Type:	Package
Title:	Plot Data on Oceanographic Maps using 'ggplot2'
Version:	2.2.0
Date:	2024-01-15
URL:	https://mikkovihtakari.github.io/ggOceanMaps/
BugReports:	https://github.com/MikkoVihtakari/ggOceanMaps/issues
Description:	Allows plotting data on bathymetric maps using 'ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using 'ggplot2' layers separated by the '+' operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the 'ggplot2' package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the 'ggOceanMapsLargeData' repository on GitHub and downloaded automatically when needed.
Depends:	R (≥ 3.5.0), ggplot2
Imports:	sf, stars, methods, utils, smoothr, units
Suggests:	ggspatial, cowplot, knitr, rmarkdown, scales, ggnewscale
License:	GPL-3
Encoding:	UTF-8
RoxygenNote:	7.2.3
LazyData:	true
LazyDataCompression:	xz
NeedsCompilation:	no
Packaged:	2024-01-15 10:56:44 UTC; a22357
Author:	Mikko Vihtakari [aut, cre] (affiliation: Institute of Marine Research), Roger Bivand [ctb], Hadley Wickham [ctb]
Maintainer:	Mikko Vihtakari <mikko.vihtakari@hi.no>
Repository:	CRAN
Date/Publication:	2024-01-15 13:10:05 UTC

Plot Data on Oceanographic Maps using ggplot2

Description

Uses ggplot2 syntax and shape files to plot research data on oceanographic maps anywhere around the globe.

Details

The general map-making function for ggOceanMaps is basemap. This function creates a "canvas" on which research data can be plotted. The basemap function is analogous to ggplot function from the ggplot2 package. Remember to use data = <<NAMEOFDATASET>> for additional geometries you plot on basemaps (basemap(60) + geom_point(data = data.frame(lon = 50, lat = 70), aes(x = lon, y = lat)) as an example). As a shortcut, you may also use qmap(data.frame(lon = c(10, 50), lat = c(60, 70))). Bathymetry is plotted using the bathymetry argument.

Author(s)

Maintainer: Mikko Vihtakari mikko.vihtakari@hi.no (ORCID) (Institute of Marine Research)

Other contributors:

• Roger Bivand [contributor]

• Hadley Wickham [contributor]

See Also

Useful links:

• https://mikkovihtakari.github.io/ggOceanMaps/

• Report bugs at https://github.com/MikkoVihtakari/ggOceanMaps/issues

Convert font sizes measured as points to ggplot font sizes

Description

Converts font sizes measured as points (as given by most programs such as MS Word etc.) to ggplot font sizes

Usage

FS(x)

Arguments

Value

Returns a numeric vector of lenght x of ggplot font sizes

See Also

Other size adjustors: LS()

Convert line sizes measured as points to ggplot line sizes

Description

Converts line sizes measured as points (as given by most programs such as Adobe Illustrator etc.) to ggplot font sizes

Usage

LS(x)

Arguments

Value

Returns a numeric vector of lenght x of ggplot line sizes

See Also

Other size adjustors: FS()

Automatic limits for basemap

Description

Find limits for a basemap from a data frame.

Usage

auto_limits(
  data,
  lon = NULL,
  lat = NULL,
  proj.in = 4326,
  proj.out = NULL,
  expand.factor = NULL,
  verbose = FALSE
)

Arguments

Details

This is an internal function, which is automatically run by the basemap function.

Value

A list of limits and projections in proj.in and proj.out formats.

Author(s)

Mikko Vihtakari

See Also

Other customize shapefiles: reorder_layers(), theme_map()

Examples

auto_limits(data = expand.grid(lon = c(-120, 180, 120),
   lat = c(60, 60, 80)))

Create a ggplot2 basemap for plotting variables

Description

Creates a ggplot2 basemap for further plotting of data.

