Bathymetric data for the Aleutians (Alaska)

Description

Bathymetric matrix of class bathy created from NOAA GEODAS data.

Usage

data(aleutians)

Details

Data imported from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/) and transformed into an object of class bathy by as.bathy.

Value

A text file.

Author(s)

see https://maps.ngdc.noaa.gov/viewers/wcs-client/

See Also

as.bathy, read.bathy, antimeridian.box

Examples

# load celt data
data(aleutians)

# class "bathy"
class(aleutians)
summary(aleutians)

# test plot.bathy
plot(aleutians,image = TRUE, 
     bpal = list(c(0,max(aleutians),"grey"),
                 c(min(aleutians),0,"darkblue","lightblue")), 
     land = TRUE, lwd = 0.1, axes = FALSE)
antimeridian.box(aleutians, 10)

Adds a box to maps including antimeridian

Description

Adds a box on maps including the antimeridian (180)

Usage

antimeridian.box(object, tick.spacing)

Arguments

Value

The function adds a box and tick marks to an existing plot which contains the antimeridian line (180 degrees).

Author(s)

Eric Pante & Benoit Simon-Bouhet

See Also

plot.bathy

Examples

data(aleutians)

# default plot:
plot(aleutians,n=1)

# plot with corrected box and labels:
plot(aleutians,n=1,axes=FALSE)
antimeridian.box(aleutians, 10)

Convert bathymetric data to a spatial grid

Description

Transforms an object of class bathy to a SpatialGridDataFrame object.

Usage

as.SpatialGridDataFrame(bathy)

Arguments

Details

as.SpatialGridDataFrame transforms bathy objects into objects of class SpatialGridDataFrame as defined in the sp package. All methods from the sp package are thus available for bathymetric data (e.g. rotations, projections...).

Value

An object of class SpatialGridDataFrame with the same characteristics as the bathy object (same longitudinal and latitudinal ranges, same resolution).

Author(s)

Benoit Simon-Bouhet

See Also

as.xyz, as.bathy, as.raster

Examples

# load Hawaii bathymetric data
data(hawaii)

# use as.SpatialGridDataFrame
sp.hawaii <- as.SpatialGridDataFrame(hawaii)

# Summaries
summary(hawaii)
summary(sp.hawaii)

# structure of the SpatialGridDataFrame object
str(sp.hawaii)

# Plots
plot(hawaii,image=TRUE,lwd=.2)
image(sp.hawaii)

Convert to bathymetric data in an object of class bathy

Description

Reads either an object of class RasterLayer, SpatialGridDataFrame or a three-column data.frame containing longitude (x), latitude (y) and depth (z) data and converts it to a matrix of class bathy.

Usage

as.bathy(x)

Arguments

Details

x can contain data downloaded from the NOAA GEODAS Grid Translator webpage (http://www.ngdc.noaa.gov/mgg/gdas/gd_designagrid.html) in the form of an xyz table. The function as.bathy can also be used to transform objects of class raster (see package raster) and SpatialGridDataFrame (see package sp).

Value

The output of as.bathy is a matrix of class bathy, which dimensions and resolution are identical to the original object. The class bathy has its own methods for summarizing and ploting the data.

Author(s)

Benoit Simon-Bouhet

See Also

summary.bathy, plot.bathy, read.bathy, as.xyz, as.raster, as.SpatialGridDataFrame.

Examples

# load NW Atlantic data
data(nw.atlantic)

# use as.bathy
atl <- as.bathy(nw.atlantic)

# class "bathy"
class(atl)

# summarize data of class "bathy"
summary(atl)

Convert bathymetric data to a raster layer

Description

Transforms an object of class bathy to a raster layer.

Usage

as.raster(bathy)

Arguments

Details

as.raster transforms bathy objects into objects of class RasterLayer as defined in the raster package. All methods from the raster package are thus available for bathymetric data (e.g. rotations, projections...).

Value

An object of class RasterLayer with the same characteristics as the bathy object (same longitudinal and latitudinal ranges, same resolution).

Author(s)

Benoit Simon-Bouhet

See Also

as.xyz, as.bathy, as.SpatialGridDataFrame

Examples

# load Hawaii bathymetric data
data(hawaii)

# use as.raster
r.hawaii <- as.raster(hawaii)

# class "RasterLayer"
class(r.hawaii)

# Summaries
summary(hawaii)
summary(r.hawaii)

# structure of the RasterLayer object
str(r.hawaii)

## Not run: 
# Plots
#require(raster)
plot(hawaii,image=TRUE,lwd=.2)
plot(r.hawaii)

## End(Not run)

Convert to xyz format

Description

Converts a matrix of class bathy into a three-column data.frame containing longitude, latitude and depth data.

Usage

as.xyz(bathy)

Arguments

Details

The use of as.bathy and as.xyz allows to swicth back and forth between the long format (xyz) and the wide format of class bathy suitable for plotting bathymetric maps, computing least cost distances, etc. as.xyz is especially usefull for exporting xyz files when data are obtained using subsetSQL, i.e. bathymetric matrices of class bathy.

Value

Three-column data.frame with a format similar to xyz files downloaded from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/). The first column contains longitude data, the second contains latitude data and the third contains depth/elevation data.

Author(s)

Benoit Simon-Bouhet

See Also

as.bathy, summary.bathy

Examples

# load celt data
data(celt)
dim(celt)
class(celt)
summary(celt)
plot(celt,deep= -300,shallow= -25,step=25)

# use as.xyz
celt2 <- as.xyz(celt)
dim(celt2)
class(celt2)
summary(celt2)

Ploting bathymetric data with ggplot

Description

Plots contour or image map from bathymetric data matrix of class bathy with ggplot2

Usage

## S3 method for class 'bathy'
autoplot(x, geom="contour", mapping=NULL, coast=TRUE, ...)

Arguments

Details

fortify.bathy is called with argument x to produce a data.frame compatible with ggplot2. Then layers are added to the plot based om the argument geom. Finally, the whole plot is projected geographically using coord_map (for geom="contour") or an approximation thereof.

Author(s)

Jean-Olivier Irisson

See Also

fortify.bathy, plot.bathy, read.bathy, summary.bathy

Examples

# load NW Atlantic data and convert to class bathy
	data(nw.atlantic)
	atl <- as.bathy(nw.atlantic)

  # basic plot
## Not run: 
  library("ggplot2")
	autoplot.bathy(atl)

  # plot images
	autoplot.bathy(atl, geom=c("tile"))
	autoplot.bathy(atl, geom=c("raster")) # faster but not resolution independant

  # plot both!
	autoplot.bathy(atl, geom=c("raster", "contour"))

  # geom names can be abbreviated
	autoplot.bathy(atl, geom=c("r", "c"))

  # do not highlight the coastline
	autoplot.bathy(atl, coast=FALSE)
    
  # better colour scale
  	autoplot.bathy(atl, geom=c("r", "c")) +
    scale_fill_gradient2(low="dodgerblue4", mid="gainsboro", high="darkgreen")

  # set aesthetics
	autoplot.bathy(atl, geom=c("r", "c"), colour="white", size=0.1)
  
  # topographical colour scale, see ?scale_fill_etopo
	autoplot.bathy(atl, geom=c("r", "c"), colour="white", size=0.1) + scale_fill_etopo()
  	
	# add sampling locations
	data(metallo)
  last_plot() + geom_point(aes(x=lon, y=lat), data=metallo, alpha=0.5)

  # an alternative contour map making use of additional mappings
  # see ?stat_contour in ggplot2 to understand the ..level.. argument
	autoplot.bathy(atl, geom="contour", mapping=aes(colour=..level..))

## End(Not run)

Bathymetric data for the North Est Atlantic

Description

Bathymetric matrix of class bathy created from NOAA GEODAS data.

Usage

data(celt)

Details

Data imported from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/) and transformed into an object of class bathy by as.bathy.

Value

A text file.

Author(s)

see https://maps.ngdc.noaa.gov/viewers/wcs-client/

See Also

as.bathy, read.bathy

Examples

# load celt data
data(celt)

# class "bathy"
class(celt)
summary(celt)

# test plot.bathy
plot(celt, deep=-300, shallow=-50, step=25)

Sort bathymetric data matrix by increasing latitude and longitude

Description

Reads a bathymetric data matrix and orders its rows and columns by increasing latitude and longitude.

Usage

check.bathy(x)

Arguments

Details

check.bathy allows to sort rows and columns by increasing latitude and longitude, which is necessary for ploting with the function image (package graphics). check.bathy is used within the marmap functions read.bathy and as.bathy (it is also used in getNOAA.bathy through as.bathy).

Value

The output of check.bathy is an ordered matrix.

Author(s)

Eric Pante

See Also

read.bathy, as.bathy, getNOAA.bathy

Examples

matrix(1:100, ncol=5, dimnames=list(20:1, c(3,2,4,1,5))) -> a
check.bathy(a)

Adds alpha transparency to a (vector of) color(s)

Description

Adds transparency to a color or a vector of colors by specifying one or several alpha values.

Usage

col2alpha(color,alpha = 0.5)

Arguments

Details

When the size of color and alpha vectors are different, alpha values are recycled.

Value

A (vector) of color code(s).

Author(s)

Benoit Simon-Bouhet

Examples

# Generate random data
dat <- rnorm(4000)

# plot with plain color for points
plot(dat,pch=19,col="red")

# Add some transparency to get a better idea of density
plot(dat,pch=19,col=col2alpha("red",.3))

# Same color for all points but with increasing alpha (decreasing transparency)
plot(dat,pch=19,col=col2alpha(rep("red",4000),seq(0,1,len=4000)))

# Two colors, same alpha
plot(dat,pch=19,col=col2alpha(rep(c("red","purple"),each=2000),.2))

# Four colors, gradient of transparency for each color
plot(dat,pch=19,col=col2alpha(rep(c("blue","purple","red","orange"),each=1000),seq(.1,.6,len=1000)))

# Alpha transparency applied to a gradient of colors
plot(dat,pch=19,col=col2alpha(rainbow(4000),.5))

Collates two bathy matrices with data from either sides of the antimeridian

Description

Collates two bathy matrices, one with longitude 0 to 180 degrees East, and the other with longitude 0 to 180 degrees West

Usage

collate.bathy(east,west)

Arguments

Details

This function is meant to be used with read.bathy() or readGEBCO.bathy(), when data is downloaded from either sides of the antimeridian line (180 degrees longitude). If, for example, data is downloaded from GEBCO for longitudes of 170E-180 and 180-170W, collate.bathy() will create a single matrix of class bathy with a coordinate system going from 170 to 190 degrees longitude.

getNOAA.bathy() deals with data from both sides of the antimeridian and does not need further processing with collate.bathy().

