R/res_custom_sk_map.R

In SWMPrExtension: Functions for Analyzing and Plotting Estuary Monitoring Data

#' Local Reserve Map With Seasonal Kendall Results for Custom Stations
#'
#' Create a stylized reserve-level map of seasonal kendall results from custom
#' station locations for use with the reserve level reporting template
#'
#' @param stations chr string of the reserve stations to include in the map
#' @param x_loc num vector of x coordinates for \code{stations}. East longitudes
#'   must be negative.
#' @param y_loc num vector of y coordinates for \code{stations}
#' @param sk_result vector of values denoting direction and significance of
#'   seasonal kendall results. Result should be c('inc', 'dec', 'insig') for
#'   sig. negative, no sig. results, and sig. positive result
#' @param bbox a bounding box associated with the reserve. Must be in the format
#'   of c(X1, Y1, X2, Y2)
#' @param shp {sf} data frame (preferred) or SpatialPolygons object
#' @param station_labs logical, should stations be labeled? Defaults to
#'   \code{TRUE}
#' @param lab_loc chr vector of 'R' and 'L', one letter for each station. if no
#'   \code{lab_loc} is specified then labels will default to the left.
#' @param bg_map a georeferenced \code{ggmap} or \code{ggplot} object used as a
#'   background map, generally provided by a call to \code{\link{base_map}}. If
#'   \code{bg_map} is specified, \code{maptype} and \code{zoom} are ignored.
#' @param maptype Background map type from Stamen Maps
#'   (\url{http://maps.stamen.com/}); one of c("terrain", "terrain-background",
#'   "terrain-labels", "terrain-lines", "toner", "toner-2010", "toner-2011",
#'   "toner-background", "toner-hybrid", "toner-labels", "toner-lines",
#'   "toner-lite", "watercolor").
#' @param zoom Zoom level for the base map created when \code{bg_map} is not
#'   specified.  An integer value, 5 - 15, with higher numbers providing  more
#'   detail.  If not provided, a zoom level is autoscaled based on \code{bbox}
#'   parameters.
#'
#' @importFrom magrittr "%>%"
#' @importFrom methods as
#' @importFrom rlang .data
#' @importFrom sf st_as_sf st_bbox st_crs st_transform
#' @importFrom utils download.file unzip
#'
#' @export
#'
#' @details Creates a stylized, reserve-level base map for displaying seasonal
#'   kendall results from \code{\link{sk_seasonal}}. The user can specify the
#'   reserve and stations to plot. The user can also specify a bounding box. For
#'   multi-component reserves, the user should specify a bounding box that
#'   highlights the component of interest.
#'
#'   To display seasonal trends, the user must specify \code{c('inc', 'dec',
#'   'insig', 'insuff')} for each station listed in the \code{stations}
#'   argument.
#'
#'
#'
#' @author Julie Padilla, Dave Eslinger
#'
#' @concept analyze
#'
#' @return returns a {ggplot} object
#'
#' @examples
#' ### set plotting parameters
#' stns <- c('Stn 1', 'Stn 2')
#' x_coords <- c(-121.735281, -121.750369)
#' y_coords <- c(36.850377, 36.806667)
#' shp_fl <- elk_spatial
#' bounding_elk <- c(-121.8005, 36.7779, -121.6966, 36.8799)
#' lab_dir <- c('R', 'L')
#' trnds <- c('inc', 'dec')
#'
#' ### Low zoom and default maptype plot (for CRAN testing, not recommended)
#' #    Lower zoom number gives coarser text and fewer features
#' (x_low <- res_custom_sk_map(stations = stns, x_loc = x_coords,
#'                   sk_result = trnds, y_loc = y_coords,
#'                   bbox = bounding_elk, lab_loc = lab_dir,
#'                   shp = shp_fl, zoom = 10))
#' \donttest{
#' ### Default zoom and maptype plot
#' x_def <- res_custom_sk_map(stations = stns, x_loc = x_coords,
#'                   sk_result = trnds, y_loc = y_coords,
#'                   bbox = bounding_elk, lab_loc = lab_dir,
#'                   shp = shp_fl)
#'
#' ### Higher zoom number gives more details, but may not be visible
#' x_14 <- res_custom_sk_map(stations = stns, x_loc = x_coords,
#'                   sk_result = trnds, y_loc = y_coords,
#'                   bbox = bounding_elk, lab_loc = lab_dir,
#'                   shp = shp_fl, zoom = 14)
#'
#'
#' ### Different maptypes may be used.  All may not be available.
#' #   Note that zoom and maptype interact, so some experimentation may be
#' #   required.
#' x_terrain <- res_custom_sk_map(stations = stns, x_loc = x_coords,
#'                   sk_result = trnds, y_loc = y_coords,
#'                   bbox = bounding_elk, lab_loc = lab_dir,
#'                   shp = shp_fl, maptype = 'terrain')
#' }

res_custom_sk_map <- function(stations
                              , x_loc
                              , y_loc
                              , sk_result = NULL
                              , bbox
                              , shp
                              , station_labs = TRUE
                              , lab_loc = NULL
                              , bg_map = NULL
                              , zoom = NULL
                              , maptype = "toner-lite") {

  # define local variables  to remove `check()` warnings
  abbrev <- lab_long <- lab_lat  <- Longitude <- Latitude <- NULL

  # check that a shape file exists
  if(!('SpatialPolygons' %in% class(shp))) {
    if(!('sf' %in% class(shp))) {
      stop('shapefile (shp) must be sf (preferred) or SpatialPolygons object')
    }
  } else {
    shp <- as(shp, "sf")   # convert SpatialPolygons to sf
  }

  # check that sk results correspond to station results
  if(length(stations) != length(sk_result))
    stop('Incorrect number of seasonal kendall results specified.')