Usage

basemap(
  x = NULL,
  limits = NULL,
  data = NULL,
  shapefiles = NULL,
  crs = NULL,
  bathymetry = FALSE,
  glaciers = FALSE,
  rotate = FALSE,
  legends = TRUE,
  legend.position = "right",
  lon.interval = NULL,
  lat.interval = NULL,
  bathy.style = NULL,
  downsample = 0,
  bathy.border.col = NA,
  bathy.size = 0.1,
  bathy.alpha = 1,
  land.col = "grey60",
  land.border.col = "black",
  land.size = 0.1,
  gla.col = "grey95",
  gla.border.col = "black",
  gla.size = 0.1,
  grid.col = "grey70",
  grid.size = 0.1,
  base_size = 11,
  projection.grid = FALSE,
  expand.factor = 1,
  verbose = FALSE
)

Arguments

Details

The function uses ggplot2, sf, stars and spatial files to plot maps of the world's oceans.

Limits

If the limits are in decimal degrees, the longitude limits ([1:2]) specify the start and end segments of corresponding angular lines that should reside inside the map area. The longitude limits are defined counter-clockwise. The latitude limits [3:4] define the parallels that should reside inside the limited region given the longitude segments. Note that the actual limited region becomes wider than the polygon defined by the coordinates (shown in Examples). Using data to limit the map, making the points barely fit into the map. The expand.factor argument can be used to adjust the space between map borders and points. If the limits are given as projected coordinates or as decimal degrees for maps with -60 < latitude < 60, limit elements represent lines encompassing the map area in cartesian space.

Projections

If the shapefiles are not specified, the function uses either the limits or data arguments to decide which projection to use. Up-to-date conditions are defined in define_shapefiles and shapefile_list functions. At the time of writing, the function uses three different projections (given as EPSG codes)

• 3995 WGS 84 / Arctic Polar Stereographic. Called "ArcticStereographic". For max latitude (limits[4]) >= 60 (if min latitude (limits[3]) >= 30), and single integer latitudes >= 30 and <= 89.

• 3031 WGS 84 / Antarctic Polar Stereographic. Called "AntarcticStereographic". For max latitude (limits[4]) <= -60 (if min latitude (limits[3]) <= -30), and single integer latitudes <= -30 and >= -89.

• 4326 WGS 84 / World Geodetic System 1984, used in GPS. Called "DecimalDegree". For min latitude (limits[3]) < 30 or > -30, max latitude (limits[4]) < 60 or > -60, and single integer latitudes < 30 and > -30.

The rotate argument changes the pre-defined projection such that mid-longitude point in the map points northward.

The crs argument can be used to define the projection, which can be useful when plotting, for instance, model data that are difficult to transform into another projection.

Bathymetry

Bathymetry can be plotted by simply specifying bathymetry = TRUE or bathy.style (you won't need to specify both any longer). The former uses a low-resolution raster file shipped with ggOceanMaps. The package contains an option to plot higher resolution bathymetries than the default binned blue alternative (bathy.style = "raster_binned_blues"). These bathymetries can be accessed by specifying the bathy.style argument and require a download from ggOceanMapsLargeData or other online repositories. The bathy.style character argument consists of three parts separated by a _. The first part gives the type: raster, poly(gon), or contour. The two latter ones use vector data. The second part gives the resolution: binned, continuous or user. The continuous and user options cannot be used for vector data. The user option accepts any raster file that can be opened using read_stars. The path to the file has to be stored in ggOceanMaps.userpath option (e.g. options(ggOceanMaps.userpath = "PATH_TO_THE_FILE")) (you can set this in .Rprofile to avoid having to type it every time). The last part defines the color: blues or grays. These options can be abbreviated by specifying the first letter of each part. Gray contour lines are an exception to the rule above and can be plotted using bathy.style = "contour_gray". Future versions may contain a combination of raster and gray contours, but these have not been implemented yet. Currently implemented bathy.style alternatives are:

• NULL (default). Bathymetry style is searched from getOption("ggOceanMaps.bathy.style"). If not found, "raster_binned_blues" is used.

• "raster_binned_blues" or "rbb" plots binned raster bathymetry filled with different shades of blue. Does not require a download.

• "raster_binned_grays" or "rbg" the same than above but uses different shades of gray.

• "raster_continuous_blues" or "rcb" plots continuous raster bathymetry filled with different shades of blue. More detailed and visually more appealing than the binned bathymetry. Recommended. Requires a download.

• "raster_continuous_grays" or "rcg" the same than above but uses different shades of gray.

• "raster_user_blues" or "rub" plots continuous raster bathymetry filled with different shades of blue from getOption("ggOceanMaps.user.path"). Any file supported by read_stars should work. The file has to be placed into the location specified by the path. Experimental feature. Has been tested using ETOPO 60 arc-second and GEBCO 15 arc-second grids. Please report any bugs you find.