Value

A single matrix of class bathy that can be interpreted by plot.bathy. When plotting collated data (with longitudes 0 to 180 and 180 to 360 degrees), plots can be modified to display the conventional coordinate system (with longitudes 0 to 180 and -180 to 0 degrees) using function antimeridian.box().

Author(s)

Eric Pante

See Also

getNOAA.bathy, summary.bathy, plot.bathy, antimeridian.box

Examples

## faking two datasets using aleutians, for this example
## "a" and "b" simulate two datasets downloaded from GEBCO, for ex.
	data(aleutians)
	aleutians[1:181,] -> a ; "bathy" -> class(a)
	aleutians[182:601,] -> b ; "bathy" -> class(b)
	-(360-as.numeric(rownames(b))) -> rownames(b) 

## check these objects with summary(): pay attention of the Longitudinal range
	summary(aleutians)
	summary(a)
	summary(b)

## merge datasets:
	collate.bathy(a,b) -> collated
	summary(collated) # should be identical to summary(aleutians)

Create a new, (non circular) composite buffer from a list of existing buffers.

Description

Creates a new bathy object from a list of existing buffers of compatible dimensions.

Usage

combine.buffers(...)

Arguments

Value

An object of class bathy of the same dimensions as the original bathy objects contained within each buffer objects. The resulting bathy object contains only NAs outside of the combined buffer and values of depth/altitude inside the combined buffer.

Author(s)

Benoit Simon-Bouhet

See Also

create.buffer, plot.buffer, plot.bathy

Examples

# load and plot a bathymetry
data(florida)
plot(florida, lwd = 0.2)
plot(florida, n = 1, lwd = 0.7, add = TRUE)

# add points around which a buffer will be computed
loc <- data.frame(c(-80,-82), c(26,24))
points(loc, pch = 19, col = "red")

# create 2 distinct buffer objects with different radii
buf1 <- create.buffer(florida, loc[1,], radius=1.9)
buf2 <- create.buffer(florida, loc[2,], radius=1.2)

# combine both buffers
buf <- combine.buffers(buf1,buf2)

## Not run: 
# Add outline of the resulting buffer in red 
# and the outline of the original buffers in blue
plot(outline.buffer(buf), lwd = 3, col = 2, add=TRUE)
plot(buf1, lwd = 0.5, fg="blue")
plot(buf2, lwd = 0.5, fg="blue")

## End(Not run)

Create a buffer of specified radius around one or several points

Description

Create a circular buffer of user-defined radius around one or several points defined by their longitudes and latitudes.

Usage

create.buffer(x, loc, radius, km = FALSE)

Arguments

Details

This function takes advantage of the buffer function from package adehabitatMA and several functions from packages sp to define the buffer around the points provided by the user.

Value

An object of class bathy of the same size as mat containing only NAs outside of the buffer and values of depth/altitude (taken from mat) within the buffer.

Author(s)

Benoit Simon-Bouhet

See Also

outline.buffer, combine.buffers, plot.bathy

Examples

# load and plot a bathymetry
data(florida)
plot(florida, lwd = 0.2)
plot(florida, n = 1, lwd = 0.7, add = TRUE)

# add a point around which a buffer will be created
loc <- data.frame(-80, 26)
points(loc, pch = 19, col = "red")

# compute and print buffer
buf <- create.buffer(florida, loc, radius=1.5)
buf

# highlight isobath with the buffer and add outline
plot(buf, outline=FALSE, n = 10, col = 2, lwd=.4)
plot(buf, lwd = 0.7, fg = 2)

Finds matrix diagonal for non-square matrices

Description

Finds either the values of the coordinates of the non-linear diagonal of non-square matrices.

Usage

diag.bathy(mat,coord=FALSE)

Arguments

Details

diag.bathy gets the values or coordinates from the first element of a matrix to its last elements. If the matrix is non-square, that is, its number of rows and columns differ, diag.bathy computes an approximate diagonal.

Value

A vector of diagonal values is coord is FALSE, or a table of diagonal coordinates ifcoord is FALSE

Author(s)

Eric Pante

See Also

get.transect, diag

Examples

	
# a square matrix: diag.bathy behaves as diag
	matrix(1:25, 5, 5) -> a ; a
	diag(a)
	diag.bathy(a)

# a non-square matrix: diag.bathy does not behaves as diag
	matrix(1:15, 3, 5) -> b ; b
	diag(b)
	diag.bathy(b)
	
# output the diagonal or its coordinates: 
	rownames(b) <- seq(32,35, length.out=3)
	colnames(b) <- seq(-100,-95, length.out=5)
	diag.bathy(b, coord=FALSE)
	diag.bathy(b, coord=TRUE)
	

Computes the shortest great circle distance between any point and a given isobath

Description

Computes the shortest (great circle) distance between a set of points and an isoline of depth or altitude. Points can be selected interactively by clicking on a map.

Usage

dist2isobath(mat, x, y=NULL, isobath=0, locator=FALSE, ...)

Arguments

Details

dist2isobath allows the user to compute the shortest great circle distance between a set of points (selected interactively on a map or not) and a user-defined isobath. dist2isobath takes advantage of functions from packages sp (Lines() and SpatialLines()) and geosphere (dist2Line) to compute the coordinates of the nearest location along a given isobath for each point provided by the user.

Value

A 5-column data.frame. The first column contains the distance in meters between each point and the nearest point located on the given isobath. Columns 2 and 3 indicate the longitude and latitude of starting points (i.e. either coordinates provided as x and y or coordinates of points selected interactively on a map when locator=TRUE) and columns 4 and 5 contains coordinates (longitudes and latitudes) arrival points i.e. the nearest points on the isobath.

Author(s)

Benoit Simon-Bouhet

See Also

linesGC, lc.dist

Examples

# Load NW Atlantic data and convert to class bathy
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)

# Create vectors of latitude and longitude
lon <- c(-70, -65, -63, -55, -48)
lat <- c(33, 35, 40, 37, 33)

# Compute distances between each point and the -200m isobath
d <- dist2isobath(atl, lon, lat, isobath = -200)
d

# Visualize the great circle distances
blues <- c("lightsteelblue4","lightsteelblue3","lightsteelblue2","lightsteelblue1")
plot(atl, image=TRUE, lwd=0.1, land=TRUE, bpal = list(c(0,max(atl),"grey"), c(min(atl),0,blues)))
plot(atl, deep=-200, shallow=-200, step=0, lwd=0.6, add=TRUE)
points(lon,lat, pch=21, col="orange4", bg="orange2", cex=.8)
linesGC(d[2:3],d[4:5])

Etopo colours

Description

Various ways to access the colors on the etopo color scale

Usage

etopo.colors(n)

scale_fill_etopo(...)
scale_color_etopo(...)

Arguments

Details

etopo.colors is equivalent to other color scales in R (e.g. grDevices::heat.colors, grDevices::cm.colors).

scale_fill/color_etopo are meant to be used with ggplot2. They allow consistent plots in various subregions by setting the limits of the scale explicitly.

Author(s)

Jean-Olivier Irisson

See Also

autoplot.bathy, palette.bathy

Examples

# load NW Atlantic data and convert to class bathy
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)

# plot with base graphics
plot(atl, image=TRUE)

# using the etopo color scale
etopo_cols <- rev(etopo.colors(8))
plot(atl, image=TRUE, bpal=list(
  c(min(atl), 0, etopo_cols[1:2]),
  c(0, max(atl), etopo_cols[3:8])
))


# plot using ggplot2; in which case the limits of the scale are automatic
library("ggplot2")
ggplot(atl, aes(x=x, y=y)) + coord_quickmap() +
  # background
  geom_raster(aes(fill=z)) +
  scale_fill_etopo() +
  # countours
  geom_contour(aes(z=z),
    breaks=c(0, -100, -200, -500, -1000, -2000, -4000),
    colour="black", size=0.2
  ) +
  scale_x_continuous(expand=c(0,0)) +
  scale_y_continuous(expand=c(0,0))

Bathymetric data around Florida, USA

Description

Bathymetric object of class bathy created from NOAA GEODAS data.

Usage

data(florida)

Details

Data imported from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/) and transformed into an object of class bathy by read.bathy.

Value

A bathymetric object of class bathy with 539 rows and 659 columns.

Author(s)

see https://maps.ngdc.noaa.gov/viewers/wcs-client/

See Also

plot.bathy, summary.bathy

Examples

# load florida data
data(florida)

# class "bathy"
class(florida)
summary(florida)

# test plot.bathy
plot(florida,asp=1)
plot(florida,asp=1,image=TRUE,drawlabels=TRUE,land=TRUE,n=40)

Extract bathymetry data in a data.frame

Description

Extract bathymetry data in a data.frame

Usage

## S3 method for class 'bathy'
fortify(model, data, ...)

Arguments

Details

fortify.bathy is really just calling as.xyz and ensuring consistent names for the columns. It then allows to use ggplot2 functions directly.

Author(s)

Jean-Olivier Irisson, Benoit Simon-Bouhet

See Also

autoplot.bathy, as.xyz

Examples

# load NW Atlantic data and convert to class bathy
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)

library("ggplot2")
# convert bathy object into a data.frame
head(fortify(atl))

# one can now use bathy objects with ggplot directly
ggplot(atl) + geom_contour(aes(x=x, y=y, z=z)) + coord_map()

# which allows complete plot configuration
atl.df <- fortify(atl)
ggplot(atl.df, aes(x=x, y=y)) + coord_quickmap() +
  geom_raster(aes(fill=z), data=atl.df[atl.df$z <= 0,]) +
  geom_contour(aes(z=z),
    breaks=c(-100, -200, -500, -1000, -2000, -4000),
    colour="white", size=0.1
  ) +
  scale_x_continuous(expand=c(0,0)) +
  scale_y_continuous(expand=c(0,0))

Get projected surface area

Description

Get projected surface area for specific depth layers

Usage

get.area(mat, level.inf, level.sup=0, xlim=NULL, ylim=NULL)

Arguments

Details

get.area calculates the projected surface area of specific depth layers (e.g. upper bathyal, lower bathyal), the projected plane being the ocean surface. The resolution of get.area depends on the resolution of the input bathymetric data. xlim and ylim can be used to restrict the area of interest. Area calculation is based on areaPolygon of package geosphere (using an average Earth radius of 6,371 km).

