admbsecr: SECR models with supplementary location information

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This package allows for the fitting of spatially explicit capture-recapture (SECR) models. In particular, it is focussed on a class of SECR model which makes use of supplementary information which is informative on animal location.

Author
Ben Stevenson <bcs5@st-andrews.ac.uk>, David Borchers <dlb@st-andrews.ac.uk>
Date of publication
2014-06-17 22:16:51
Maintainer
Ben Stevenson <bcs5@st-andrews.ac.uk>
License
GPL
Version
1.0.6
URLs

View on R-Forge

Man pages

admbsecr
Fitting SECR models in ADMB
AIC.admbsecr
Extract AIC from an admbsecr model object
bearings
Calculating bearings between two sets of points
boot.admbsecr
Bootstrapping SECR data
coef.admbsecr
Extract admbsecr model coefficients
confint.admbsecr
Confidence intervals for admbsecr model parameters
convert.capt
Convert capture history object
convert.mask
Convert mask object
convert.pamguard
Create a capture history object from a PAMGuard output file
convert.traps
Convert traps object
create.capt
Creating capture history object.
create.mask
Create mask object
distances
Calculating distances between two sets of points
example
Example data
get.bias
Extracting estimated biases
get.mask
Extracting mask point locations
get.mce
Extracting Monte Carlo error
get.par
Extract estimated or fixed parameter values from an...
get.traps
Extracting trap locations
lightfooti
_Arthroleptella lightfooti_ survey data
locations
Plotting estimated locations
make.acoustic.captures
Assigning ID numbers to sounds.
show.detfn
Plotting a detection function.
show.detsurf
Plotting the detection probability surface
show.survey
Plotting mask and trap layout
sim.capt
Simulating SECR data
stdEr.admbsecr
Extract standard errors from an admbsecr model fit
stdEr.admbsecr.boot
Extract standard errors from a bootstrapped admbsecr model...
summary.admbsecr
Summarising admbsecr model fits
test.admbsecr
Run admbsecr tests
vcov.admbsecr
Extract the variance-covariance matrix from an admbsecr model...
vcov.admbsecr.boot
Extract the variance-covariance matrix from a bootstrapped...

Files in this package

admbsecr/BinaryFiles
admbsecr/DESCRIPTION
admbsecr/NAMESPACE
admbsecr/NEWS
admbsecr/R
admbsecr/R/RcppExports.R
admbsecr/R/admbsecr.r
admbsecr/R/autofuns.r
admbsecr/R/boot.r
admbsecr/R/convert.r
admbsecr/R/detfns.r
admbsecr/R/helpers.r
admbsecr/R/locations.r
admbsecr/R/methods.r
admbsecr/R/simcapt.r
admbsecr/R/surveyplots.r
admbsecr/R/test.r
admbsecr/README.md
admbsecr/data
admbsecr/data/example.RData
admbsecr/data/lightfooti.RData
admbsecr/inst
admbsecr/inst/ADMB
admbsecr/inst/ADMB/bin
admbsecr/inst/ADMB/bin/linux
admbsecr/inst/ADMB/bin/linux/secr
admbsecr/inst/ADMB/bin/linux/secr_new
admbsecr/inst/ADMB/bin/mac
admbsecr/inst/ADMB/bin/mac/secr
admbsecr/inst/ADMB/bin/windows
admbsecr/inst/ADMB/bin/windows/secr.exe
admbsecr/inst/ADMB/src
admbsecr/inst/ADMB/src/densfuns.cpp
admbsecr/inst/ADMB/src/detfuns.cpp
admbsecr/inst/ADMB/src/invlinkfuns.cpp
admbsecr/inst/ADMB/src/secr.tpl
admbsecr/inst/data-simulation.r
admbsecr/inst/testthat
admbsecr/inst/testthat/test-args.r
admbsecr/inst/testthat/test-boot.r
admbsecr/inst/testthat/test-convert.r
admbsecr/inst/testthat/test-detfns.r
admbsecr/inst/testthat/test-errors.r
admbsecr/inst/testthat/test-fits.r
admbsecr/inst/testthat/test-helpers.r
admbsecr/inst/testthat/test-plots.r
admbsecr/inst/testthat/test-simcapt.r
admbsecr/man
admbsecr/man/AIC.admbsecr.Rd
admbsecr/man/admbsecr.Rd
admbsecr/man/bearings.Rd
admbsecr/man/boot.admbsecr.Rd
admbsecr/man/coef.admbsecr.Rd
admbsecr/man/confint.admbsecr.Rd
admbsecr/man/convert.capt.Rd
admbsecr/man/convert.mask.Rd
admbsecr/man/convert.pamguard.Rd
admbsecr/man/convert.traps.Rd
admbsecr/man/create.capt.Rd
admbsecr/man/create.mask.Rd
admbsecr/man/distances.Rd
admbsecr/man/example.Rd
admbsecr/man/get.bias.Rd
admbsecr/man/get.mask.Rd
admbsecr/man/get.mce.Rd
admbsecr/man/get.par.Rd
admbsecr/man/get.traps.Rd
admbsecr/man/lightfooti.Rd
admbsecr/man/locations.Rd
admbsecr/man/make.acoustic.captures.Rd
admbsecr/man/show.detfn.Rd
admbsecr/man/show.detsurf.Rd
admbsecr/man/show.survey.Rd
admbsecr/man/sim.capt.Rd
admbsecr/man/stdEr.admbsecr.Rd
admbsecr/man/stdEr.admbsecr.boot.Rd
admbsecr/man/summary.admbsecr.Rd
admbsecr/man/test.admbsecr.Rd
admbsecr/man/vcov.admbsecr.Rd
admbsecr/man/vcov.admbsecr.boot.Rd
admbsecr/src
admbsecr/src/Makevars
admbsecr/src/Makevars.win
admbsecr/src/RcppExports.cpp
admbsecr/src/funs.cpp