secrdesign-package: Spatially Explicit Capture-Recapture Study Design

Description Details Author(s) See Also


Tools to assist the design of spatially explicit capture–recapture studies of animal populations.


Package: secr
Type: Package
Version: 2.5.4
Date: 2017-12-05
License: GNU General Public License Version 2 or later

The primary use of secrdesign is to predict by Monte Carlo simulation the precision or bias of density estimates from different detector layouts, given pilot values for density and the detection parameters lambda0/g0 and sigma.

The simulation functions in secrdesign are:

make.scenarios generate dataframe of parameter values etc.
run.scenarios perform simulations, with or without model fitting
fit.models fit SECR model(s) to rawdata output from run.scenarios
predict.fittedmodels infer `real' parameter estimates from fitted models
select.stats collect output for a particular parameter
summary.selectedstatistics numerical summary of results
plot.selectedstatistics histogram or CI plot for each scenario

Other functions not used exclusively for simulation are:

Enrm expected numbers of individuals n, re-detections r and movements m
minnrRSE approximate RSE(D-hat) given sample size (n, r)
costing compute various cost components
saturation expected detector saturation (trap success)
scenarioSummary applies Enrm, minnrRSE, and other summaries to each scenario in a dataframe
optimalSpacing optimal detector spacing by rule-of-thumb and simulation RSE(D-hat)
scenariosFromStatistics match specified n, r

A vignette documenting the simulation functions is available at secrdesign-vignette.pdf. An Appendix in that vignette has code for various examples that should help get you started.

Documentation for expected counts is in secrdesign-Enrm.pdf. Another vignette secrdesign-tools.pdf demonstrates other tools. These include the optimalSpacing function, for finding the detector spacing that yields the greatest precision for a given detector geometry, number of sampling occasions, density and detection parameters.

Help pages are also available as ../doc/secrdesign-manual.pdf.


Murray Efford [email protected]

See Also

make.grid, sim.popn, sim.capthist,

secrdesign documentation built on Dec. 5, 2017, 1:02 a.m.