Value

A list of four objects: the projeced surface area in squared kilometers, a matrix with the cells used for calculating the projected surface area, the longitude and latitude of the matrix used for the calculations.

Author(s)

Benoit Simon-Bouhet and Eric Pante

See Also

plotArea, plot.bathy, contour, areaPolygon

Examples

## get area for the entire hawaii dataset:
	data(hawaii)
	plot(hawaii, lwd=0.2)
	
	mesopelagic <- get.area(hawaii, level.inf=-1000, level.sup=-200)
	bathyal <- get.area(hawaii, level.inf=-4000, level.sup=-1000)
	abyssal <- get.area(hawaii, level.inf=min(hawaii), level.sup=-4000)
	
	col.meso <- rgb(0.3, 0, 0.7, 0.3) 
	col.bath <- rgb(0.7, 0, 0, 0.3) 
	col.abys <- rgb(0.7, 0.7, 0.3, 0.3) 

	plotArea(mesopelagic, col = col.meso)
	plotArea(bathyal, col = col.bath)
	plotArea(abyssal, col = col.abys)
	
	me <- round(mesopelagic$Square.Km, 0)
	ba <- round(bathyal$Square.Km, 0)
	ab <- round(abyssal$Square.Km, 0)

	legend(x="bottomleft",
		legend=c(paste("mesopelagic:",me,"km2"),
		         paste("bathyal:",ba,"km2"), 
		         paste("abyssal:",ab,"km2")), 
		col="black", pch=21, 
		pt.bg=c(col.meso,col.bath,col.abys))

# Use of xlim and ylim
	data(hawaii)
	plot(hawaii, lwd=0.2)
	
	mesopelagic <- get.area(hawaii, xlim=c(-161.4,-159), ylim=c(21,23),
	                        level.inf=-1000, level.sup=-200)
	bathyal <- get.area(hawaii, xlim=c(-161.4,-159), ylim=c(21,23),
	                        level.inf=-4000, level.sup=-1000)
	abyssal <- get.area(hawaii, xlim=c(-161.4,-159), ylim=c(21,23),
	                        level.inf=min(hawaii), level.sup=-4000)
	
	col.meso <- rgb(0.3, 0, 0.7, 0.3) 
	col.bath <- rgb(0.7, 0, 0, 0.3) 
	col.abys <- rgb(0.7, 0.7, 0.3, 0.3) 
	
	plotArea(mesopelagic, col = col.meso)
	plotArea(bathyal, col = col.bath)
	plotArea(abyssal, col = col.abys)
	
	me <- round(mesopelagic$Square.Km, 0)
	ba <- round(bathyal$Square.Km, 0)
	ab <- round(abyssal$Square.Km, 0)
	
	legend(x="bottomleft",
		legend=c(paste("mesopelagic:",me,"km2"),
		         paste("bathyal:",ba,"km2"), 
		         paste("abyssal:",ab,"km2")), 
		col="black", pch=21, 
		pt.bg=c(col.meso,col.bath,col.abys))

Get bathymetric information of a belt transect

Description

get.box gets depth information of a belt transect of width width around a transect defined by two points on a bathymetric map.

Usage

get.box(bathy,x1,x2,y1,y2,width,locator=FALSE,ratio=FALSE, ...)

Arguments

Details

get.box allows the user to get depth data for a rectangle area of the map around an approximate linear transect (belt transect). Both the position and size of the belt transect are user defined. The position of the transect can be specified either by inputing start and stop coordinates, or by clicking on a map created with plot.bathy. In its interactive mode, this function uses the locator function (graphics package) to retrieve and plot the coordinates of the selected transect. The argument width allows the user to specify the width of the belt transect in degrees.

Value

A matrix containing depth values for the belt transect. rownames indicate the kilometric distance from the start of the transect and colnames indicate the distance form the central transect in degrees. If ratio=TRUE, a list of two elements: depth, a matrix containing depth values for the belt transect similar to the description above and ratios a vector of length two specifying the ratio between (i) the width and length of the belt transect and (ii) the depth range and the length of the belt transect. These ratios can be used by the function wireframe to produce realistic 3D bathymetric plots of the selected belt transect.

Author(s)

Benoit Simon-Bouhet and Eric Pante

See Also

plot.bathy, get.transect, get.depth

Examples

# load and plot bathymetry
	data(hawaii)
	plot(hawaii,im=TRUE)

# get the depth matrix for a belt transect
	depth <- get.box(hawaii,x1=-157,y1=20,x2=-155.5,y2=21,width=0.5,col=2)
	
# plotting a 3D bathymetric map of the belt transect
	require(lattice)
	wireframe(depth,shade=TRUE)
	
# get the depth matrix for a belt transect with realistic aspect ratios
	depth <- get.box(hawaii,x1=-157,y1=20,x2=-155.5,y2=21,width=0.5,col=2,ratio=TRUE)

# plotting a 3D bathymetric map of the belt transect with realistic aspect ratios
	require(lattice)
	wireframe(depth[[1]],shade=TRUE,aspect=depth[[2]])

Get depth data by clicking on a map

Description

Outputs depth information based on points selected by clicking on a map

Usage

get.depth(mat, x, y=NULL, locator=TRUE, distance=FALSE, ...)

Arguments

Details

get.depth allows the user to get depth data by clicking on a map created with plot.bathy or by providing coordinates of points of interest. This function uses the locator function (graphics package); after creating a map with plot.bathy, the user can click on the map once or several times (if locator=TRUE), press the Escape button, and get the depth of those locations in a three-coumn data.frame (longitude, latitude and depth). Alternatively, when locator=FALSE, the user can submit a list of longitudes and latitudes, a two-column matrix or data.frame of longitudes and latitudes (as input for x), or one vector of longitudes (x) and one vector of latitudes (y). The non-interactive mode is well suited to get depth information for each point provided by GPS tracking devices. While get.transect gets every single depth value available in the bathymetric matrix between two points along a user-defined transect, get.depth only provides depth data for the specific points provided as input by the user.

Value

A data.frame with at least, longitude, latitude and depth with one line for each point of interest. If distance=TRUE, a fourth column containing the kilometric distance from the first point is added.

Author(s)

Benoit Simon-Bouhet and Eric Pante

See Also

path.profile, get.transect, read.bathy, summary.bathy, subsetBathy, nw.atlantic

Examples

# load NW Atlantic data and convert to class bathy
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)

# create vectors of latitude and longitude
lon <- c(-70, -65, -63, -55)
lat <- c(33, 35, 40, 37)

# a simple example
plot(atl, lwd=.5)
points(lon,lat,pch=19,col=2)

# Use get.depth to get the depth for each point
get.depth(atl, x=lon, y=lat, locator=FALSE)

# alternativeley once the map is plotted, use the iteractive mode:
## Not run: 
get.depth(atl, locator=TRUE, pch=19, col=3)

## End(Not run)
# click several times and press Escape

Get sample data by clicking on a map

Description

Outputs sample information based on points selected by clicking on a map

Usage

get.sample(mat, sample, col.lon, col.lat, ...)

Arguments

Details

get.sample allows the user to get sample data by clicking on a map created with plot.bathy. This function uses the locator function (graphics package). After creating a map with plot.bathy, the user can click twice on the map to delimit an area (for example, lower left and upper right corners of a rectangular area of interest), and get a dataframe corresponding to the sample points present within the selected area.

Value

a dataframe of the elements of sample present within the area selected

Warning

clicking once or more than twice on the map will return a warning message: "Please choose two points from the map"

Author(s)

Eric Pante

See Also

read.bathy, summary.bathy, nw.atlantic, metallo

Examples

## Not run: 
# load metallo sampling data and add a third field containing a specimen ID
data(metallo)
metallo$id <- factor(paste("Metallo",1:38))

# load NW Atlantic data, convert to class bathy, and plot
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)
plot(atl, deep=-8000, shallow=0, step=1000, col="grey")

# once the map is plotted, use get.sample to get sampling info!
get.sample(atl, metallo, 1, 2)
# click twice

## End(Not run)

Compute approximate cross section along a depth transect

Description

Compute the depth along a linear transect which bounds are specified by the user.

Usage

get.transect(mat, x1, y1, x2, y2, locator=FALSE, distance=FALSE, ...)

Arguments

Details

get.transect allows the user to compute an approximate linear depth cross section either by inputing start and stop coordinates, or by clicking on a map created with plot.bathy. In its interactive mode, this function uses the locator function (graphics package); after creating a map with plot.bathy, the user can click twice to delimit the bound of the transect of interest (for example, lower left and upper right corners of a rectangular area of interest), press Escape, and get a table with the transect information.

Value

A table with, at least, longitude, latitude and depth along the transect, and if specified (distance=TRUE), the distance in kilometers from the start of the transect. The number of elements in the resulting table depends on the resolution of the bathy object.

Warning

Clicking once or more than twice on the map will return a warning message: "Please choose only two points from the map". Manually entering coordinates that are outside the geographical range of the input bathy matrix will return a warning message.

Note

The distance option of get.transect is calculated based on the haversine formula for getting the great circle distance (takes into account the curvature of the Earth). get.transect uses an internal function called diag.bathy that extracts the approximate diagonal of a matrix, when that matrix has uneven dimentions (different numbers of columns and rows).

Author(s)

Eric Pante and Benoit Simon-Bouhet

See Also

read.bathy, nw.atlantic, nw.atlantic.coast, get.depth, get.sample

Examples

	
# load datasets
	data(nw.atlantic); as.bathy(nw.atlantic) -> atl
	data(nw.atlantic.coast)

# Example 1. get.transect(), without use of locator()
	get.transect(atl, -65, 43,-59,40) -> test ; plot(test[,3]~test[,2],type="l")
	get.transect(atl, -65, 43,-59,40, distance=TRUE) -> test ; plot(test[,4]~test[,3],type="l")

# Example 2. get.transect(), without use of locator(); pretty plot
	par(mfrow=c(2,1),mai=c(1.2, 1, 0.1, 0.1))
	plot(atl, deep=-6000, shallow=-10, step=1000, lwd=0.5, col="grey50",drawlabels=TRUE)
	lines(nw.atlantic.coast)

	get.transect(atl, -75, 44,-46,32, loc=FALSE, dis=TRUE) -> test
	points(test$lon,test$lat,type="l",col="blue",lwd=2,lty=2)
	plotProfile(test)

# Example 3. get.transect(), with use of locator(); pretty plot
## Not run: 
	par(mfrow=c(2,1),mai=c(1.2, 1, 0.1, 0.1))
	plot(atl, deep=-6000, shallow=-10, step=1000, lwd=0.5, col="grey50",drawlabels=TRUE)
	lines(nw.atlantic.coast)
	
	get.transect(atl, loc=TRUE, dis=TRUE, col=2, lty=2) -> test
	plotProfile(test)
	
## End(Not run)

Import bathymetric data from the NOAA server

Description

Imports bathymetric data from the NOAA server, given coordinate bounds and resolution.

