R/atlantisfmsy.R

In rgirardi/atlantisfmsy: Estimation of a functional group's Fmsy in Atlantis ecosystem model

#' atlantisfmsy: Estimate a functional group's Fmsy in Atlantis ecosystem model
#'
#' @description An estimation of a functional group's Fmsy in Atlantis ecosystem
#'   model in R. It iteratively searchs for Fmsy of a specified functional group
#'   in a calibrated Atlantis model. The iterative simulations protocole was
#'   defined by Dr. Elisabeth Fulton (CSIRO) for the IndiSeas project
#'   (\url{http://www.indiseas.org/}, 03/01/2018).
#'
#' @section Methods:
#'   It is designed first to gradualy increase F for a particular functional
#'   group in the model up to the collapse of the stock. Then, it narrows down
#'   the value of Fmsy (in y-1) with a precision of two decimals. To do so, it
#'   copies/pastes all the files necessary to run the calibrated model into a
#'   seperate directory and then modifies the fishing mortality parameter (mFC)
#'   of the selected functinoal group in the harvest parameters file within this
#'   directory before each simulation. A new name is provided for the output
#'   files in the bach/shell file and finally the Atlantis model is run. It
#'   starts at F = 0 , with a step of F = 0.4, until reaching collapse
#'   \strong{(NEED TO BE MODIFY AS B = 0.1*B0)}. Then in the interval containing
#'   FMSY, reduce F-step by 50% progressively until a sufficiently smooth curve
#'   is obtained to enable estimation of FMSY at a precision of 10E-02.For each
#'   simulation allow a burn in time of at least 20 years (depends on the time
#'   that your model needs to stabilize), then run for another 30 years, and
#'   take average of the last 5 years to estimates the yield.
#'   See Atlantis website for more information on the ecosystem model
#'   (\url{https://research.csiro.au/atlantis/}, 03/01/2018).
#'
#' @author Raphael Girardin \email{raphael.girardin@@ifremer.fr}
#'
#' @seealso
#'
#' @docType package
#' @name atlantisfmsy
"_PACKAGE"
#> [1] "_PACKAGE"