• "raster_user_grays" or "rug" the same than above but uses different shades of gray.

• "poly_binned_blues", "poly_blues", "pbb" or "pb" plots polygon bathymetry filled with different shades of blue. Default in the versions older than 2.0 of ggOceanMaps. Requires a download.

• "poly_binned_grays", "poly_grays", "pbg" or "pg" same than above but uses different shades of gray.

• "contour_binned_blues", "contour_blues", "cbb" or "cb" contour lines with different shades of blue. Requires a download.

• "contour_gray", "contour_gray" or "cg" plots gray contour lines. Requires a download.

The default can be changed by setting the ggOceanMaps.bathy.style option. options(ggOceanMaps.bathy.style = "poly_blues") would make the style similar to older pre-2.0 versions of ggOceanMaps.

Pre-made shapefiles

If the limits are not defined as decimal degrees (any longitude outside the range [-180, 180] or latitude [-90, 90]), the function will ask to specify shapefiles. The shapefiles can be defined by partially matching the names of the pre-made shapefiles in shapefile_list (e.g. "Ar" would be enough for "ArcticStereographic") or by specifying custom shapefiles.

Custom shapefiles

Custom shapefiles have to be a named list containing at least the following elements:

• land Object name of the spatial polygon containing land. Required.

• glacier Object name of the spatial polygon containing glaciers. Not required if glaciers are not needed.

• bathy Object name of the spatial polygon or raster containing bathymetry data. Not required if bathymetry is not needed.

See Examples.

Line width and font size

The line size aesthetics in ggplot2 generates approximately 2.13 wider lines measured in pt than the given values. If you want a specific line width in pt, use the internal function LS to convert the desired line width to the ggplot2 equivalent. A similar function is also available for font sizes (FS).

Value

Returns a ggplot map, which can be assigned to an object and modified as any ggplot object.

Author(s)

Mikko Vihtakari

References

Note that if you use this function to generate maps for a publication, it is advised to cite the underlying data. The spatial data used by this function have been acquired from the following sources:

• Land polygons. Natural Earth Data 1:10m Physical Vectors with the Land and Minor Island datasets combined. Distributed under the CC Public Domain license (terms of use).

• Glacier polygons. Natural Earth Data 1:10m Physical Vectors with the Glaciated Areas and Antarctic Ice Shelves datasets combined. Distributed under the CC Public Domain license (terms of use)

• Bathymetry. NOAA National Centers for Environmental Information. 2022: ETOPO 2022 15 Arc-Second Global Relief Model. NOAA National Centers for Environmental Information. doi:10.25921/fd45-gt74. Distributed under the U.S. Government Work license.

See Also

ggplot

Other basemap functions: qmap(), shapefile_list(), transform_coord()

Examples

# The easiest way to produce a map is to use the limits
# argument and decimal degrees:

basemap(limits = 60) # synonym to basemap(60)

# Bathymetry can be added using the respective argument:
basemap(limits = -60, bathymetry = TRUE)

## Not run: 
# Glaciers require a download in the new version:
basemap(limits = -60, glaciers = TRUE, shapefiles = "Arctic")

## End(Not run)

# The easiest way to add data on the maps is to use the ggspatial functions:
dt <- data.frame(lon = c(-150, 150), lat = c(60, 90))
if(requireNamespace("ggspatial", quietly = TRUE)) {
basemap(data = dt, bathymetry = TRUE) +
  ggspatial::geom_spatial_point(data = dt, aes(x = lon, y = lat), 
    color = "red")
}
## Not run: 
# Note that writing out data = dt is required because there are multiple
# underlying ggplot layers plotted already:
basemap(data = dt) +
ggspatial::geom_spatial_point(dt, aes(x = lon, y = lat), color = "red")
#> Error: `mapping` must be created by `aes()`

## End(Not run)

# If you want to use native ggplot commands, you need to transform your data
# to the projection used by the map:
dt <- transform_coord(dt, bind = TRUE)

basemap(data = dt) + 
  geom_point(data = dt, aes(x = lon.proj, y = lat.proj), color = "red")