Usage

getNOAA.bathy(lon1, lon2, lat1, lat2, resolution = 4,
              keep = FALSE, antimeridian = FALSE, path = NULL)

Arguments

Details

getNOAA.bathy queries the ETOPO 2022 database hosted on the NOAA website, given the coordinates of the area of interest and desired resolution. Users have the option of directly writing the downloaded data into a file (keep = TRUE argument ; see below). If an identical query is performed (i.e. using identical lat-long and resolution), getNOAA.bathy will load data from the file previously written to the disk instead of querying the NOAA database. This behavior should be used preferentially (1) to reduce the number of uncessary queries to the NOAA website, and (2) to reduce data load time. If the user wants to make multiple, identical queries to the NOAA website without loading the data written to disk, the data file name must be modified by the user. Alternatively, the data file can be moved outside of the present working directory.

getNOAA.bathy allows users to download bathymetric data in the antimeridian region when antimeridian=TRUE. The antimeridian is the 180th meridian and is located about in the middle of the Pacific Ocean, east of New Zealand and Fidji, west of Hawaii and Tonga. For a given pair of longitude values, e.g. -150 (150 degrees West) and 150 (degrees East), you have the possibility to get data for 2 distinct regions: the area centered on the antimeridian (60 degrees wide, when antimeridian = TRUE) or the area centered on the prime meridian (300 degrees wide, when antimeridian = FALSE). It is recommended to use keep = TRUE in combination with antimeridian = TRUE since gathering data for an area around the antimeridian requires two distinct queries to NOAA servers.

Value

The output of getNOAA.bathy is a matrix of class bathy, which dimensions depends on the resolution of the grid uploaded from the NOAA server. The class bathy has its own methods for summarizing and plotting the data. If keep=TRUE, a csv file containing the downloaded data is produced. This file is named using the following format: 'marmap_coord_COORDINATES_res_RESOLUTION.csv' (COORDINATES separated by semicolons, and the RESOLUTION in degrees).

Author(s)

Eric Pante and Benoit Simon-Bouhet

References

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

See Also

read.bathy, readGEBCO.bathy, plot.bathy

Examples

## Not run: 
# you must have an internet connection. This line queries the NOAA ETOPO 2022 database
# for data from North Atlantic, for a resolution of 10 minutes.

getNOAA.bathy(lon1=-20,lon2=-90,lat1=50,lat2=20, resolution=10) -> a
plot(a, image=TRUE, deep=-6000, shallow=0, step=1000)

# download speed for a matrix of 10 degrees x 10 degrees x 30 minutes
system.time(getNOAA.bathy(lon1=0,lon2=10,lat1=0,lat2=10, resolution=30))

## End(Not run)

Fill a grid with irregularly spaced data

Description

Transforms irregularly spaced xyz data into a raster object suitable to create a bathy object with regularly spaced longitudes and latitudes.

Usage

griddify(xyz, nlon, nlat)

Arguments

Details

griddify takes anys dataset with irregularly spaced xyz data and transforms it into a raster object (i.e. a grid) with user specified dimensions. griddify relies on several functions from the raster package, especially rasterize and resample. If a cell of the user-defined grig does not contain any depth/altitude value in the original xyz matrix/data.frame, a NA is added in that cell. A bilinear interpolation is then applied in order to fill in most of the missing cells. For cells of the user-defined grig containing more than one depth/altitude value in the original xyz matrix/data.frame, the mean depth/altitude value is computed.

Value

The output of griddify is an object of class raster, with nlon unique longitude values and nlat unique latitude values.

Author(s)

Eric Pante and Benoit Simon-Bouhet

References

Robert J. Hijmans (2015). raster: Geographic Data Analysis and Modeling. R package version 2.4-20. https://CRAN.R-project.org/package=raster

See Also

read.bathy, readGEBCO.bathy, plot.bathy

Examples

# load irregularly spaced xyz data
data(irregular)
head(irregular)

# use griddify to create a 40x60 grid
reg <- griddify(irregular, nlon = 40, nlat = 60)

# switch to class "bathy"
class(reg)
bat <- as.bathy(reg)
summary(bat)

# Plot the new bathy object and overlay the original data points
plot(bat, image = TRUE, lwd = 0.1)
points(irregular$lon, irregular$lat, pch = 19, cex = 0.3, col = col2alpha(3))

Bathymetric data for Hawaii, USA

Description

Bathymetric object of class bathy created from NOAA GEODAS data and arbitrary locations around the main Hawaiian islands.

Usage

data(hawaii)
data(hawaii.sites)

Details

hawaii contains data imported from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/) and transformed into an object of class bathy by read.bathy. hawaii.sites is a 2-columns data.frame containing longitude and latitude of 6 locations spread at sea around Hawaii.

Value

hawaii: a bathymetric object of class bathy with 539 rows and 659 columns. hawaii.sites: data.frame (6 rows, 2 columns)

Author(s)

see https://maps.ngdc.noaa.gov/viewers/wcs-client/

See Also

plot.bathy, summary.bathy

Examples

# load hawaii data
	data(hawaii)
	data(hawaii.sites)

# class "bathy"
	class(hawaii)
	summary(hawaii)

## Not run: 
## use of plot.bathy to produce a bathymetric map
# creation of a color palette
	pal <- colorRampPalette(c("black","darkblue","blue","lightblue"))

# Plotting the bathymetry
	plot(hawaii,image=TRUE,draw=TRUE,bpal=pal(100),asp=1,col="grey40",lwd=.7)

# Adding coastline
	require(mapdata)
	map("worldHires",res=0,fill=TRUE,col=rgb(.8,.95,.8,.7),add=TRUE)

# Adding hawaii.sites location on the map
	points(hawaii.sites,pch=21,col="yellow",bg=col2alpha("yellow",.9),cex=1.2)

## End(Not run)

Irregularly spaced bathymetric data.

Description

Three-column data.frame of irregularly-spaced longitudes, latitudes and depths.

Usage

data(irregular)

Value

A three-columns data.frame containing longitude, latitude and depth/elevation data.

Author(s)

Data modified form a dataset kindly provided by Noah Lottig from the university of Wisconsin https://limnology.wisc.edu/staff/lottig-noah/ in the framework of the North Temperate Lakes Long Term Ecological Research program https://lter.limnology.wisc.edu

See Also

griddify

Examples

# load data
data(irregular)

# use griddify
reg <- griddify(irregular, nlon = 40, nlat = 60)

# switch to class "bathy"
class(reg)
bat <- as.bathy(reg)
summary(bat)

# Plot the new bathy object along with the original data
plot(bat, image = TRUE, lwd = 0.1)
points(irregular$lon, irregular$lat, pch = 19, cex = 0.3, col = col2alpha(3))

Test whether an object is of class bathy

Description

Test whether an object is of class bathy

Usage

is.bathy(xyz)

Arguments

Value

The function returns TRUE or FALSE

Author(s)

Eric Pante

See Also

as.bathy, summary.bathy, read.bathy

Examples

# load NW Atlantic data
data(nw.atlantic)

# test class "bathy"
is.bathy(nw.atlantic)

# use as.bathy
atl <- as.bathy(nw.atlantic)

# class "bathy"
class(atl)
is.bathy(atl)

# summarize data of class "bathy"
summary(atl)

Computes least cost distances between two or more locations

Description

Computes least cost distances between two or more locations

Usage

lc.dist(trans, loc, res = c("dist", "path"), meters = FALSE, round = 0)

Arguments

Details

lc.dist computes least cost distances between 2 or more locations. This function relies on the package gdistance (van Etten, 2011. https://CRAN.R-project.org/package=gdistance) and on the trans.mat function to define a range of depths where the paths are possible.

Value

Results can be presented either as a kilometric distance matrix between all possible pairs of locations (argument res="dist") or as a list of paths (i.e. 2-columns matrices of routes) between pairs of locations (res="path").

Author(s)

Benoit Simon-Bouhet

References

Jacob van Etten (2011). gdistance: distances and routes on geographical grids. R package version 1.1-2. https://CRAN.R-project.org/package=gdistance

See Also

trans.mat

Examples

# Load and plot bathymetry
	data(hawaii)
	pal <- colorRampPalette(c("black","darkblue","blue","lightblue"))
	plot(hawaii,image=TRUE,bpal=pal(100),asp=1,col="grey40",lwd=.7,
	     main="Bathymetric map of Hawaii")

# Load and plot several locations
	data(hawaii.sites)
	sites <- hawaii.sites[-c(1,4),]
	rownames(sites) <- 1:4
	points(sites,pch=21,col="yellow",bg=col2alpha("yellow",.9),cex=1.2)
	text(sites[,1],sites[,2],lab=rownames(sites),pos=c(3,4,1,2),col="yellow")

## Not run: 
# Compute transition object with no depth constraint
	trans1 <- trans.mat(hawaii)

# Compute transition object with minimum depth constraint:
# path impossible in waters shallower than -200 meters depth
	trans2 <- trans.mat(hawaii,min.depth=-200)

# Computes least cost distances for both transition matrix and plots the results on the map
	out1 <- lc.dist(trans1,sites,res="path")
	out2 <- lc.dist(trans2,sites,res="path")
	lapply(out1,lines,col="yellow",lwd=4,lty=1) # No depth constraint (yellow paths)
	lapply(out2,lines,col="red",lwd=1,lty=1) # Min depth set to -200 meters (red paths)

# Computes and display distance matrices for both situations
	dist1 <- lc.dist(trans1,sites,res="dist")
	dist2 <- lc.dist(trans2,sites,res="dist")
	dist1
	dist2

# plots the depth profile between location 1 and 3 in the two situations
	dev.new()
	par(mfrow=c(2,1))
	path.profile(out1[[2]],hawaii,pl=TRUE,
                 main="Path between locations 1 & 3\nProfile with no depth constraint")
	path.profile(out2[[2]],hawaii,pl=TRUE,
                 main="Path between locations 1 & 3\nProfile with min depth set to -200m")

## End(Not run)

Add Great Circle lines on a map

Description

linesGC draws Great Circle lines between a set of start and end points on an existing map.

