Tools to assist the design of spatially explicit capture--recapture studies of animal populations.
| Package: | secr |
| Type: | Package |
| Version: | 2.5.5 |
| Date: | 2018-12-07 |
| 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.