In MikkoVihtakari/ggOceanMaps: Plot Data on Oceanographic Maps using 'ggplot2'

library(knitr)
knitr::opts_chunk$set(collapse = TRUE, 
                      message = FALSE, 
                      warning = FALSE, 
                      eval = FALSE,
                      comment = "#>"
)

library(ggOceanMaps); library(sf); library(stars)

Shapefiles used by this package are stored in two places: 1) the low-resolution shapefiles used frequently are stored in the ggOceanMapsData package which should be installed automatically together with ggOceanMaps. 2) High-resolution shapefiles of selected locations are stored in the ggOceanMapsLargeData repository and downloaded automatically as needed. This document describes how each of the shapefiles is created. The maps are shown in the Premade maps document.

1. Low-resolution shapefiles in ggOceanMapData

Download the datasets specified in Data sources to folders on your computer. Replace the paths under with the correct folder paths on your computer.

etopoPath <- ""
NEDPath <- ""
gebcoPath <- ""
outPath <- ""
EEAPath <- ""

Define the the coordinate reference systems.

arcticCRS <- sf::st_crs(shapefile_list("Arctic")$crs)
antarcticCRS <- sf::st_crs(shapefile_list("Antarctic")$crs)
ddCRS <- sf::st_crs(shapefile_list("Decimal")$crs)

Decimal degrees

Bathymetry:

# Binned raster bathymetry
dd_rbathy <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO_2022_v1_60s_N90W180_surface.nc"),
  depths = c(50, 300, 500, 1000, 1500, 2000, 4000, 6000, 10000), 
  proj.out = 4326,
  downsample = 1
)

save(dd_rbathy, file = file.path(outPath, "ggOceanMapsData/dd_rbathy.rda"), compress = "bzip2")

# Vector bathymetry
dd_bathy <- vector_bathymetry(dd_rbathy, drop.crumbs = 25, smooth = TRUE) 
save(dd_bathy, file = file.path(outPath, "ggOceanMapsData/dd_bathy.rda"), compress = "xz")

# Continuous raster bathymetry
dd_rbathy_cont <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO_2022_v1_60s_N90W180_surface.nc"),
  depths = NULL, 
  proj.out = 4326,
  downsample = 1
)

save(dd_rbathy_cont, file = file.path(outPath, "ggOceanMapsData/dd_rbathy_cont.rda"), compress = "bzip2")

Land:

# Natural Earth Data require s2 turned off.
s2_mode <- sf::sf_use_s2()
suppressMessages(sf::sf_use_s2(FALSE))
on.exit({suppressMessages(sf::sf_use_s2(s2_mode))})

world <- sf::st_read(file.path(NEDPath, "ne_10m_land/ne_10m_land.shp"))
islands <- sf::st_read(file.path(NEDPath, "ne_10m_minor_islands/ne_10m_minor_islands.shp"))

world <- rbind(world, islands)
world <- sf::st_make_valid(world)
dd_land <- clip_shapefile(world, c(-180, 180, -90, 90))
all(sf::st_is_valid(dd_land))

save(dd_land, file = file.path(outPath, "ggOceanMapsData/dd_land.rda"), compress = "xz")

Glaciers:

glaciers <- sf::st_read(file.path(NEDPath, "ne_10m_glaciated_areas/ne_10m_glaciated_areas.shp"))
iceshelves <- sf::st_read(file.path(NEDPath, "ne_10m_antarctic_ice_shelves_polys/ne_10m_antarctic_ice_shelves_polys.shp"))

glaciers <- rbind(glaciers, iceshelves)
glaciers <- sf::st_make_valid(glaciers)
dd_glacier <- clip_shapefile(glaciers, c(-180, 180, -90, 90))
all(sf::st_is_valid(dd_glacier))

save(dd_glacier, file = file.path(outPath, "ggOceanMapsData/dd_glacier.rda"), compress = "xz")

Arctic stereographic

Bathymetry:

# Vector bathymetry
rb <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO_2022_v1_60s_N90W180_surface.nc"),
  depths = c(50, 300, 500, 1000, 1500, 2000, 4000, 6000, 10000), 
  proj.out = arcticCRS,
  boundary = c(-180, 180, 1, 90),
  downsample = 1
)

arctic_bathy <- vector_bathymetry(rb)
save(arctic_bathy, file = file.path(outPath, "ggOceanMapsData/arctic_bathy.rda"), compress = "xz")

# Raster bathymetry
dd_rbathy <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO_2022_v1_60s_N90W180_surface.nc"),
  depths = NULL, 
  proj.out = ddCRS,
  downsample = 1
)

# save(rb, file = file.path(outPath, "ggOceanMapsData/dd_rbathy_agg.rda"), compress = "xz")
save(dd_rbathy, file = file.path(outPath, "ggOceanMapsData/dd_rbathy.rda"), compress = "xz")

rb <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO_2022_v1_60s_N90W180_surface.nc"), 
  depths = c(50, 300, 500, 1000, 1500, 2000, 4000, 6000, 10000), 
  proj.out = arcticCRS, 
  boundary = c(-180.0083, 180.0083, 1, 90), 
  aggregation.factor = 2
)

arctic_bathy <- vector_bathymetry(rb)
save(arctic_bathy, file = file.path(outPath, "ggOceanMapsData/arctic_bathy.rda"), compress = "xz")

Land:

arctic_land <- clip_shapefile(world, c(-180, 180, 1, 90))
arctic_land <- sp::spTransform(arctic_land, sp::CRS(arcticCRS))
arctic_land <- rgeos::gBuffer(arctic_land, byid = TRUE, width = 0)

save(arctic_land, file = file.path(outPath, "ggOceanMapsData/arctic_land.rda"), compress = "xz")

