R/drawTracks.R

In ABindoff/TwilightFree: Reconstruct animal tracks from GLS tag data

#' Plot tracks with map
#' @param gls a trip object returned from `trip()` with `Lon` and `Lat` columns in time order at minimum
#' @param gps optional data.frame of reference data with `Lon` and `Lat` columns in time order
#' @param col line colour for trip
#' @param gps.col line colour for gps
#' @param point.cols optional gradient colours for points, NULL if points not required
#' @param main optional title
#' @param pacific TRUE if map uses Pacific-centred co-ordinates
#' @export
#' @import maptools
#' @import polyclip
#' @importFrom viridisLite viridis
#' @importFrom graphics abline par points
#' @importFrom utils data
drawTracks <- function(gls,
                       gps = NULL,
                       point.cols = TRUE,
                       line.col = "grey60",
                       main = "",
                       pacific = F){
  xlm <- range(c(gls$Lon, gps$Lon))
  ylm <- range(c(gls$Lat, gps$Lat))
  data(wrld_simpl, package = "maptools", envir = environment())

  if(pacific){
    wrld_simpl <- nowrapRecenter(wrld_simpl, avoidGEOS = TRUE)}
  plot(wrld_simpl,xlim=xlm,ylim=ylm,
       col="grey90",border="grey80", main = main, axes = T)
  xlm <- par()$usr[1:2]
  ylm <- par()$usr[3:4]
  border <- cbind(c(xlm[1], xlm[2], xlm[2], xlm[1], xlm[1]),
                  c(ylm[1], ylm[1], ylm[2], ylm[2], ylm[1]))
  lines(border, col = "black")

  if(point.cols){
    points(cbind(jitter(gls$Lon), jitter(gls$Lat)), col = viridisLite::viridis(nrow(gls), end = 0.95))}

  if(!is.null(gps)){
    d <- nrow(gls)
    for (i in c(seq(d, nrow(gps), by = d),nrow(gps))){
      lines(cbind(gps$Lon[(i-d+1):i], gps$Lat[(i-d+1):i]), col = viridisLite::viridis(nrow(gps)/d, end = 0.95)[i/d])
    }}

  lines(cbind(gls$Lon, gls$Lat), col = line.col)

}