Usage

linesGC(start.points, end.points, n = 10, antimeridian = FALSE, ...)

Arguments

Details

linesGCD takes advantage of the gcIntermediate function from package geosphere to plot lines following a great circle. When working with marmap maps encompassing the antimeridian, longitudes are numbered from 0 to 360 (as opposed to the classical numbering from -180 to +180). It is thus critical to set antimeridian=TRUE to avoid plotting incoherent great circle lines.

Author(s)

Benoit Simon-Bouhet

See Also

dist2isobath, lc.dist

Examples

# Load NW Atlantic data and convert to class bathy
data(nw.atlantic)
atl <- as.bathy(nw.atlantic)

# Create vectors of latitude and longitude
lon <- c(-70, -65, -63, -55, -48)
lat <- c(33, 35, 40, 37, 33)

# Compute distances between each point and the -200m isobath
d <- dist2isobath(atl, lon, lat, isobath = -200)
d

# Create a nice palette of bleus for the bathymetry
blues <- c("lightsteelblue4","lightsteelblue3","lightsteelblue2","lightsteelblue1")

# Visualize the great circle distances
plot(atl, image=TRUE, lwd=0.1, land=TRUE, 
	 bpal = list(c(0,max(atl),"grey"), c(min(atl),0,blues)))
points(lon,lat, pch=21, col="orange4", bg="orange2", cex=.8)
linesGC(d[2:3],d[4:5])

# Load aleutians data and plot the map
data(aleutians)
plot(aleutians, image=TRUE, lwd=0.1, land=TRUE, 
	 bpal = list(c(0,max(aleutians),"grey"), c(min(aleutians),0,blues)))

# define start and end points
start <- matrix(c(170,55, 190, 60), ncol=2, byrow=TRUE, dimnames=list(1:2, c("lon","lat")))
end <- matrix(c(200, 56, 201, 57), ncol=2, byrow=TRUE, dimnames=list(1:2, c("lon","lat")))
start
end

# Add points and great circle distances on the map
points(start, pch=21, col="orange4", bg="orange2", cex=.8)
points(end, pch=21, col="orange4", bg="orange2", cex=.8)
linesGC(start, end, antimeridian=TRUE)

Import, plot and analyze bathymetric and topographic data

Description

marmap is a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. It can query the ETOPO 2022 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information, etc...) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances.

Details

Import, plot and analyze bathymetric and topographic data

Author(s)

Eric Pante, Benoit Simon-Bouhet and Jean-Olivier Irisson

Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>

References

Pante E, Simon-Bouhet B (2013) marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS ONE 8(9): e73051. doi:10.1371/journal.pone.0073051

Coral sampling information from the North West Atlantic

Description

Coral sampling data from Thoma et al 2009 (MEPS)

Usage

data(nw.atlantic)

Details

Sampling locations (longitude, latitude, depth in meters) for the deep-sea octocoral species Metallogorgia melanotrichos (see Thoma et al 2009 for details, including cruise information)

Value

A 3-column data frame

References

Thoma, J. N., E. Pante, M. R. Brugler, and S. C. France. 2009. Deep-sea octocorals and antipatharians show no evidence of seamount-scale endemism in the NW Atlantic. Marine Ecology Progress Series 397:25-35. https://www.int-res.com/articles/theme/m397p025.pdf

See Also

nw.atlantic

Examples

# load NW Atlantic data and convert to class bathy
data(nw.atlantic,metallo)
atl <- as.bathy(nw.atlantic)

## the function plot below plots:
## - the coastline in blue,
## - isobaths between 8000-4000 in light grey,
## - isobaths between 4000-500 in dark grey (to emphasize seamounts)

# 1st example: function points uses first two columns ; 3rd column contains depth info
plot(atl, deep=c(-8000,-4000,0), shallow=c(-4000,-500,0), step=c(500,500,0),
 	 lwd=c(0.5,0.5,1.5),lty=c(1,1,1),
 	 col=c("grey80", "grey20", "blue"),
 	 drawlabels=c(FALSE,FALSE,FALSE) )
points(metallo, cex=1.5, pch=19,col=rgb(0,0,1,0.5))

# 2nd example: plot points according to coordinates
plot(atl, deep=c(-8000,-4000,0), shallow=c(-4000,-500,0), step=c(500,500,0),
 	 lwd=c(0.5,0.5,1.5),lty=c(1,1,1),
 	 col=c("grey80", "grey20", "blue"),
 	 drawlabels=c(FALSE,FALSE,FALSE) )
subset(metallo, metallo$lon>-55) -> s # isolate points from the Corner Rise seamounts:
points(s, cex=1.5, pch=19,col=rgb(0,0,1,0.5)) # only plot those points

# 3rd example: point colors corresponding to a depth gradient:
par(mai=c(1,1,1,1.5))
plot(atl, deep=c(-6500,0), shallow=c(-50,0), step=c(500,0),
     lwd=c(0.3,1), lty=c(1,1),
     col=c("black","black"),
     drawlabels=c(FALSE,FALSE,FALSE))

max(metallo$depth, na.rm=TRUE) -> mx
colorRamp(c("white","lightyellow","lightgreen","blue","lightblue1","purple")) -> ramp
rgb( ramp(seq(0, 1, length = mx)), max = 255) -> blues

points(metallo, col="black", bg=blues[metallo$depth], pch=21,cex=1.5)
require(shape); colorlegend(zlim=c(-mx,0), col=rev(blues), main="depth (m)",posx=c(0.85,0.88))

Bathymetric data for the North West Atlantic

Description

Data imported from the NOAA GEODAS server

Usage

data(nw.atlantic)

Details

Data imported from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/). To prepare data from NOAA, fill the custom grid form, and choose "XYZ (lon,lat,depth)" as the "Output Grid Format", "No Header" as the "Output Grid Header", and either of the space, tab or comma as the column delimiter (either can be used, but "comma" is the default import format of read.bathy). Choose "omit empty grid cells" to reduce memory usage.

Value

A three-columns data.frame containing longitude, latitude and depth/elevation data.

Author(s)

see https://maps.ngdc.noaa.gov/viewers/wcs-client/

See Also

plot.bathy, summary.bathy

Examples

# load NW Atlantic data
data(nw.atlantic)

# use as.bathy
atl <- as.bathy(nw.atlantic)

# class "bathy"
class(atl)
summary(atl)

# test plot.bathy
plot(atl, deep=-8000, shallow=-1000, step=1000)

Coastline data for the North West Atlantic

Description

Coastline data for the North West Atlantic, as downloaded using the NOAA Coastline Extractor tool.

Usage

data(nw.atlantic.coast)

Details

Coastline data for the NW Atlantic was obtained using the NOAA Coastline Extractor tool. To get more coastline data, go to https://www.ngdc.noaa.gov/mgg/shorelines/.

Value

A 2-column data frame

References

see https://www.ngdc.noaa.gov/mgg/shorelines/

See Also

nw.atlantic

Examples

# load NW Atlantic data and convert to class bathy
data(nw.atlantic,nw.atlantic.coast)
atl <- as.bathy(nw.atlantic)

## the function plot below plots only isobaths:
## - isobaths between 8000-4000 in light grey, 
## - isobaths between 4000-500 in dark grey (to emphasize seamounts)

plot(atl, deep=c(-8000,-4000), shallow=c(-4000,-500), step=c(500,500), 
 	 lwd=c(0.5,0.5,1.5),lty=c(1,1,1),
 	 col=c("grey80", "grey20", "blue"), 
 	 drawlabels=c(FALSE,FALSE,FALSE) )
 	 
## the coastline can be added from a different source, 
## and can therefore have a different resolution:
lines(nw.atlantic.coast)

## add a geographical reference on the coast:
points(-71.064,42.358, pch=19); text(-71.064,42.358,"Boston", adj=c(1.2,0))

Get a composite buffer in a format suitable for plotting its outline

Description

Get a buffer (i.e. a non-circular buffer as produced by combine.buffers()) in a format suitable for plotting its outline. outline.buffer() replaces any NA values in a buffer or bathy object by 0 and non-NA values by -1.

Usage

outline.buffer(buffer)

Arguments

Details

This function is essentially used to prepare a composite buffer for plotting its outline on a bathymetric map. Plotting a single circular buffer should be done using the plot.buffer() function since it offers a more straightforward method for plotting and much smoother outlines, especially for low-resolution bathymetries.

Value

An object of class bathy of the same dimensions as buffer containing only zeros (outside the buffer area) and -1 values (within the buffer).

Author(s)

Benoit Simon-Bouhet

See Also

create.buffer, combine.buffers, plot.bathy

Examples

# load and plot a bathymetry
data(florida)
plot(florida, lwd = 0.2)
plot(florida, n = 1, lwd = 0.7, add = TRUE)

# add points around which a buffer will be computed
loc <- data.frame(c(-80,-82), c(26,24))
points(loc, pch = 19, col = "red")

# create 2 distinct buffer objects with different radii
buf1 <- create.buffer(florida, loc[1,], radius=1.9)
buf2 <- create.buffer(florida, loc[2,], radius=1.2)

# combine both buffers
buf <- combine.buffers(buf1,buf2)

## Not run: 
# Add outline of the resulting buffer in red 
# and the outline of the original buffers in blue
plot(outline.buffer(buf), lwd = 3, col = 2, add=TRUE)
plot(buf1, lwd = 0.5, fg="blue")
plot(buf2, lwd = 0.5, fg="blue")

## End(Not run)

Builds a bathymetry- and/or topography-constrained color palette

Description

Builds a constrained color palette based on depth / altitude bounds and given colors.

Usage

palette.bathy(mat, layers, land=FALSE, default.col="white")

Arguments

Details

palette.bathy allows the production of color palettes for specified bathymetric and/or topographic layers. The layers argument must be a list of vectors. Each vector corresponds to a bathymetry/topography layer (for example, one layer for bathymetry and one layer for topography). The first and second elements of the vector are the minimum and maximum bathymetry/topography, respectively. The other elements of the vector (3, onward) correspond to colors (see example below). palette.bathy is called internally by plot.bathy when the image argument is set to TRUE.

Value

A vector of colors which size depends on the depth / altitude range of the bathy matrix.