# The limits argument of length 4 plots a map anywhere in the world:
basemap(limits = c(100, 160, -20, 30), bathymetry = TRUE)

# The limits are further expanded when using the data argument:

dt <- data.frame(lon = c(-160, 160, 160, -160), lat = c(80, 80, 60, 60))

if(requireNamespace("ggspatial", quietly = TRUE)) {
basemap(data = dt) +
  ggspatial::geom_spatial_polygon(data = dt, aes(x = lon, y = lat),
    fill = NA, color = "red")

# Rotate:
basemap(data = dt, rotate = TRUE) +
  ggspatial::geom_spatial_polygon(data = dt, aes(x = lon, y = lat),
    fill = NA, color = "red")
}

# Alternative:
basemap(data = dt, rotate = TRUE) +
  geom_polygon(data = transform_coord(dt, rotate = TRUE), 
    aes(x = lon, y = lat), fill = NA, color = "red")

## To find UTM coordinates to limit a polar map:
basemap(limits = 60, projection.grid = TRUE)

## Not run: 
# (Arctic shapes require a download in 2.0)
basemap(limits = c(2.5e4, -2.5e6, 2e6, -2.5e5), shapefiles = "Arctic")

# Using custom shapefiles (requires download):
data(bs_shapes, package = "ggOceanMapsData")
basemap(shapefiles = list(land = bs_land))#' 

# Premade shapefiles from ggOceanMapsLargeData (requires download):
basemap("BarentsSea", bathymetry = TRUE)

## End(Not run)

# grid.col = NA removes grid lines, rotate = TRUE rotates northwards: 
basemap(limits = c(-180, -140, 50, 70), grid.col = NA, rotate = TRUE)

# Rename axis labels

basemap(limits = c(-140, -105, 20, 40), bathymetry = TRUE) + xlab("Lat")

# Remove axis labels

basemap(limits = c(0, 60, 68, 80)) + labs(x = NULL, y = NULL)

basemap(limits = c(0, 60, 68, 80), rotate = TRUE) +
theme(axis.title = element_blank(),
      axis.text = element_blank(),
      axis.ticks.x = element_blank(),
      axis.ticks.y = element_blank()
      )

Create basemapData object for basemap plotting

Description

Internal function to create a basemapData object for basemap

Usage

basemap_data(
  limits = NULL,
  data = NULL,
  shapefiles = NULL,
  crs = NULL,
  bathymetry = FALSE,
  bathy.type = NULL,
  downsample = 0,
  glaciers = FALSE,
  lon.interval = NULL,
  lat.interval = NULL,
  expand.factor = 1.1,
  rotate = FALSE,
  verbose = FALSE
)

Arguments

Details

This is an internal function, which is automatically run by the basemap function. Common users do not need to worry about these details.

Value

A list of class basemapData containing information required for plotting a basemap.

Author(s)

Mikko Vihtakari

See Also

basemap

Clip a shapefile using a bounding area

Description

Clips an area from a larger shapefile provided in sf or sp formats.

Usage

clip_shapefile(
  x,
  limits,
  proj.limits = 4326,
  simplify = FALSE,
  tol = 60,
  return.boundary = FALSE,
  extra.validate = FALSE
)

Arguments

Details

The function uses the st_intersection function to clip smaller polygons from larger ones. The clip area is constrained by either a numeric vector or a spatial object in the limits argument. Defining limits by a sf object gives greater freedom for the clip area as the area does not have to be rectangular.

Value

Clipped spatial object. If return.boundary = TRUE, a list containing the shapefile together with the clip boundary.

Author(s)

Mikko Vihtakari

See Also

Other create shapefiles: geonorge_bathymetry(), raster_bathymetry(), vector_bathymetry()

Create clip boundary from decimal degree limits

Description

Creates a clip boundary for map cropping from decimal degree limits counter-clockwise following parallels

Usage

dd_clip_boundary(limits, crs, expand.factor = NULL)

Arguments

Author(s)

Mikko Vihtakari

Decimal degree land shapes

Description

Decimal degree land shapes

Usage

dd_land

Format

Simple feature collection land shapes in decimal degrees (EPSG:4326). Obtained from Natural Earth Data (10m vectors). Includes the islands dataset.

