MapData.r

#' Plot tows on a map. This function produces a plot (originally designed by John Wallace) showing tows in strata by depth and latitude. If a folder name is given a plot called TowMap.jpg is created.
#'
#' @param Data The data frame storing raw tow data
#' @param strata.limits A file (e.g. defaultLimits.csv), indicating an alphabetic character for each strata (A, B, C, ...), as well as the depth and latitude ranges for each stratum.
#' @param SA A flat data file, with area ID, min / max depth, min / max latitude, and the area of each strata in hectares.
#' @param FileName The name of the output file -- this will be species and model specific. Defaults to 'TowMap.jpg'
#' @param Folder Where the output is stored
#'
#' @import grDevices
#' @export
#'
MapData <- function(Data, strata.limits, SA = SA3, FileName = "TowMap.jpg", Folder = NULL) {

  # Distilled from line 426-539 of "Survey.Biomass.GlmmBUGS.ver.3.00.R" from John Wallace's code

  if (!is.null(Folder)) {
    jpeg(filename = paste(Folder, FileName, sep = ""), width = 8, height = 8, res = 200, units = "in")
  }

  # Draw box
  plot(c(-55, -1280), c(32, 50.5), xlab = "Depth (m)", ylab = "Latitude", xlim = c(-1280, -55), ylim = c(32, 49), type = "n")
  abline(v = -unique(c(SA$MIN_DEPTH_M, SA$MAX_DEPTH_M)), h = unique(c(SA$MIN_LAT_DD, SA$MAX_LAT_DD)), col = "grey78")
  abline(h = 34.5, v = -c(30, 100, 300, 700) * 1.8288, col = "red")

  # Draw centroid of bins
  avelat <- apply(cbind(SA$MIN_LAT_DD, SA$MAX_LAT_DD), 1, mean)
  avedep <- apply(cbind(SA$MIN_DEPTH_M, SA$MAX_DEPTH_M), 1, mean)
  points(-avedep, avelat, cex = 0.5)

  # Label areas
  text(-1235, 34.7, "Starting in 2004 NWFSC survey sampling density changes at Pt. Conception (34.5)", adj = 0, col = "red")
  text(-1235, 49.25, "INPFC Areas", adj = 0, col = "blue")
  abline(h = c(32, 36, 40.5, 43, 47.5), col = "blue")
  text(-1235, 33.25, "Conception", adj = 0, col = "blue")
  text(-1235, 38.25, "Monterey", adj = 0, col = "blue")
  text(-1235, 41.75, "Eureka", adj = 0, col = "blue")
  text(-1235, 44.5, "Columbia", adj = 0, col = "blue")
  text(-1235, 48.25, "Vancouver", adj = 0, col = "blue")

  # Plot strata
  S <- strata.limits
  for (i in 1:nrow(S)) {
    polygon(-c(S$MinDepth[i], S$MaxDepth[i], S$MaxDepth[i], S$MinDepth[i]), c(S$SLat[i], S$SLat[i], S$NLat[i], S$NLat[i]), col = rainbow(nrow(S), alpha = 0.3)[i])
    text(-mean(c(S$MinDepth[i], S$MaxDepth[i])), mean(c(S$SLat[i], S$NLat[i])), S$STRATA[i], cex = 1.2)
  }

  # Plot Absence tows
  points(-Data$BEST_DEPTH_M[Data$HAUL_WT_KG == 0], Data$BEST_LAT_DD[Data$HAUL_WT_KG == 0], pch = 16, cex = 0.5, col = rgb(red = 1, 0, 0, alpha = 0.2))

  # Plot presence tows by year
  DataPos <- Data[Data$HAUL_WT_KG > 0 & !is.na(Data$HAUL_WT_KG), ] # Temp Sp.pos - redefined below
  CU <- c("black", "green", "blue", "cyan", "purple", "grey", "orange", "hotpink", "brown", "darkolivegreen2", "darkslategrey", "deepskyblue1", "violet", "cyan", "magenta", "lightsalmon", "gold")
  for (i in 1:length(unique(DataPos$PROJECT_CYCLE))) {
    Which <- which(DataPos$PROJECT_CYCLE == unique(DataPos$PROJECT_CYCLE)[i])
    points(-DataPos$BEST_DEPTH_M[Which], DataPos$BEST_LAT_DD[Which], pch = 16, cex = 0.5, col = CU[i])
  }

  if (!is.null(Folder)) {
    dev.off()
  }
}