R/brw.R

In ianjonsen/simsmolt: simulate Atlantic salmon smolt migration and detections on acoustic arrays

#' @title biased random walk function
#' 
#' @description utility function not to be called by user
#' 
#' @importFrom CircStats rwrpcauchy
#' @importFrom stats rweibull
#' @importFrom raster extract xyFromCell
#' @export
#' 
brw <- function(n = 1, data, xy = NULL, coa = NULL, dir = NULL, buffer = NULL, rho, a, b, shelf, beta) {
  
  if(is.null(coa) & is.null(dir)) stop("Cannot implement a biased random walk without a centre of attraction or direction")
#  if(!is.null(coa) & !is.null(dir)) stop("Only one of a centre of attraction or direction may be specified, not both")
 
  if (a > 0)
    st <- rweibull(n, a, b)
  else if(a == 0 & b > 0) {
    st <- b
  } else {
    st <- 0
  }
  
  d2l <- extract(data$land, rbind(xy))

  if(d2l > buffer | xy[1] < 300) {
    if(!is.null(coa)) {
      ## bias move step toward centre of attraction
      mu <- atan2(coa[1] - xy[1], coa[2] - xy[2]) 
    } else {
      ## bias move step to a fixed direction
      mu <- dir
    }
    
  } else if (xy[1] >= 300 & !all(xy[1] >= data$sobi.box[1], 
                                 xy[1] <= data$sobi.box[1], 
                                 xy[2] >= data$sobi.box[1], 
                                 xy[2] <= data$sobi.box[1]) & 
             d2l <= buffer) {
    
    ## direct smolt to move eastward & parallel to shore (avoid land) only after passing through most of GoM
    mu <- (extract(data$land_dir, rbind(xy)) + 0.5 * pi) %% (2*pi)
    if(d2l <= 2) {
      mu <- mu + 0.5 * pi %% (2*pi) ## move in opposite direction of land if within 2km
      rho <- 0.95
      }
  } 
  
  phi <- rwrpcauchy(n, mu, rho)
  
  new.xy <- c(xy[1] + sin(phi) * st, xy[2] + cos(phi) * st)
  if(shelf) {
    pv <- c(extract(data$shelf[[1]], rbind(new.xy))[1],
            extract(data$shelf[[2]], rbind(new.xy))[1])
    new.xy <- new.xy + pv * beta
  }
  new.d2l <- extract(data$land, rbind(new.xy))

  ## if new location on land (0) then adjust so it's in water
  if(!is.na(new.d2l) & new.d2l == 0) {
    ## find all nearby cells within 3 km & select the one farthest from land
    cells <- extract(data$land, rbind(new.xy), buffer = 3, cellnumbers = TRUE, df = TRUE)
    cell.max <- cells[cells[, 3] == max(cells[, 3], na.rm = TRUE), 2][1]
    new.xy <- xyFromCell(data$land, cell.max)
    
    return(new.xy)
    
  } else if(is.na(new.d2l)) {
    return(cbind(NA,NA))
    
  } else if(!is.na(new.d2l) & new.d2l > 0) {
    return(new.xy)
  }
  
  
}