail Possum Trapping Dataset |
possum.model.0 | Brushtail Possum Trapping Dataset |
possum.model.b | Brushtail Possum Trapping Dataset |
possum.model.Dh2 | Brushtail Possum Trapping Dataset |
possum.model.Dsh2 | Brushtail Possum Trapping Dataset |
possum.model.h2 | Brushtail Possum Trapping Dataset |
possumarea | Brushtail Possum Trapping Dataset |
possumCH | Brushtail Possum Trapping Dataset |
possummask | Brushtail Possum Trapping Dataset |
possumremovalarea | Brushtail Possum Trapping Dataset |
predict.secr | SECR Model Predictions |
predict.secrlist | SECR Model Predictions |
predictDsurface | Predict Density Surface |
print.capthist | Print Detections |
print.Dsurface | Density Surfaces |
print.secr | Print secr Object |
print.summary.capthist | Summarise Detections |
print.summary.mask | Summarise Habitat Mask |
print.summary.traps | Summarise Detector Array |
print.traps | Print Detectors |
proximity | Detector Type |
randomHabitat | Random Landscape |
rbind.capthist | Combine capthist Objects |
rbind.mask | Subset Mask Object |
rbind.popn | Combine popn Objects |
rbind.traps | Combine traps Objects |
read.capthist | Import or export data |
read.DA | Convert Data To Or From BUGS Format |
read.mask | Read Habitat Mask From File |
read.SPACECAP | Exchange data with SPACECAP package |
read.traps | Read Detector Data From File |
rectangularMask | Rectangular Mask |
reduce | Combine Columns |
reduce.capthist | Combine Occasions Or Detectors |
reduce.default | Combine Columns |
reduce.traps | Combine Occasions Or Detectors |
region.N | Population Size |
RMarkInput | Convert Data to RMark Input Format |
rotate | Transform Point Array |
rotate.popn | Transform Point Array |
rotate.traps | Transform Point Array |
RPSV | Home Range Statistics |
score.table | Score Test for SECR Models |
score.test | Score Test for SECR Models |
searcharea | Detector Attributes |
secr | Spatially Explicit Capture-Recapture Models |
secr density models | Density Models |
secr detection models | Models for Detection Parameters |
secr models | Spatially Explicit Capture-Recapture Models |
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 | Spatially Explicit Capture-Recapture Models |
secr.model.density | Density Models |
secr.model.detection | Models for Detection Parameters |
secrdemo | SECR Models Fitted to Demonstration Data |
secrdemo.0 | SECR Models Fitted to Demonstration Data |
secrdemo.b | SECR Models Fitted to Demonstration Data |
secrdemo.CL | SECR Models Fitted to Demonstration Data |
secrlist | Compare SECR Models |
session | Session Vector |
session<- | Session Vector |
shift | Transform Point Array |
shift.popn | Transform Point Array |
shift.traps | Transform Point Array |
signal | Dissect Spatial Capture History Object |
signal<- | Dissect Spatial Capture History Object |
signalCH | Ovenbird Acoustic Dataset |
signalframe | Dissect Spatial Capture History Object |
signalframe<- | Dissect Spatial Capture History Object |
signalmatrix | Reformat Signal Data |
sim.capthist | Simulate Detection Histories |
sim.popn | Simulate 2-D Population |
sim.resight | Simulate Detection Histories |
sim.secr | Simulate From Fitted secr Model |
simulate | Simulate From Fitted secr Model |
simulate.secr | Simulate From Fitted secr Model |
single | Detector Type |
skink | Skink Pitfall Data |
snip | Slice Transect Into Shorter Sections |
sort.capthist | Sort Rows of capthist Object |
spacing | Detector or Mask Spacing |
spacing.mask | Detector or Mask Spacing |
spacing.traps | Detector or Mask Spacing |
spacing<- | Detector or Mask Spacing |
speed | Speed Tips |
Speed tips | Speed Tips |
split.capthist | Subset or Split capthist Object |
split.traps | Subset traps Object |
spotHeight | Plot Habitat Mask or Density Surface |
stoat.model.EX | Stoat DNA Data |
stoat.model.HN | Stoat DNA Data |
stoat.model.HZ | Stoat DNA Data |
stoatCH | Stoat DNA Data |
stoatDNA | Stoat DNA Data |
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.Dsurface | Density Surfaces |
summary.mask | Summarise Habitat Mask |
summary.traps | Summarise Detector Array |
tail.capthist | First or Last Part of an Object |
tail.Dsurface | First or Last Part of an Object |
tail.mask | First or Last Part of an Object |
tail.traps | First or Last Part of an Object |
tile | Simulate 2-D Population |
timevaryingcov | Time-varying Detector Covariates |
timevaryingcov<- | Time-varying Detector Covariates |
transect | Detector Type |
transectID | Detector Attributes |
transectID<- | Detector Attributes |
transectlength | Detector Attributes |
transectX | Detector Type |
transformations | Transform Point Array |
trap | Dissect Spatial Capture History Object |
trap.builder | Complex Detector Layouts |
traps | Detector Array |
traps object | Detector Array |
traps<- | Detector Array |
trapXY | SECR Models Fitted to Demonstration Data |
trim | Drop Unwanted List Components |
trim.default | Drop Unwanted List Components |
trim.secr | Drop Unwanted List Components |
Troubleshooting | Problems in Fitting SECR Models |
unjoin | Combine or Split Sessions of capthist Object |
unRMarkInput | Convert Data to RMark Input Format |
usage | Detector Usage |
usage<- | Detector Usage |
usagePlot | Plot Usage |
vcov.secr | Variance - Covariance Matrix of SECR Parameters |
verify | Check SECR Data |
verify.capthist | Check SECR Data |
verify.default | Check SECR Data |
verify.mask | Check SECR Data |
verify.traps | Check SECR Data |
write.capthist | Import or export data |
write.captures | Write Data to Text File |
write.DA | Convert Data To Or From BUGS Format |
write.SPACECAP | Exchange data with SPACECAP package |
write.traps | Write Data to Text File |
writeGPS | Upload to GPS |
WSG.0 | Deermouse Live-trapping Datasets |
WSG.b | Deermouse Live-trapping Datasets |
WSG.h2 | Deermouse Live-trapping Datasets |
WSG.t | Deermouse Live-trapping Datasets |
xy | Dissect Spatial Capture History Object |
xy<- | Dissect Spatial Capture History Object |