man-roxygen/covariance_template.R

In colemonnahan/admbtools: Bayesian analyses using ADMB

#' @param model.path The directory path to the folder containing the model.
#' @param cov.user (Numeric matrix) A covariance matrix (in bounded space)
#' to write to file. This matrix will be read in by ADMB and can be used in
#' subsequent calculations.
#' @export
#' @author Cole Monnahan
#' @details The \code{admodel.hes} and \code{admodel.cov} files are written
#' by ADMB during the optimization phase. The Hessian matrix contains the
#' second derivatives evaluated at the maximum likelihood estimates. The
#' inverse of the Hessian is the covariance matrix used to determine
#' standard errors and in the MCMC algorithm. The \code{admodel.hes} file
#' is written even if the matrix is not invertible (not positive definite).
#' @return The \code{write} functions return nothing, but have the side
#' effect of changing ADMB files (including creating a backup of the
#' original). The \code{get} functions return a list of the number of
#' parameters (\code{num.pars}), the covariance or Hessian matrix in
#' unbounded space (\code{cov} or \code{hes}), the hybrid bounded flag
#' (\code{hybrid_bounded_flag}) which controls which bounding functions are
#' used, and the \code{scales}, which are the second derivatives of the
#' bounding functions evaluated at the MLE.