make_transition: Create transition layer from spatial object.

In ocean-tracking-network/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

Create transition layer from spatial object.

Description

Create transition layer for interpolate_path() spatial object.

Usage

make_transition(poly, res, receiver_points = NULL, epsg = 3175, buffer = NULL)

Arguments

poly	A spatial polygon object of class SpatialPolygonsDataFrame or a sf::sf() object with a geometry column of polygon and/or multipolygon objects.
res	two element vector that specifies the x and y dimension of output raster cells. Units are same as poly crs. May be calculated from desired resolution in meters using scale_meters_to_degrees().
receiver_points	Object containing coordinates of receiver locations. Must be of class SpatialPointsDataFrame, SpatialPoints, sf, glatos_receivers, or glatos_detections.
epsg	coordinate reference code that describes projection used for buffers. Defaults to NAD83/Great Lakes and St. Lawrence Albers.
buffer	Buffer, in same units as epsg, that will be added to poly before rasterization.

Details

make_transition uses jarasterize() to convert a polygon shapefile into a raster layer and geo-corrected transition layer interpolate_path(). Raster cell values on land equal 0, cells in water equal 1. Output is a two-object list containing the raster layer and transition layer.

If receiver_points is provided, any receiver not in water is buffered by the distance from the receiver to the nearest water. This allows all receivers to be coded as in water if the receiver is on land.

Poly object is transformed into planer map projection specified by epsg argument for calculation of transition object if receiver_points is provided. Output is projected to crs of input poly.

output transition layer is corrected for projection distortions using gdistance::geoCorrection. Adjacent cells are connected by 16 directions and transition function returns 0 (land) for movements between land and water and >0 for all over-water movements.

Note that this function underwent breaking changes between 0.7.3 and 0.8.0 (uses jasterize instead of gdalUtilities::gdal_rasterize see NEWS).

Value

A list with two elements:

transition

a geo-corrected transition raster layer where land = 0 and water = 1 (see gdistance::Transition)

rast

rasterized input layer of class raster

Author(s)

Todd Hayden, Chris Holbrook

Examples

# Example 1 - read from sf polygon object
# use example polygon for Great lakes

# calculate resolution in degrees (from meters)
#  note this applies to cell at center, cell sizes will vary
res <- scale_meters_to_degrees(5000, sf = great_lakes_polygon)

# make_transition layer
tst <- make_transition(great_lakes_polygon, res = res)

## Not run: 
# plot raster layer (notice water = 1, land = 0)
raster::plot(tst$rast)

# compare to polygon
plot(sf::st_geometry(great_lakes_polygon), add = TRUE)

## End(Not run)

# Example 2 - add 1 km buffer (same resolution)

# make_transition layer
tst2 <- make_transition(great_lakes_polygon,
  res = res,
  buffer = 3000
)

## Not run: 
# plot raster layer (notice water = 1, land = 0)
raster::plot(tst2$rast)

# compare to polygon
plot(sf::st_geometry(great_lakes_polygon), add = TRUE)

## End(Not run)

# Example 3 - read from ESRI Shapefile and include receiver file
# to account for any receivers outside of great lakes polygon

# path to polygon shapefile
poly <- system.file("extdata", "shoreline.zip", package = "glatos")
poly <- sf::st_read(paste0("/vsizip/", poly))

# read in glatos receivers object
rec_file <- system.file("extdata", "sample_receivers.csv",
  package = "glatos"
)
recs <- read_glatos_receivers(rec_file)

# change a coordinate to on-land to show impact...
recs[1, "deploy_lat"] <- recs[1, "deploy_lat"] + 4

# make_transition layer (roughly 500 m res)
tst <- make_transition(poly, res = c(0.065, 0.046), receiver_points = recs)

## Not run: 
# plot raster layer
# notice the huge circle rasterized as "water"  north of Lake Superior.
# This occurred because we had a "receiver" deployed at that locations
raster::plot(tst$rast)
points(recs$deploy_long, recs$deploy_lat, col = "red", pch = 20)

# plot transition layer
raster::plot(raster::raster(tst$transition))

## End(Not run)

# Example 4- transition layer of Lake Huron only with receivers

# transform to great lakes projection
poly <- sf::st_transform(great_lakes_polygon, crs = 3175)

# set attribute-geometry relationship to constant.
# this avoids error when cropping
sf::st_agr(poly) <- "constant"

# crop Great lakes polygon file
poly <- sf::st_crop(
  x = poly, xmin = 829242.55, ymin = 698928.27,
  xmax = 1270000.97, ymax = 1097196.15
)

# read in glatos receivers object
rec_file <- system.file("extdata", "sample_receivers.csv",
  package = "glatos"
)
recs <- read_glatos_receivers(rec_file)

# extract receivers in "HECWL" project
# all receiver stations except one is in Lake Huron
recs <- recs[recs$glatos_project == "HECWL", ]

# remove two stations not in Lake Huron
recs <- recs[!recs$glatos_array %in% c("MAU", "LVD"), ]

# convert recs to simple feature  object (sf)
recs <- sf::st_as_sf(recs,
  coords = c("deploy_long", "deploy_lat"),
  crs = 4326
)

# transform receivers to same projection as great lakes polygon
recs <- sf::st_transform(recs, crs = 3175)

## Not run: 
# check by plotting
plot(sf::st_geometry(poly), col = NA)
plot(sf::st_geometry(recs), col = "red", add = TRUE)

## End(Not run)

# create slightly higher resolution transition layer
#   (note that res in in meters here because crs is 3175)
tst1 <- make_transition(poly, res = 5000, receiver_points = recs)

## Not run: 
# plot raster layer
raster::plot(tst1$rast)

plot(sf::st_geometry(recs),
  add = TRUE, col = "red", pch = 20
)

# plot transition layer
raster::plot(raster::raster(tst1$transition))

## End(Not run)

ocean-tracking-network/glatos documentation built on April 17, 2025, 10:38 p.m.