Glaciers:

arctic_glacier <- clip_shapefile(glaciers, c(-180, 180, 40, 90))
arctic_glacier <- sp::spTransform(arctic_glacier, sp::CRS(arcticCRS))
arctic_glacier <- rgeos::gBuffer(arctic_glacier, byid = FALSE, width = 1000)
arctic_glacier <- rgeos::gBuffer(arctic_glacier, byid = FALSE, width = -1000)

save(arctic_glacier, file = file.path(outPath, "ggOceanMapsData/arctic_glacier.rda"), compress = "xz")

Antarctic steregraphic

Bathymetry:

rb <- raster_bathymetry(
  bathy = file.path(etopoPath, "ETOPO1_Ice_g_gmt4.grd"), 
  depths = c(50, 300, 500, 1000, 1500, 2000, 4000, 6000, 10000), 
  proj.out = antarcticCRS, 
  boundary = c(-180.0083, 180.0083, -80, -30), 
  aggregation.factor = 2
)

antarctic_bathy <- vector_bathymetry(rb)

save(antarctic_bathy, file = file.path(outPath, "ggOceanMapsData/antarctic_bathy.rda"), compress = "xz")

Land:

antarctic_land <- clip_shapefile(world, c(-180, 180, -90, -30))
antarctic_land <- sp::spTransform(antarctic_land, sp::CRS(antarcticCRS))
antarctic_land <- rgeos::gBuffer(antarctic_land, byid = TRUE, width = 0)

save(antarctic_land, file = file.path(outPath, "ggOceanMapsData/antarctic_land.rda"), compress = "xz")

Glaciers:

antarctic_glacier <- clip_shapefile(glaciers, c(-180, 180, -90, -30))
antarctic_glacier <- sp::spTransform(antarctic_glacier, sp::CRS(antarcticCRS))
antarctic_glacier <- rgeos::gBuffer(antarctic_glacier, byid = FALSE, width = 1000)
antarctic_glacier <- rgeos::gBuffer(antarctic_glacier, byid = FALSE, width = -1000)

save(antarctic_glacier, file = file.path(outPath, "ggOceanMapsData/antarctic_glacier.rda"), compress = "xz")

2. High-resolution shapefiles in ggOceanMapsLargeData

Europe

Download the EEA landshapes from here: https://www.eea.europa.eu/en/datahub/datahubitem-view/af40333f-9e94-4926-a4f0-0a787f1d2b8f

Unzip the file and paste the folder path to the EEAPath object as a string.

europe_land <- sf::read_sf(file.path(EEAPath, "EEA_Coastline_20170228.shp"))
all(sf::st_is_valid(europe_land))

save(europe_land, 
     file = file.path(outPath, "ggOceanMapsLargeData/europe_land.rda"),
     compress = "xz"
)

Barents Sea

Bathymetry:

bound.limits <- c(-21, 85, 63, 85)

rb <- raster_bathymetry(
  bathy = file.path(gebcoPath, "GEBCO_2021.nc"), 
  depths = c(50, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 
             2500, 3000, 3500, 4000, 5000, 6000, 10000), 
  proj.out = paste0("EPSG:", shapefile_list("Barents")$crs), 
  boundary = bound.limits
)

barentssea_bathy <- vector_bathymetry(rb)

# Raster bathymetry
Sys.time()

barentssea_rbathy <- raster_bathymetry(
  bathy = file.path(gebcoPath, "GEBCO_2021.nc"), 
  depths = NULL, 
  proj.out = paste0("EPSG:", shapefile_list("Barents")$crs),
  boundary = bound.limits,
  warp = TRUE
)

Sys.time()

# save(rb, file = file.path(outPath, "ggOceanMapsData/dd_rbathy_agg.rda"), compress = "xz")
save(barentssea_rbathy, file = file.path(outPath, "ggOceanMapsData/barentssea_rbathy.rda"), compress = "xz")

Land:

barentssea_land <- clip_shapefile(
  world, c(-400000, 1300000, 7400000, 9350000), 
  proj.limits = convert_crs(32636))
barentssea_land <- sp::spTransform(
  barentssea_land, 
  sp::CRS(paste0("EPSG:", shapefile_list("Barents")$crs))
)
barentssea_land <- rgeos::gBuffer(barentssea_land, byid = TRUE, width = 0)

Glaciers:

barentssea_glacier <- clip_shapefile(
  glaciers,  c(-400000, 1300000, 7400000, 9350000), 
  proj.limits = convert_crs(32636))
barentssea_glacier <- sp::spTransform(
  barentssea_glacier, 
  sp::CRS(paste0("EPSG:", shapefile_list("Barents")$crs))
)
barentssea_glacier <- rgeos::gBuffer(barentssea_glacier, byid = TRUE, width = 0)

Save the data

save(barentssea_land, barentssea_glacier, barentssea_bathy,
     file = paste(outPath, "ggOceanMapsLargeData/barentssea.rda", sep = "/"),
     compress = "xz"
)

High resolution Arctic stereographic

rb <- raster_bathymetry(
  bathy = file.path(gebcoPath, "GEBCO_2021.nc"), 
  depths = c(50, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 
             3000, 4000, 5000, 6000, 10000), 
  proj.out = arcticCRS, 
  boundary = c(-180.0083, 180.0083, 10, 90)
)

gebco_bathy <- vector_bathymetry(rb)

save(gebco_bathy, 
     file = file.path(outPath, "ggOceanMapsLargeData/gebco_bathy.rda"),
     compress = "xz"
)

Data sources

The data used by the package are not the property of the Institute of Marine Research nor the author of the package. It is, therefore, important that you cite the data sources used in a map you generate with the package. Please see here for a list of data sources.

MikkoVihtakari/ggOceanMaps documentation built on Oct. 26, 2024, 9:39 a.m.