make_transition3: Create transition layer from polygon shapefile

In jsta/glatos: A package for the Great Lakes Acoustic Telemetry Observation System

Create transition layer from polygon shapefile

Description

Create transition layer for interpolate_path from polygon shapefile.

Usage

make_transition3(poly, res = c(0.1, 0.1), receiver_points = NULL,
  epsg = 3175)

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 of res are same as input shapefile.
receiver_points	A SpatialPointsDataFrame object that contains coordinates of receivers dataset or a "glatos_receivers" object.
epsg	coordinate reference code that describes projection used for map calculation and rasterization. Defaults to NAD83/Great Lakes and St. Lawrence Albers.

Details

make_transition uses fasterize to convert a polygon shapefile into a raster layer and geo-corrected transition layer interpolate_path. Raster cell values on land equal 1 cells in water equal 0. Output is a two-object list containing the raster layer and transition layer. Both objects have the same extents and geographic projection as input shapefile.

@details 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 WGS84 (epsg- 4326).

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 1 for all over-water movements.

Value

A list with two elements:

transition

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

rast

rasterized input layer of class raster

Additonally, rasterized version of input shapefile (*.tif extension) is written to computer at output_dir

Author(s)

Todd Hayden, Tom Binder, Chris Holbrook

Examples

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

library(sp) #for loading greatLakesPoly
library(raster) # for plotting rasters

#get polygon of the Great Lakes
data(greatLakesPoly) #glatos example data; a SpatialPolygonsDataFrame

# make_transition layer
tst <- make_transition3(greatLakesPoly, res = c(0.1, 0.1))

# plot raster layer
# notice land = 1, water = 0
plot(tst$rast)

#compare to polygon
plot(greatLakesPoly, add = TRUE)

#Example 2 - 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 <- unzip(poly, exdir = tempdir())
poly <- sf::st_read(poly[grepl("*.shp", 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
tst <- make_transition3(poly, res = c(0.1, 0.1), receiver_points = recs)

# 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))

Example 3- transition layer of Lake Huron only with receivers

# read polygon shapefile
poly <- system.file("extdata", "shoreline.zip", package = "glatos")
poly <- unzip(poly, exdir = tempdir())
poly <- sf::st_read(poly[grepl("*.shp", poly)])


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

# check by plotting
plot(sf::st_geometry(poly), col = NA)
plot(sf::st_geometry(recs), col = "red", add = TRUE)

# create slightly higher resolution transition layer
tst1 <- make_transition3(poly, res = c(0.01, 0.01), receiver_points = recs)

# plot raster layer
raster::plot(tst1$rast)
 plot(sf::st_transform(sf::st_geometry(recs), crs = 4326), add = TRUE, col = "red", pch = 20)

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

jsta/glatos documentation built on July 11, 2022, 7:01 a.m.