Author(s)

Eric Pante and Benoit Simon-Bouhet

See Also

plot.bathy

Examples

# load NW Atlantic data and convert to class bathy
	data(nw.atlantic)
	atl <- as.bathy(nw.atlantic)

# creating depth-constrained palette for the ocean only
    newcol <- palette.bathy(mat=atl,
		layers = list(c(min(atl), 0, "purple", "blue", "lightblue")),
		land = FALSE, default.col = "grey" )
	plot(atl, land = FALSE, n = 10, lwd = 0.5, image = TRUE,
		bpal = newcol, default.col = "grey")

# same:
	plot(atl, land = FALSE, n = 10, lwd = 0.5, image = TRUE,
		bpal = list(c(min(atl), 0, "purple", "blue", "lightblue")),
		default.col = "gray")

# creating depth-constrained palette for 3 ocean "layers"
	newcol <- palette.bathy(mat = atl, layers = list(
		c(min(atl), -3000, "purple", "blue", "grey"),
		c(-3000, -150, "white"),
		c(-150, 0, "yellow", "green", "brown")),
		land = FALSE, default.col = "grey")
	plot(atl, land = FALSE, n = 10, lwd = 0.7, image = TRUE,
		bpal = newcol, default.col = "grey")

# same
	plot(atl, land = FALSE, n = 10, lwd = 0.7, image = TRUE,
		bpal = list(c(min(atl), -3000, "purple","blue","grey"),
					c(-3000, -150, "white"),
					c(-150, 0, "yellow", "green", "brown")),
		default.col = "grey")

# creating depth-constrained palette for land and ocean
	newcol <- palette.bathy(mat= atl, layers = list(
		c(min(atl),0,"purple","blue","lightblue"),
		c(0, max(atl), "gray90", "gray10")),
		land = TRUE)
	plot(atl, land = TRUE, n = 10, lwd = 0.5, image = TRUE, bpal = newcol)

# same
	plot(atl, land = TRUE, n = 10, lwd = 0.7, image = TRUE,
		bpal = list(
			c(min(atl), 0, "purple", "blue", "lightblue"),
			c(0, max(atl), "gray90", "gray10")))

Geographic coordinates, kilometric distance and depth along a path

Description

Computes and plots the depth/altitude along a transect or path

Usage

path.profile(path,bathy,plot=FALSE, ...)

Arguments

Value

a four-columns matrix containing longitude, latitude, kilometric distance from the start of a route and depth for a set of points along a route. Optionally (i.e. when plot=TRUE) a bivariate plot of depth against the kilometric distance from the starting point of a transect or least cost path.

Author(s)

Benoit Simon-Bouhet

See Also

plotProfile

Examples

# Loading an object of class bathy and a data.frame of locations
	require(mapdata)
	data(hawaii)
	data(hawaii.sites)

# Preparing a color palette for the bathymetric map
	pal <- colorRampPalette(c("black","darkblue","blue","lightblue"))

# Plotting the bathymetric data and the path between locations
# (the path starts on location 1)
	plot(hawaii,image=TRUE,bpal=pal(100),col="grey40",lwd=.7, 
	     main="Bathymetric map of Hawaii")
	map("worldHires",res=0,fill=TRUE,col=rgb(.8,.95,.8,.7),add=TRUE)
	lines(hawaii.sites,type="o",lty=2,lwd=2,pch=21,
	      col="yellow",bg=col2alpha("yellow",.9),cex=1.2)
	text(hawaii.sites[,1], hawaii.sites[,2], 
	     lab=rownames(hawaii.sites),pos=c(3,3,4,4,1,2),col="yellow")

# Computing and plotting the depth profile for this path
	profile <- path.profile(hawaii.sites,hawaii,plot=TRUE, 
	                        main="Depth profile along the path\nconnecting the 6 sites")
	summary(profile)

Ploting bathymetric data

Description

Plots contour map from bathymetric data matrix of class bathy

Usage

## S3 method for class 'bathy'
plot(x, image=FALSE, bpal=NULL, land=FALSE,
           deepest.isobath, shallowest.isobath, step, n=20,
           lwd=1, lty=1, col="black", default.col="white", drawlabels = FALSE,
           xlab="Longitude", ylab="Latitude", asp=1, ...)

Arguments

Details

plot.bathy uses the base contour and image functions. If a vector of isobath characteristics is provided, different types of isobaths can be added to the same plot using a single call of plot.bathy (see examples)

If image=TRUE, the user has three choices for colors: (1) bpal can be set to NULL, in which case a default blue color palette is generated; (2) colors can be user-defined as in example 4, in which case the palette can be generated with function colorRampPalette (colors are then supplied as a vector to plot.bathy) ; (3) colors can be constrained to bathymetry- and/or topography. In this last case, a list of vectors is supplied to plot.bathy (example 7): each vector corresponds to a bathymetry/topography layer (for example, one layer for bathymetry and one layer for topography). The first and second elements of the vector are the minimum and maximum bathymetry/topography, respectively. The other elements of the vector (3, onward) correspond to colors (see example 7).

Value

a bathymetric map with isobaths

Note

plot.bathy uses a matrix of class bathy, and can therefore be substituted for plot.

Author(s)

Eric Pante and Benoit Simon-Bouhet

References

Eric Pante, Benoit Simon-Bouhet (2013) marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS ONE 8(9): e73051. doi:10.1371/journal.pone.0073051. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073051

See Also

read.bathy, summary.bathy, nw.atlantic, metallo

Examples

# load NW Atlantic data and convert to class bathy
	data(nw.atlantic)
	atl <- as.bathy(nw.atlantic)

## Example 1: a simple marine chart
	plot(atl) # without specifying any isobath parameters
	plot(atl, n=5, drawlabels=TRUE) # with about 5 isobaths
	plot(atl, deep=-8000, shallow=0, step=1000) # with isobath parameters

## Example 2: taking advantage of multiple types of isobaths
	plot(atl, deep=c(-8000,-2000,0), shallow=c(-2000,-100,0), step=c(1000,100,0),
		 lwd=c(0.5,0.5,1),lty=c(1,1,1),col=c("grey80","red", "blue"),
		 drawlabels=c(FALSE,FALSE,FALSE) )

## Example 3: plotting a colored map with the default color palette
	plot(atl, image=TRUE, deep=c(-8000,0), shallow=c(-1000,0), step=c(1000,0),
	     lwd=c(0.5,1), lty=c(1,1), col=c("grey","black"), drawlabels=c(FALSE,FALSE))

## Example 4: make a pretty custom color ramp
	colorRampPalette(c("purple","lightblue","cadetblue2","cadetblue1","white")) -> blues

	plot(atl, image=TRUE, bpal=blues(100), deep=c(-6500,0), shallow=c(-50,0), step=c(500,0),
	     lwd=c(0.3,1), lty=c(1,1), col=c("black","black"), drawlabels=c(FALSE,FALSE))

	scaleBathy(atl, deg=3, x="bottomleft", inset=5)

## Example 5: add points corresponding to sampling locations
##            point colors correspond to the sampling depth
	par(mai=c(1,1,1,1.5))
	plot(atl, deep=c(-4500,0), shallow=c(-50,0), step=c(500,0),
	     lwd=c(0.3,1), lty=c(1,1), col=c("black","black"), drawlabels=c(FALSE,FALSE))

	# add a title to the plot
	title(main="Distribution of coral samples\non the New England and Corner Rise seamounts")
	# add a scale
	scaleBathy(atl, deg=3, x="bottomleft", inset=5)

	# add a geographical reference on the coast:
	points(-71.064,42.358, pch=19)
	text(-71.064,42.358,"Boston", adj=c(1.2,0))

	# prepare colors for the sampling locations:
	data(metallo) ## see dataset metallo
	max(metallo$depth, na.rm=TRUE) -> mx
	colorRampPalette(c("white","lightyellow","lightgreen","blue","lightblue1","purple")) -> ramp
	blues <- ramp(max(metallo$depth))

	# plot sampling locations:
	points(metallo, col="black", bg=blues[metallo$depth], pch=21,cex=1.5)
	library(shape)
	colorlegend(zlim=c(-mx,0), col=rev(blues), main="depth (m)",posx=c(0.85,0.88))

## Example 6: use packages maps and mapdata in combination with marmap
	# use maps and mapdata to plot the coast
	library(maps)
	library(mapdata)
	map('worldHires',xlim=c(-75,-46),ylim=c(32,44), fill=TRUE, col="grey")
	box();axis(1);axis(2)

	# add bathymetric data from 'bathy' data
    plot(atl, add=TRUE, lwd=.3, deep=-4500, shallow=-10, step=500,
		drawlabel=FALSE, col="grey50")

## Example 7: provide a list of depths and colors to argument bpal to finely tune palette
	# check out ?palette.bathy to see details on how the palette is handled

	# creating depth-constrained palette for the ocean only
	plot(atl, land = FALSE, n = 10, lwd = 0.5, image = TRUE,
	     bpal = list(c(min(atl), 0, "purple", "blue", "lightblue")),
	     default.col = "gray")

	# creating depth-constrained palette for 3 ocean "layers"
	plot(atl, land = FALSE, n = 10, lwd = 0.7, image = TRUE,
	     bpal = list(c(min(atl), -3000, "purple","blue","grey"),
	                 c(-3000, -150, "white"),
	                 c(-150, 0, "yellow", "green", "brown")),
	     default.col = "grey")

	# creating depth-constrained palette for land and ocean
	plot(atl, land = TRUE, n = 10, lwd = 0.7, image = TRUE,
	     bpal = list(c(min(atl), 0, "purple", "blue", "lightblue"),
	                 c(0, max(atl), "gray90", "gray10")))

Plots a circular buffer and or its outline

Description

plot.buffer is a generic function that allows the plotting of objects of class buffer, either as new plots or as a new layer added on top of an existing one. The plotting of both the bathymetry/hypsometry as well as the outline of the buffer is possible.

