R/TuneSelec.R

In JVAdams/artiFISHal: A Pelagic Fish Community Simulator

#' Tune Midwater Trawl Selectivity
#'
#' Interactive visualization of midwater trawl selectivity curve for aid in
#' tuning selectivity parameters used in \code{\link{AcMtEst}}.
#'
#' @details
#'   Interactive sliders are provided for the four parameters of interest which
#'   are required for defining the midwater trawl selectivity
#'   of the mesh panel zones as a double logistic curve:
#'   \itemize{
#'     \item \code{MtL50Small} the length (in mm) at which small fish have a
#'       50\% probability of being captured by the trawl
#'     \item \code{MtSlopeSmall} the slope at which small fish probability of
#'       capture increases with length
#'     \item \code{MtL50Large} the length (in mm) at which large fish have a
#'       50\% probability of being captured by the trawl
#'     \item \code{MtSlopeLarge} the (absolute value of the) slope at which
#'       large fish probability of capture decreases with length
#'    }
#'
#'   Note that the sliders pop up in a separate R window, which may be hidden if
#'     you click on another window.
#'
#' @export
#' @import
#'   rpanel
#' @seealso
#'   \code{\link{AcMtEst}}, \code{\link{logit2}}
#' @examples
#'
#' \dontrun{
#' TuneSelec()
#' }

TuneSelec <- function() {

  # no idea why, but doesn't seem to work unless this package is attached
  library(rpanel)

  # probability graphing function
  double.draw <- function(panel) {
    y <- logit2(panel$x, panel$L501, panel$SR1, panel$L502, -panel$SR2)
    plot(0, 0, xlim=range(panel$x[y>0.001]), ylim=0:1, type="n", las=1,
      xlab="Fish length  (mm)", ylab="Midwater trawl selectivity")
    abline(v=c(panel$L501, panel$L502), col="gray", lwd=2)
    abline(h=c(0, 0.5, 1), col="gray", lwd=2)
    lines(spline(panel$x, y, 1000), lwd=3)
    panel
  }

  # plot it, with a slider to adjust coeficients of the double logistic function
#  dev.new()
  par(mar=c(4, 4, 1, 1))
  plot(1, 1)
  panel <- rp.control(x=1:2000, L501=10.1, SR1=10.1, L502=200.1, SR2=20.1)
  # draw an initial plot, so user isn't staring at a gray window
  #   before clicking on the slider
  double.draw(panel)
  rp.slider(panel, L501, 0.1, 1000, resolution=0.1, showvalue=T,
    action=double.draw, title=
    "MtL50Small:   length at 50% for small fish                                                                                                                 ")
  rp.slider(panel, SR1, 0.1, 200, resolution=0.1, showvalue=T,
    action=double.draw, title="MtSlopeSmall:   slope for small fish")
  rp.slider(panel, L502, 0.1, 1000, resolution=0.1, showvalue=T,
    action=double.draw, title="MtL50Large:   length at 50% for large fish")
  rp.slider(panel, SR2, 0.1, 200, resolution=0.1, showvalue=T,
    action=double.draw, title="MtSlopeLarge:   slope for large fish")

}