Source

Natural Earth Data

See Also

Other mapfiles: dd_rbathy

Decimal degree bathymetry

Description

Decimal degree bathymetry

Usage

dd_rbathy

Format

Raster bathymetry in decimal degrees (EPSG:4326). Downsampled from ETOPO 60 arc-second grid.

Source

NOAA National Centers for Environmental Information. 2022: ETOPO 2022 15 Arc-Second Global Relief Model. NOAA National Centers for Environmental Information. doi:10.25921/fd45-gt74

See Also

Other mapfiles: dd_land

Convert decimal degree values to angular degrees

Description

Converts decimal degree values to angular degrees. Used in decimal degree limit calculations.

Usage

dd_to_deg(x)

Arguments

Value

A vector of angular degrees

Author(s)

Mikko Vihtakari

See Also

Other degree converters: deg_to_dd()

Define bathymetry style for basemap

Description

Defines bathymetry style to be used in basemap

Usage

define_bathy_style(x)

Arguments

Value

Returns a named character vector with the name pointing to the bathymetry style and value to internal map element command for basemap (see map_cmd).

Author(s)

Mikko Vihtakari

Define a shapefile to use in plotting from the limits argument

Description

An internal function to make basemap code more readable

Usage

define_shapefiles(limits, force_dd = FALSE)

Arguments

Details

This is an internal function, which is automatically run by the basemap function.

Value

A list containing the correct shapefile, a logical statement whether the limits were supplied as decimal degrees and coordinate reference system.

Author(s)

Mikko Vihtakari

See Also

basemap

Convert angular degrees to decimal degree values

Description

Converts angular degree values to decimal degrees. Used in decimal degree limit calculations.

Usage

deg_to_dd(x)

Arguments

Value

A vector of decimal degrees

Author(s)

Mikko Vihtakari

See Also

Other degree converters: dd_to_deg()

Calculate distance to the closest land for coordinates

Description

Calculates the closest distance to land for coordinates in a data frame

Usage

dist2land(
  data,
  lon = NULL,
  lat = NULL,
  shapefile = "DecimalDegree",
  proj.in = 4326,
  bind = TRUE,
  dist.col = "ldist",
  binary = FALSE,
  verbose = TRUE
)

Arguments

Details

The function calculates great circle spherical distances using the st_distance function by default. The function can be slow for large datasets. If you only want to use the function to remove (wrong) observations reported on land, set the binary argument to TRUE. This speeds up the calculations by a factor of ten.

Value

Returns a vector if bind = FALSE, otherwise a data frame. The distances are given in a new column defined by the dist.col argument. The distances are kilometers if binary = FALSE, otherwise logical (TRUE = the position is in the ocean, FALSE = the position is on land).

Author(s)

Mikko Vihtakari

Examples

# Simple example:
dt <- data.frame(lon = seq(-20, 80, length.out = 41), lat = 50:90)
dt <- dist2land(dt, verbose = FALSE)

qmap(dt, color = ldist) + scale_color_viridis_c()

# Datasets covering the entire Earth seem to work now, except 0,0 lon/lat point
lon = deg_to_dd(seq(0,360,30)); lat = c(80,50,20,0,-20,-50,-80)

dt <- data.frame(
 lon = rep(lon, length(lat)), lat = rep(lat, each = length(lon)))

qmap(dist2land(dt, verbose = FALSE), color = ldist) +
 scale_color_viridis_c()

## Not run: 
dt <- data.frame(
  lon = deg_to_dd(seq(0,360,length.out = 1e3)), 
  lat = rep(60, 1000))
  
# The distance calculation is slow for large datasets
system.time(dist2land(dt))
# user  system elapsed 
# 12.677   0.146  12.849 

# binary = TRUE speeds the function up
system.time(dist2land(dt, binary = TRUE))
# user  system elapsed 
# 1.239   0.120   1.369 

## End(Not run)

Major fisheries areas (hovedomraade) of Norway

Description

Major fisheries areas (hovedomraade) of Norway

Usage

fdir_main_areas

Format

sf object containing major fishing zones defined by the Norwegian Directorate of Fisheries. Contains also Northwest Atlantic Fisheries Organization's divisions where Norwegian vessels tend to fish.

