admbsecr: SECR models with supplementary location information
Version 1.0.6

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.

AuthorBen Stevenson <bcs5@st-andrews.ac.uk>, David Borchers <dlb@st-andrews.ac.uk>
Date of publication2014-06-17 22:16:51
MaintainerBen Stevenson <bcs5@st-andrews.ac.uk>
LicenseGPL
Version1.0.6
URL https://github.com/b-steve/admbsecr
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("admbsecr", repos="http://R-Forge.R-project.org")

Getting started

README.md

Popular man pages

bearings: Calculating bearings between two sets of points
boot.admbsecr: Bootstrapping SECR data
coef.admbsecr: Extract admbsecr model coefficients
convert.traps: Convert traps object
create.capt: Creating capture history object.
locations: Plotting estimated locations
show.detfn: Plotting a detection function.
See all...

All man pages Function index File listing

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...

Functions

AIC.admbsecr Man page Source code
admbsecr Man page Source code
animalIDvec Source code
autoD Source code
autoalpha Source code
autob0.ss Source code
autob1.ss Source code
autog0 Source code
autokappa Source code
autoscale Source code
autoshape Source code
autosigma Source code
autosigma.ss Source code
autosigma.toa Source code
autoz Source code
bearing.density Source code
bearings Man page Source code
boot.admbsecr Man page Source code
calc.cis Source code
calc.detfn Source code
calc.hn Source code
calc.hr Source code
calc.log.ss Source code
calc.lth Source code
calc.ss Source code
calc.th Source code
circles Source code
coef.admbsecr Man page Source code
coef.admbsecr.boot Man page Source code
confint.admbsecr Man page Source code
confint.admbsecr.boot Man page Source code
convert.capt Man page Source code
convert.mask Man page Source code
convert.pamguard Man page Source code
convert.traps Man page Source code
create.capt Man page Source code
create.mask Man page Source code
dist.density Source code
distances Man page Source code
erf Source code
example Man page
find_local Source code
get.bias Man page Source code
get.detfn Source code
get.mask Man page Source code
get.mce Man page Source code
get.par Man page Source code
get.traps Man page Source code
inv.logit Source code
inv.scaled.logit.link Source code
lightfooti Man page
locations Man page Source code
log.link Source code
logit.link Source code
make.acoustic.captures Man page Source code
make_toa_ssq Source code
p.dot Source code
print.summary.admbsecr Source code
read.admbsecr Source code
scaled.log.link Source code
scaled.logit.link Source code
show.arrows Source code
show.circles Source code
show.contour Source code
show.detfn Man page Source code
show.detsurf Man page Source code
show.survey Man page Source code
sim.capt Man page Source code
ss.density Source code
stdEr.admbsecr Man page Source code
stdEr.admbsecr.boot Man page Source code
summary.admbsecr Man page Source code
test.admbsecr Man page Source code
toa.density Source code
trapvec Source code
vcov.admbsecr Man page Source code
vcov.admbsecr.boot Man page Source code

Files

BinaryFiles
DESCRIPTION
NAMESPACE
NEWS
R
R/RcppExports.R
R/admbsecr.r
R/autofuns.r
R/boot.r
R/convert.r
R/detfns.r
R/helpers.r
R/locations.r
R/methods.r
R/simcapt.r
R/surveyplots.r
R/test.r
README.md
data
data/example.RData
data/lightfooti.RData
inst
inst/ADMB
inst/ADMB/bin
inst/ADMB/bin/linux
inst/ADMB/bin/linux/secr
inst/ADMB/bin/linux/secr_new
inst/ADMB/bin/mac
inst/ADMB/bin/mac/secr
inst/ADMB/bin/windows
inst/ADMB/bin/windows/secr.exe
inst/ADMB/src
inst/ADMB/src/densfuns.cpp
inst/ADMB/src/detfuns.cpp
inst/ADMB/src/invlinkfuns.cpp
inst/ADMB/src/secr.tpl
inst/data-simulation.r
inst/testthat
inst/testthat/test-args.r
inst/testthat/test-boot.r
inst/testthat/test-convert.r
inst/testthat/test-detfns.r
inst/testthat/test-errors.r
inst/testthat/test-fits.r
inst/testthat/test-helpers.r
inst/testthat/test-plots.r
inst/testthat/test-simcapt.r
man
man/AIC.admbsecr.Rd
man/admbsecr.Rd
man/bearings.Rd
man/boot.admbsecr.Rd
man/coef.admbsecr.Rd
man/confint.admbsecr.Rd
man/convert.capt.Rd
man/convert.mask.Rd
man/convert.pamguard.Rd
man/convert.traps.Rd
man/create.capt.Rd
man/create.mask.Rd
man/distances.Rd
man/example.Rd
man/get.bias.Rd
man/get.mask.Rd
man/get.mce.Rd
man/get.par.Rd
man/get.traps.Rd
man/lightfooti.Rd
man/locations.Rd
man/make.acoustic.captures.Rd
man/show.detfn.Rd
man/show.detsurf.Rd
man/show.survey.Rd
man/sim.capt.Rd
man/stdEr.admbsecr.Rd
man/stdEr.admbsecr.boot.Rd
man/summary.admbsecr.Rd
man/test.admbsecr.Rd
man/vcov.admbsecr.Rd
man/vcov.admbsecr.boot.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/funs.cpp
admbsecr documentation built on May 21, 2017, 1:17 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.