Usage

## S3 method for class 'buffer'
plot(x, outline = TRUE, add = TRUE, ...)

Arguments

Value

Either a plot of the outline of a buffer (default) or a bathymetric map with isobaths of a buffer when outline = FALSE

Author(s)

Benoit Simon-Bouhet

See Also

create.buffer, combine.buffers, plot.bathy

Examples

# load and plot a bathymetry
data(florida)
plot(florida, lwd = 0.2)
plot(florida, n = 0, lwd = 0.7, add = TRUE)

# add points around which a buffer will be computed
loc <- data.frame(-80, 26)
points(loc, pch = 19, col = "red")

# compute buffer
buf <- create.buffer(florida, loc, radius=1.5)

# plot buffer bathymetry 
plot(buf, outline=FALSE, n=10, lwd=.5, col=2)

# add buffer outline
plot(buf, lwd=.7, fg=2)

Plotting projected surface areas

Description

Highlights the projected surface area for specific depth layers on an existing bathymetric/hypsometric map

Usage

plotArea(area, col)

Arguments

Author(s)

Benoit Simon-Bouhet

See Also

get.area, plot.bathy, areaPolygon

Examples

# load and plot a bathymetry
data(florida)
plot(florida, lwd = 0.2)
plot(florida, n = 1, lwd = 0.7, add = TRUE)

# Create a point and a buffer around this point
loc <- data.frame(-80, 26)
buf <- create.buffer(florida, loc, radius=1.8)

# Get the surface within the buffer for several depth slices
surf1 <- get.area(buf, level.inf=-200, level.sup=-1)
surf2 <- get.area(buf, level.inf=-800, level.sup=-200)
surf3 <- get.area(buf, level.inf=-3000, level.sup=-800)

s1 <- round(surf1$Square.Km)
s2 <- round(surf2$Square.Km)
s3 <- round(surf3$Square.Km)

# Add buffer elements on the plot
col.surf1 <- rgb(0.7, 0.7, 0.3, 0.3)
col.surf2 <- rgb(0, 0.7, 0.3, 0.3)
col.surf3 <- rgb(0.7, 0, 0, 0.3)

plotArea(surf1, col = col.surf1)
plotArea(surf2, col = col.surf2)
plotArea(surf3, col = col.surf3)
plot(buf, lwd = 0.7)
points(loc, pch = 19, col = "red")

## Add legend
legend("topleft", fill = c(col.surf1, col.surf2, col.surf3),
       legend = c(paste("]-200 ; -1] -",s1,"km2"),
	   			  paste("]-800 ; -200] -",s2,"km2"),
				  paste("]-3000 ; -800] -",s3,"km2")))

Ploting bathymetric data along a transect or path

Description

Plots the depth/altitude along a transect or path

Usage

plotProfile(profile,shadow=TRUE,xlim,ylim,col.sea,col.bottom,xlab,ylab, ...)

Arguments

Value

a bivariate plot of depth against the kilometric distance from the starting point of a transect or least cost path.

Note

path.profile with argument plot set to TRUE plots depth profiles with default values for all arguments of plotProfile.

Author(s)

Benoit Simon-Bouhet

See Also

path.profile, plot.bathy

Examples

# Example 1:
	data(celt)
	layout(matrix(1:2,nc=1),height=c(2,1))
	par(mar=c(4,4,1,1))
	plot(celt,n=40,draw=TRUE)
	points(c(-6.34,-5.52),c(52.14,50.29),type="o",col=2)
	
	tr <- get.transect(celt, x1 = -6.34, y1 = 52.14, x2 = -5.52, y2 = 50.29, distance = TRUE)
	plotProfile(tr)

# Example 2: 
	layout(matrix(1:2,nc=1),height=c(2,1))
	par(mar=c(4,4,1,1))
	plot(celt,n=40,draw=TRUE)
	points(c(-5,-6.34),c(49.8,52.14),type="o",col=2)
	
	tr2 <- get.transect(celt, x1 = -5, y1 = 49.8, x2 = -6.34, y2 = 52.14, distance = TRUE)
	plotProfile(tr2)

# Example 3: click several times on the map and press ESC
## Not run: 
	layout(matrix(1:2,nc=1),height=c(2,1))
	par(mar=c(4,4,1,1))
	data(florida)
	plot(florida,image=TRUE,dra=TRUE,land=TRUE,n=40)
	
	out <- path.profile(as.data.frame(locator(type="o",col=2,pch=19,cex=.8)),florida)
	plotProfile(out)

## End(Not run)

Read bathymetric data in XYZ format

Description

Reads a three-column table containing longitude (x), latitude (y) and depth (z) data.

Usage

read.bathy(xyz, header = FALSE, sep = ",", ...)

Arguments

Details

Allows direct import of data from the NOAA GEODAS Grid Translator webpage (https://maps.ngdc.noaa.gov/viewers/wcs-client/). To prepare data from NOAA, fill the custom grid form, and choose "XYZ (lon,lat,depth)" as the "Output Grid Format", "No Header" as the "Output Grid Header", and either of the space, tab of comma as the column delimiter (either can be used, but "comma" is the default import format of read.bathy). Choose "omit empty grid cells" to reduce memory usage.

Value

The output of read.bathy is a matrix of class bathy, which dimensions depends on the resolution of the grid uploaded from the NOAA GEODAS server (Grid Cell Size). The class bathy has its own methods for summarizing and ploting the data.

Author(s)

Eric Pante

See Also

summary.bathy, plot.bathy, readGEBCO.bathy

Examples

# load NW Atlantic data
data(nw.atlantic)

# write example file to disk
write.table(nw.atlantic, "NW_Atlantic.csv", sep=",", quote=FALSE, row.names=FALSE)

# use read.bathy
read.bathy("NW_Atlantic.csv", header=TRUE) -> atl

# remove temporary file
system("rm NW_Atlantic.csv") # remove file, for unix-like systems

# class "bathy"
class(atl)

# summarize data of class "bathy"
summary(atl)

Read bathymetric data from a GEBCO file

Description

Imports 30-sec and 1-min bathymetric data from a .nc file downloaded on the GEBCO website.

Usage

readGEBCO.bathy(file, resolution = 1, sid = FALSE)

Arguments

Details

readGEBCO.bathy reads a 30 arcseconds or 1 arcminute bathymetry file downloaded from the GEBCO (General Bathymetric Chart of the Oceans) website (British Oceanographic Data Center). The website allows the download of bathymetric data in the netCDF format. readGEBCO.bathy uses the ncdf4 package to load the data into R, and parses it into an object of class bathy.

Data can be downloaded from the 30 arcseconds database (GEBCO_08) or the 1 arcminute database (GEBCO_1min, the default). A third database type, GEBCO_08 SID, is available from the website. This database includes a source identifier specifying which grid cells have depth information based on soundings ; it does not include bathymetry or topography data. readGEBCO.bathy can read this type of database when sid is set to TRUE. Then only the SID information will be included in the object of class bathy. Therefore, to display a map with both the bathymetry and the SID information, you will have to download both datasets from GEBCO, and import and plot both independently.

The argument resolution specifies the resolution of the object of class bathy. Because the resolution of GEBCO data is rather fine, we offer the possibility of downsizing the dataset with resolution. resolution is in units of the selected database: in "GEBCO_1min", resolution is in minutes; in "GEBCO_08", resolution is in 30 arcseconds (that is, resolution = 3 corresponds to 3x30sec, or 1.5 arcminute).

Value

The output of readGEBCO.bathy is a matrix of class bathy, which dimensions depends on the resolution specified (one-minute, the original GEBCO resolution, is the default). The class bathy has its own methods for summarizing and ploting the data.

Author(s)

Eric Pante and Benoit Simon-Bouhet

References

British Oceanographic Data Center: General Bathymetric Chart of the Oceans gridded bathymetric data sets (accessed July 10, 2020) https://www.bodc.ac.uk/data/hosted_data_systems/gebco_gridded_bathymetry_data/

General Bathymetric Chart of the Oceans website (accessed Oct 5, 2013) https://www.gebco.net

David Pierce (2019). ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. R package version 1.17. https://cran.r-project.org/package=ncdf4

See Also

getNOAA.bathy, read.bathy, plot.bathy

Examples

## Not run: 
# This example will not run, and we do not provide the dummy "gebco_file.nc" file,
# because a copyright license must be signed on the GEBCO website before the data can be
# downloaded and used. We just provide this line as an example for synthax.
  readGEBCO.bathy(file="gebco_file.nc", resolution=1) -> nw.atl

# Second not-run example, with GEBCO_08 and SID:
  readGEBCO.bathy("gebco_08_7_38_10_43_corsica.nc") -> med
  summary(med) # the bathymetry data

  readGEBCO.bathy("gebco_SID_7_38_10_43_corsica.nc")-> sid
  summary(sid) # the SID data

  colorRampPalette(c("lightblue","cadetblue1","white")) -> blues # custom col palette
  plot(med, n=1, im=T, bpal=blues(100)) # bathymetry

  as.numeric(rownames(sid)) -> x.sid
  as.numeric(colnames(sid)) -> y.sid
  contour(x.sid, y.sid, sid, drawlabels=FALSE, lwd=.1, add=TRUE) # SID

## End(Not run)

Adds a scale to a map

Description

Uses geographic information from object of class bathy to calculate and plot a scale in kilometer.

Usage

scaleBathy(mat, deg=1, x="bottomleft", y=NULL, inset=10, angle=90, ...)

Arguments

Details

scaleBathy is a simple utility to add a scale to the lower left corner of a bathy plot. The distance in kilometers between two points separated by 1 degree longitude is calculated based on the minimum latitude of the bathy object used to plot the map. Option deg allows the user to plot the distance separating more than one degree (default is one).

The plotting coordinates x and y either correspond to two points on the map (i.e. longitude and latitude of the point where the scale should be plotted), or correspond to a keyword (set with x, y being set to NULL) from the list "bottomright", "bottomleft", "topright", "topleft". When a keyword is used, the option inset controls how far the scale will be from the edges of the plot.

Value

a scale added to the active graphical device

Note

The calculation formula is from function map.scale of package maps. 6372.798 km is used as the Earth radius.

Author(s)

Eric Pante

See Also

plot.bathy

Examples

# load NW Atlantic data and convert to class bathy
	data(nw.atlantic)
	atl <- as.bathy(nw.atlantic)

# a simple example
	plot(atl, deep=-8000, shallow=-1000, step=1000, lwd=0.5, col="grey")
	scaleBathy(atl, deg=4)

# using keywords to place the scale with inset=10%
	par(mfrow=c(2,2))
	plot(atl, deep=-8000, shallow=-1000, step=1000, lwd=0.5, col="grey")
	scaleBathy(atl, deg=4, x="bottomleft", y=NULL)
	plot(atl, deep=-8000, shallow=-1000, step=1000, lwd=0.5, col="grey")
	scaleBathy(atl, deg=4, x="bottomright", y=NULL)

# using keywords to place the scale with inset=20%
	plot(atl, deep=-8000, shallow=-1000, step=1000, lwd=0.5, col="grey")
	scaleBathy(atl, deg=4, x="topleft", y=NULL, inset=20)
	plot(atl, deep=-8000, shallow=-1000, step=1000, lwd=0.5, col="grey")
	scaleBathy(atl, deg=4, x="topright", y=NULL, inset=20) 

Automatic placement of piecharts on maps

Description

Attemps to automatically place piecharts on maps, avoiding overlap. Work in progress...

