R/countCells.R

In gunpowder78/pathtrackr: Video Tracking and Analysis of Animal Movement

#' Overlay a grid and count cell crossings
#'
#' This function overlays a grid on the track generated by the \code{trackPath} function and counts the number of cells crossed by the animal. It is useful for returning count and proportional data abount an animal's path.
#' @param path.list a list object created by the \code{trackPath} function
#' @param xgrid an integer specifying the number of grid cells the arena should be divided into along its width
#' @param ygrid an integer specifying the number of grid cells the arena should be divided into along its height
#' @return If assigned to an object, a list containing the number of cells crossed and the proportion of total cells crossed; if not assigned to an object, a message in the console is returned.
#' @importFrom marmap diag.bathy
#' @export
countCells = function(path.list, xgrid, ygrid) {

  grid.matrix = matrix(ncol = 2, nrow = (xgrid * ygrid))
  colnames(grid.matrix) = c("x", "y")
  grid.matrix[, 1] = rep(seq(from = (path.list$dim.pix[1]/xgrid)/2, to = path.list$dim.pix[1] - (path.list$dim.pix[1]/xgrid)/2, by = path.list$dim.pix[1]/xgrid), times = ygrid)
  grid.matrix[, 2] = rep(seq(from = (path.list$dim.pix[2]/ygrid)/2, to = path.list$dim.pix[2] - (path.list$dim.pix[2]/ygrid)/2, by = path.list$dim.pix[2]/ygrid), each = xgrid)

  xtrack = c()
  ytrack = c()
  dat = na.lomf(path.list$position)

  for (i in 2:length(path.list$position[,1])) {

    track = matrix(ncol = length(round(dat[,1][i - 1]):round(dat[,1][i])), nrow = length(round(dat[,2][i - 1]):round(dat[,2][i])))
    colnames(track) = round(dat[,1][i - 1]):round(dat[,1][i])
    rownames(track) = round(dat[,2][i - 1]):round(dat[,2][i])
    diag.bathy(track, coord = T)

    xtrack = append(xtrack, diag.bathy(track, coord = T)[,2])
    ytrack = append(ytrack, diag.bathy(track, coord = T)[,1])
  }

  cells = c()
  cells.cross = c()

  for (j in 1:length(xtrack)) {

    for (k in 1:nrow(grid.matrix)) {
      A = abs(xtrack[j] - grid.matrix[k, 1])
      B = abs(ytrack[j] - grid.matrix[k, 2])
      cells[k] = sqrt((A^2) + (B^2))
    }
    cells.cross[j] = which(cells == min(cells))[1]
  }

  message(paste("The animal crossed a total of ", length(unique(cells.cross)), "  unique grid cells (", round((length(unique(cells.cross))/(xgrid * ygrid)) * 100), "% of total grid cells)", sep = ""))
  flush.console()

  invisible(list(cell.count = length(unique(cells.cross)), proportion.cells = length(unique(cells.cross))/(xgrid * ygrid)))

}