Source

Norwegian Directorate of Fisheries and Northwest Atlantic Fisheries Organization

See Also

Other datasets: fdir_sub_areas, ices_areas

Examples

if(requireNamespace("ggspatial")) {
 
basemap(fdir_main_areas) + 
ggspatial::annotation_spatial(fdir_main_areas, fill = NA)

}

Norwegian sub-areas (lokasjon) for commercial fishing

Description

Norwegian sub-areas (lokasjon) for commercial fishing

Usage

fdir_sub_areas

Format

sf object containing major fishing zones defined by the Norwegian Directorate of Fisheries.

Source

Norwegian Directorate of Fisheries

See Also

Other datasets: fdir_main_areas, ices_areas

Examples

if(requireNamespace("ggspatial")) {

basemap(fdir_sub_areas) + 
ggspatial::annotation_spatial(fdir_sub_areas, fill = NA)

}

Open Geonorge bathymetry shapefiles

Description

Opens and formats Geonorge bathymetry shapefiles ready for plotting in ggOceanMaps

Usage

geonorge_bathymetry(filepath, layer = NULL, verbose = FALSE)

Arguments

Details

You can download the bathymetry polygon shapefiles from Geonorge. Download the file in GLM format.

Value

An sf object containing the depth polygons. Uses same projection than bathy (see CRS).

Author(s)

Mikko Vihtakari

See Also

Other create shapefiles: clip_shapefile(), raster_bathymetry(), vector_bathymetry()

Extract depth for coordinates from a raster bathymetry dataset

Description

Extracts depth from basemap bathymetry raster dataset for coordinates in a data frame

Usage

get_depth(
  data,
  bathy.style = "raster_continuous",
  lon = NULL,
  lat = NULL,
  shapefile = "DecimalDegree",
  proj.in = 4326,
  bind = TRUE,
  depth.col = "depth",
  verbose = FALSE
)

Arguments

Details

Uses the st_extract function to extract values from basemap bathymetry raster grids. Does not work for vector bathymetries.

Value

Returns a vector if bind = FALSE, otherwise a data frame. The depths are given in a new column defined by the dist.col argument. The distances are kilometers. NA distance means that the position is on land.

Author(s)

Mikko Vihtakari

Examples

## Not run: 
dt <- data.frame(lon = seq(-20, 80, length.out = 41), lat = 50:90)
dt <- get_depth(dt)
qmap(dt, color = depth) + scale_color_viridis_c()

## End(Not run)

Guess longitude and latitude columns in a data frame

Description

An internal function to make basemap code more readable

Usage

guess_coordinate_columns(data, lon = NULL, lat = NULL)

Arguments

Details

This is an internal function, which is automatically run by the basemap function.

Value

A named vector of colummn names.

Author(s)

Mikko Vihtakari

See Also

auto_limits, transform_coord, basemap

ICES Advisory Areas

Description

ICES Advisory Areas

Usage

ices_areas

Format

sf object containing ICES Advisory Areas.

Source

International Council for the Exploration of the Sea

See Also

Other datasets: fdir_main_areas, fdir_sub_areas

Examples

if(requireNamespace("ggspatial")) {

basemap(ices_areas) + 
ggspatial::annotation_spatial(ices_areas, fill = NA)

}

Test whether a limit argument is specified as decimal degrees.

Description

An internal function to make basemap code more readable

Usage

is_decimal_limit(limits)

Arguments

Details

This is an internal function, which is automatically run by the basemap function.

Value

A logical value

Author(s)

Mikko Vihtakari

See Also

basemap

Load large shapefile objects

Description

Internal function to load large shapefile objects. Downloads the files if they are not found getOption("ggOceanMaps.datapath")

Usage

load_map_data(x, force = FALSE, downsample = 0)

Arguments

Details

This is an internal function, which is automatically run by the basemap function. Common users do not need to worry about these details.

Value

A list of spatial objects

Author(s)

Mikko Vihtakari

See Also

basemap

Return map elements for basemap

Description

An internal function to make basemap code more readable

Usage

map_cmd(command, alternative = FALSE)

Arguments

Details

This is an internal function, which is automatically run by the basemap function. Common users do not need to worry about these details. Basemap elements can added together using this function, parse and eval.

Value

A character string containing a ggplot2 plotting command. Use eval(parse(text=...)) to plot the string.

