\name{secrdesign-package}
\alias{secrdesign-package}
\alias{secrdesign}

\docType{package}

\title{Spatially Explicit Capture--Recapture Study Design }

\description{
Tools to assist the design of spatially explicit capture--recapture studies of animal populations.
}

\details{
\tabular{ll}{
Package: \tab secr\cr
Type: \tab Package\cr
Version: \tab 2.5.1\cr
Date: \tab 2017-10-09\cr
License: \tab GNU General Public License Version 2 or later\cr
}

The primary use of \pkg{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 \pkg{secrdesign} are:
\tabular{ll}{
  \code{\link{make.scenarios}} \tab generate dataframe of parameter values etc. \cr
  \code{\link{run.scenarios}} \tab perform simulations, with or without model fitting \cr
  \code{\link{fit.models}} \tab fit SECR model(s) to rawdata output from \code{run.scenarios} \cr
  \code{\link{predict.fittedmodels}} \tab infer `real' parameter
  estimates from fitted models \cr
  \code{\link{select.stats}} \tab collect output for a particular
  parameter \cr
  \code{\link{summary.selectedstatistics}} \tab numerical summary of results \cr 
  \code{\link{plot.selectedstatistics}} \tab histogram or CI plot for
  each scenario \cr 
}

Documentation for simulation functions is provided in a vignette \url{../doc/secrdesign-vignette.pdf}. An Appendix has code for various examples that should help get you started. 

Other functions not used exclusively for simulation are:
\tabular{ll}{
  \code{\link{Enrm}} \tab expected numbers of individuals \eqn{n}, re-detections \eqn{r} and movements \eqn{m} \cr
  \code{\link{minnrRSE}} \tab approximate RSE(D-hat) given sample size (\eqn{n}, \eqn{r}) \cr
  \code{\link{costing}} \tab compute various cost components \cr
  \code{\link{scenarioSummary}} \tab applies \code{Enrm}, \code{minnrRSE}, and other summaries to each scenario in a dataframe \cr
  \code{\link{optimalSpacing}} \tab optimal detector spacing by rule-of-thumb and simulation RSE(D-hat)\cr
  \code{\link{scenariosFromStatistics}} \tab match specified \eqn{n}, \eqn{r} \cr
}

Documentation for expected counts is in \url{../doc/secrdesign-Enrm.pdf}. Another vignette \url{../doc/secrdesign-tools.pdf} demonstrates other tools. These include the \code{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 \url{../doc/secrdesign-manual.pdf}.

}

\seealso{

\code{\link{make.grid}}, \code{\link[secr]{sim.popn}}, \code{\link[secr]{sim.capthist}},  \code{\link[secr]{secr.fit}}
 
}

\author{ Murray Efford \email{murray.efford@otago.ac.nz} }

\keyword{ package }