  # # check that length(lab_loc) = length(stations)
  # if(!is.null(station_labs) && length(lab_loc) != length(stations))
  #   stop('Incorrect number of label location identifiers specified. R or L designation must be made for each station.' )

  # check that the bb has the right dimensions
  if(is.null(bbox))
    stop('Specify a bounding box (bbox) in the form of c(X1, Y1, X2, Y2)')
  if(length(bbox) != 4)
    stop('Incorrect number of elements specified for bbox. Specify a bounding box (bbox) in the form of c(X1, Y1, X2, Y2)')
  # Get min-max bounding coordinates, and format bbox correctly:
  xmin <- min(bbox[c(1,3)])
  xmax <- max(bbox[c(1,3)])
  ymin <- min(bbox[c(2,4)])
  ymax <- max(bbox[c(2,4)])
  bbox <- c(xmin, ymin, xmax, ymax)

  #check that stations, x_loc, and y_loc match
  if(length(stations) != length(x_loc))
    stop('An incorrect number of x coordinates were specified. One x coordinate must be specified for each station')
  if(length(stations) != length(y_loc))
    stop('An incorrect number of y coordinates were specified. One y coordinate must be specified for each station')

  # generate location labels
  loc <- data.frame(abbrev = stations, Latitude = y_loc, Longitude = x_loc,
                    sk_result = sk_result, stringsAsFactors = FALSE)

  # Default all labels to left and then change if there is location information
  loc$align <- -1.25
  if(!is.null(lab_loc))
    loc$align[lab_loc == 'R'] <- 1.25

  # If longitudes are positive and print warning
  if(sum(loc$Longitude > 0) > 0) {
    # loc$Longitude[loc$Longitude > 0] <- -loc$Longitude[loc$Longitude > 0]
    warning("Positive longitudes given, please double check")
  }
  # convert location info to sf object
  # use lat/lon, WGS84 projection, EPSG:4326.
  loc_sf <- sf::st_as_sf(loc, coords = c("Longitude","Latitude"))
  sf::st_crs(loc_sf) <- 4326

  # Define vectors for the colors, shapes and sizes as needed:
  #   1 - 4 are for showing S-K trend results: 1 = increasing, 2 = decreasing,
  #   3 = insignificant, and 4 = insufficient data.
  # This convention holds for colors, shapes and size parameters. The order is
  #   consistent with the original order.

  # These are the codes for the fill color, size and shape legends.
  break_vals <- c("inc", "dec", "insig", "insuff")
  res_png_shape <-  c(system.file("extdata", "up_arrow.png", package="SWMPrExtension"),
                      system.file("extdata", "down_arrow.png", package="SWMPrExtension"),
                      system.file("extdata", "dash.png", package="SWMPrExtension"),
                      system.file("extdata", "ex_square.png", package="SWMPrExtension"))

  master_key <- as.data.frame(cbind(break_vals, res_png_shape))
  loc_keys <- merge(loc, master_key, by.x = "sk_result", by.y = "break_vals")

   print(paste("maptype is ",maptype))

  if(is.null(bg_map)) {
    bg_map <- base_map(bbox, crs = st_crs(shp),
                     maptype = maptype,
                     zoom = zoom)
  }

  m <- bg_map +
    geom_sf(data = shp, aes(), inherit.aes = FALSE,
            fill = "yellow", col = '#B3B300', alpha = 0.3) +
    ggthemes::theme_map() +
    geom_image(data = loc_keys,
               aes(x = Longitude, y = Latitude,
                   image = res_png_shape),
               size = 0.045)

  if(station_labs) {
    # Define lat/long for labels, based on stations, alignment, and bbox
    loc$lab_long <- loc$Longitude + 0.06 * loc$align * (bbox[3] - bbox[1])
    loc$lab_lat <- loc$Latitude + 0.015 * (bbox[4] - bbox[2])

    # convert Labels info to sf object, use lat/lon, WGS84 projection, EPSG:4326.
    labels_sf <- loc %>%
      select(abbrev, lab_long, lab_lat) %>%
      sf::st_as_sf(coords = c("lab_long","lab_lat"))
    sf::st_crs(labels_sf) <- 4326

    m <- m +
      geom_sf_label(data = labels_sf, inherit.aes = FALSE,
                    aes(label = abbrev))
  }

  m <- m +
    coord_sf(
      xlim = c(bbox[1], bbox[3]),
      ylim = c(bbox[2], bbox[4]),
      expand = FALSE,
      crs = st_crs(shp),
      default_crs = NULL,
      datum = sf::st_crs(4326),
      # label_graticule = waiver(),
      # label_axes = waiver(),
      lims_method = c("cross", "box", "orthogonal", "geometry_bbox"),
      ndiscr = 100,
      default = FALSE,
      clip = "on"
    )

  return(m)
}