Author(s)

Mikko Vihtakari

See Also

basemap

Examples

## An example for utm map without glaciers or bathymetry
## Not run: eval(parse(text=paste(map_cmd("base"), map_cmd("land_utm"),
map_cmd("grid_utm"), map_cmd("defs_utm"), sep = "+")))
## End(Not run)

Quick map

Description

qmap is a shortcut similar to ggplot2's qplot designed to quickly plot data with a limited range of options.

Usage

qmap(
  data,
  ...,
  x = NULL,
  y = NULL,
  geom = "point",
  limits = NULL,
  shapefiles = NULL,
  crs = NULL,
  bathymetry = FALSE,
  glaciers = FALSE,
  rotate = FALSE,
  legends = TRUE,
  legend.position = "right",
  lon.interval = NULL,
  lat.interval = NULL,
  bathy.style = NULL,
  downsample = 0,
  bathy.border.col = NA,
  bathy.size = 0.1,
  bathy.alpha = 1,
  land.col = "grey60",
  land.border.col = "black",
  land.size = 0.1,
  gla.col = "grey95",
  gla.border.col = "black",
  gla.size = 0.1,
  grid.col = "grey70",
  grid.size = 0.1,
  base_size = 11,
  projection.grid = FALSE,
  expand.factor = 1.1,
  verbose = FALSE
)

Arguments

Value

Returns a ggplot map, which can be assigned to an object and modified as any ggplot object.

Author(s)

Mikko Vihtakari

See Also

Other basemap functions: basemap(), shapefile_list(), transform_coord()

Examples

dt <- data.frame(lon = c(-100, -80, -60), lat = c(10, 25, 40), var = c("a", "a", "b"))

# Quickly see position of data
qmap(dt)


# Set color
qmap(dt, color = I("blue")) 

# Map color to a variable
qmap(dt, color = var) 
 
# Map text to a variable 
qmap(dt, label = var) 

# All basemap arguments work in qmap()
dt <- data.frame(lon = c(-80, -80, -50, -50), lat = c(65, 80, 80, 65))
qmap(dt, rotate = TRUE)

Return function output quietly

Description

Returns function output without printed cat messages

Usage

quiet(x)

Arguments

Value

Output of x

Author(s)

Hadley Wickham

Simplify a bathymetry raster ready for vectorization

Description

Simplifies bathymetry raster ready for the vector_bathymetry function. Warning: processing may take a long time if the bathymetry raster is large.

Usage

raster_bathymetry(
  bathy,
  depths,
  proj.out = NULL,
  proj.bathy = NULL,
  boundary = NULL,
  warp = FALSE,
  estimate.land = FALSE,
  downsample = NULL,
  verbose = TRUE
)

Arguments

Details

You can use GEBCO, IBCAO, ETOPO bathymetry grids downloaded from respective sources as the bathy argument. The bathymetry grids read from files must be in any format read by read_stars. Alternatively use the marmap::getNOAA.bathy function to download ETOPO1 bathymetry and convert it to a raster object using the marmap::as.raster function.

Note that the size of the output is heavily influenced by the number of depth contours (depths) as well as the resolution of bathy and choice of downsample. To make the vector_bathymetry function and consequent plotting faster, limiting the details of the bathymetry raster may be desirable.

Value

A list with a stars object the containing projected bathymetry defined by the proj.out argument and a data frame of depth intervals.

Author(s)

Mikko Vihtakari

References

GEBCO Compilation Group (2019) GEBCO 2019 15-arcsecond grid (doi:10.5285/836f016a-33be-6ddc-e053-6c86abc0788e). URL: https://www.gebco.net/data_and_products/gridded_bathymetry_data/gebco_2019/gebco_2019_info.html. NOAA National Centers for Environmental Information. 2022: ETOPO 2022 15 Arc-Second Global Relief Model. NOAA National Centers for Environmental Information. doi:10.25921/fd45-gt74.

See Also

Other create shapefiles: clip_shapefile(), geonorge_bathymetry(), vector_bathymetry()

Move basemap land, glacier and grid layers on top of other ggplot layers

Description

Moves existing land, glacier and grid layers on top of other layers. Useful for hiding region polygons under land.

Usage

reorder_layers(p)

Arguments

Details

This function has not been tested properly yet and is likely to contain bugs.

Value

Returns a ggplot object with land, glacier and grid layers on top.

Author(s)

Mikko Vihtakari

See Also

Other customize shapefiles: auto_limits(), theme_map()

Examples

if(requireNamespace("ggspatial", quietly = TRUE)) {

 data("ices_areas")
 p <- basemap(c(-20, 15, 50, 70)) + 
   ggspatial::annotation_spatial(ices_areas, aes(fill = Area_Full), show.legend = FALSE)
 
 # Polygons on top of land
 p
 
 # Move land on top
 reorder_layers(p)
 
 }

Rotate CRS

Description

Rotates a CRS such that North is in the middle of two meridians

Usage

rotate_crs(crs, meridians)

Arguments

Value

Rotated CRS in st_crs format

Author(s)

Mikko Vihtakari

Round to multiple of any number

Description

Round to multiple of any number

Usage

round_any(x, accuracy, f = round)

Arguments

Value

Rounded numeric vector

Author(s)

Hadley Wickham

Select an element of each vector from a list

Description

Selects y'th element of each vector from a list

Usage

select_element(x, y)

Arguments

Value

The selected element from the list

A list of pre-made shapefiles for basemap

Description

Lists available pre-made shapefiles for plotting in the basemap function. Gives also instructions how to make custom ones.

Usage

shapefile_list(name, get.data = FALSE)

Arguments

Details

Custom shapefiles for basemap should be defined as lists with (at least) following names (everything should be provided as characters):

• land Name of the object containing land polygons. Required.

• glacier Name of the object containing glacier polygons. Use NULL if glaciers are not needed.

• bathy Name of the object containing land polygons. Use NULL if bathymetry is not needed.

All linked spatial data objects must be in same projection. High-resolution pre-made data are still under development and may not be available. Pre-made shapefiles contain additional elements that are used in the basemap function, but not required for custom shapefile datasets.

Value

Returns a data frame of provided pre-made shapefiles, if name = "all". Returns a shapefile list containing the information for a particular map otherwise.

Author(s)

Mikko Vihtakari

See Also

Other basemap functions: basemap(), qmap(), transform_coord()

Examples

shapefile_list("all")
shapefile_list("Arctic") # partial matching

A ggplot2 theme for maps

Description

A ggplot2 theme for maps.

Usage

theme_map(..., grid.col, grid.size)

Arguments

Value

A ggplot2 theme layer.

See Also

Other customize shapefiles: auto_limits(), reorder_layers()

Transform spatial coordinates to another projection

Description

Transforms spatial coordinates from original projection (decimal degrees assumed) to another projection.

Usage

transform_coord(
  x = NULL,
  lon = NULL,
  lat = NULL,
  new.names = "auto",
  rotate = FALSE,
  proj.in = 4326,
  proj.out = NULL,
  verbose = FALSE,
  bind = FALSE,
  na = "ignore"
)

Arguments

Details

If x is specified, the function guesses longitude and latitude columns from x by default.

Value

Returns a data frame with transformed spatial coordinates.

Author(s)

Mikko Vihtakari

See Also

Other basemap functions: basemap(), qmap(), shapefile_list()

Examples

# Coordinates are automatically transformed to the pre-made shapefile
# projections:
x <- data.frame(lon = c(-150, 150), lat = c(60, 90))
transform_coord(x)
transform_coord(x, bind = TRUE)

x <- data.frame(lon = c(-150, 150), lat = c(20, 50))
transform_coord(x, bind = TRUE) # no transformation required.

Create a polygon bathymetry from a raster bathymetry file

Description

Vectorizes bathymetry rasters. Designed to be used for the output of raster_bathymetry function. Warning: processing may take a long time if the bathymetry raster is large.

Usage

vector_bathymetry(
  bathy,
  drop.crumbs = NULL,
  remove.holes = NULL,
  smooth = FALSE
)

Arguments

Details

The drop.crumbs and remove.holes arguments can be used to make the resulting object smaller in file size. The smooth argument can be used to remove the pixelated contours, but often increases file size. Note also that using this option will bias the contours with respect to real world.

Value

An sf object containing the depth polygons. Uses same projection than bathy (see CRS).

Author(s)

Mikko Vihtakari

See Also

Other create shapefiles: clip_shapefile(), geonorge_bathymetry(), raster_bathymetry()