Usage

space.pies(x, y, pie.slices, pie.colors=NULL, pie.radius=1, pie.space=5,
              link=TRUE, seg.lwd=1, seg.col=1, seg.lty=1, coord=NULL)

Arguments

Details

space.pies tries to position piecharts on a map while avoiding overlap between them. The function heavily relies on two other functions. floating.pie from package plotrix is used to draw individual piecharts. floating.pie treats one pie at a time; space.pies can handle one or multiple pies by looping floating.pie. pointLabels from package maptools was modified to find the best placement for the pies, given their size and distance from their anchor point. pointLabels was originally meant to automatically place text labels, not objects; the modified version contained in space.pies uses the coordinates chosen by pointLabels for text. The algorithm used is simulating annealing (SANN). You can get a different result each time you run space.pies, because pointLabel finds one good solution out of many. If you are not satisfied by the solution, you can try running the function again.

The argument coord allows to choose between the automatic placement outlined above, and a user-defined list of longitudes and latitudes (in a two-column table format) for plotting the piecharts.

Anchor point: spatial location of the data corresponding to the piechart (e.g. a sampling point).

Value

Piechart(s) added to a plot.

Author(s)

Eric Pante, using functions plotrix::floating.pie and maptools::pointLabel.

References

Bivand, R. and Lewin-Koh, N. (2013) maptools: Tools for reading and handling spatial objects. R package version 0.8-25. http://CRAN.R-project.org/package=maptools

Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4): 8-12.

SANN code implemented in pointLabel based on: Jon Christensen, Joe Marks, and Stuart Shieber. Placing text labels on maps and diagrams. In Paul Heckbert, editor, Graphics Gems IV, pages 497-504. Academic Press, Boston, MA, 1994.

See Also

plot.bathy, plotrix::floating.pie, maptools::pointLabel

Examples

# fake frequencies to feed to space.pies()
	sample(seq(10,90,5), 11)-> freq.a
	100-freq.a -> freq.b
	rep("lightblue",11) -> col.a
	rep("white",11) -> col.b

# some coordinates on the NW Atlantic coast, and on seamounts
	x = c(-74.28487,-73.92323,-73.80753,-72.51728,-71.12418,
		  -69.81176,-69.90715,-70.43201,-70.17135,-69.43912,-65.49608)
	y = c(39.36714,39.98515,40.40316,40.79654,41.49872,41.62076,
		  41.99805,42.68061,43.40714,43.81499,43.36471)
	pts.coast = data.frame(x,y, freq.a, freq.b, col.a, col.b)

	x = c(-66.01404,-65.47260,-63.75456,-63.26082,-62.12838,
	      -60.46885,-59.96952,-56.90925,-52.20397,-51.32288,-50.72461)
	y = c(39.70769,39.39064,38.83020,38.56479,38.01881,38.95405,
	      37.55675,34.62617,36.15592,36.38992,35.91779)
	pts.smt = data.frame(x,y, freq.a, freq.b, col.a, col.b)

# prepare the plot
	data(nw.atlantic) ; atl <- as.bathy(nw.atlantic)
	plot(atl, deep=-8000, shallow=0, step=1000,col="grey")
	points(pts.coast,pch=19,col="blue", cex=0.5)
	points(pts.smt,pch=19,col="blue", cex=0.5)

# automatic placement of piecharts with space.pies
	space.pies(pts.coast[,1], pts.coast[,2],
	           pie.slices=pts.coast[,3:4], pie.colors=pts.coast[,5:6], pie.radius=0.5)
	space.pies(pts.smt[,1], pts.smt[,2],
	           pie.slices=pts.smt[,3:4], pie.colors=pts.coast[,5:6], pie.radius=0.5)

Creates bathy objects from larger bathy objects

Description

Generates rectangular or non rectangular bathy objects by extracting bathymetric data from larger bathy objects.

Usage

subsetBathy(mat, x, y=NULL, locator=TRUE, ...)

Arguments

Details

subsetBathy allows the user to generate new bathy objects by extracting data from larger bathy objects. The extraction of bathymetric data can be done interactively by clicking on a bathymetric map, or by providing longitudes and latitudes for the boundaries for the new bathy object. If two data points are provided, a rectangular area is selected. If more than two points are provided, a polygon is defined by linking the points and the bathymetic data is extracted within the polygon only. subsetBathy relies on the point.in.polygon function from package sp to identify which points of the initial bathy matrix lie witin the boundaries of the user-defined polygon.

Value

A matrix of class bathy.

Author(s)

Benoit Simon-Bouhet

References

Pebesma, EJ, RS Bivand, (2005). Classes and methods for spatial data in R. R News 5 (2), https://cran.r-project.org/doc/Rnews/

Bivand RS, Pebesma EJ, Gomez-Rubio V (2013). Applied spatial data analysis with R, Second edition. Springer, NY. https://asdar-book.org

See Also

plot.bathy, get.depth, summary.bathy, aleutians

Examples

# load aleutians dataset
data(aleutians)

# create vectors of latitude and longitude to define the boundary of a polygon
lon <- c(188.56, 189.71, 191, 193.18, 196.18, 196.32, 196.32, 194.34, 188.83)
lat <- c(54.33, 55.88, 56.06, 55.85, 55.23, 54.19, 52.01, 50.52, 51.71)


# plot the initial bathy and overlay the polygon
plot(aleutians, image=TRUE, land=TRUE, lwd=.2)
polygon(lon,lat)

# Use of subsetBathy to extract the new bathy object
zoomed <- subsetBathy(aleutians, x=lon, y=lat, locator=FALSE)

# plot the new bathy object
dev.new() ; plot(zoomed, land=TRUE, image=TRUE, lwd=.2)

# alternativeley once the map is plotted, use the interactive mode:
## Not run: 
plot(aleutians, image=TRUE, land=TRUE, lwd=.2)
zoomed2 <- subsetBathy(aleutians, pch=19, col=3)
dev.new() ; plot(zoomed2, land=TRUE, image=TRUE, lwd=.2)

## End(Not run)
# click several times and press Escape

Creating and querying local SQL database for bathymetric data

Description

subsetSQL queries the local SQL database created with setSQL to extract smaller data subsets.

Usage

setSQL(bathy, header = TRUE, sep = ",", db.name = "bathy_db")
subsetSQL(min_lon, max_lon, min_lat, max_lat, db.name = "bathy_db")

Arguments

Details

Functions setSQL and subsetSQL were built to work together. setSQL builds an SQL database and saves it on disk. subsetSQL queries that local database and the fields min_lon, max_lon, etc, are used to extract a subset of the database. The functions were built as two entities so that multiple queries can be done multiple times, without re-building the database each time. These functions were designed to access the very large (>5Go) ETOPO 2022 file that can be downloaded from the NOAA website (https://www.ncei.noaa.gov/products/etopo-global-relief-model)

Value

setSQL returns TRUE if the database was successfully created. subsetSQL returns a matrix of class bathy that can directly be used with plot.bathy.

Note

If unspecified, db.name is set to "bathy_db" by default. Thus, theere must be no database file called bathy_db in the working directory prior to running setSQL unless a different name is used for the new database. Make sure that your "bathy" input is a xyz text file (for function setSQL) with 3 columns containing longitude, latitude and depth data, in that order. setSQL and subsetSQL were modified on Nov. 2, 2014 to comply with RSQLite 1.0.0.

Author(s)

Eric Pante

References

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

Examples

## Not run: 
# load NW Atlantic data
data(nw.atlantic)

# write data to disk as a comma-separated text file
write.table(nw.atlantic, "NW_Atlantic.csv", sep=",", quote=FALSE, row.names=FALSE)

# prepare SQL database
setSQL(bathy="NW_Atlantic.csv")

# uses data from the newly-created SQL database:
subsetSQL(min_lon=-70,max_lon=-50,
             min_lat=35, max_lat=41) -> test

# visualize the results (of class bathy)
summary(test)

# remove temporary database and CSV files
system("rm bathy_db") # remove file, for unix-like systems
system("rm NW_Atlantic.csv") # remove file, for unix-like systems

## End(Not run)

Summary of bathymetric data of class bathy

Description

Summary of bathymetric data of class bathy. Provides geographic bounds and resolution (in minutes) of the dataset, statistics on depth data, and a preview of the bathymetric matrix.

Usage

## S3 method for class 'bathy'
summary(object, ...)

Arguments

Value

Information on the geographic bounds of the dataset (minimum and maximum latitude and longitude), resolution of the matrix in minutes, statistics on the depth data (e.g. min, max, median...), and a preview of the data.

Author(s)

Eric Pante and Benoit Simon-Bouhet

See Also

read.bathy, plot.bathy

Examples

# load NW Atlantic data
data(nw.atlantic)

# use as.bathy
atl <- as.bathy(nw.atlantic)

# class bathy
class(atl)

# summarize data of class bathy
summary(atl)

Transition matrix

Description

Creates a transition object to be used by lc.dist to compute least cost distances between locations.

Usage

trans.mat(bathy,min.depth=0,max.depth=NULL)

Arguments

Details

trans.mat creates a transition object usable by lc.dist to computes least cost distances between a set of locations. trans.mat rely on the function raster from package raster (Hijmans & van Etten, 2012. https://CRAN.R-project.org/package=raster) and on transition from package gdistance (van Etten, 2011. https://CRAN.R-project.org/package=gdistance).

The transition object contains the probability of transition from one cell of a bathymetric grid to adjacent cells and depends on user defined parameters. trans.mat is especially usefull when least cost distances need to be calculated between several locations at sea. The default values for min.depth and max.depth ensure that the path computed by lc.dist will be the shortest path possible at sea avoiding land masses. The path can be constrained to a given depth range by setting manually min.depth and max.depth. For instance, it is possible to limit the possible paths to the continental shelf by setting max.depth=-200. Inaccuracies of the bathymetric data can occasionally result in paths crossing land masses. Setting min.depth to low negative values (e.g. -10 meters) can limit this problem.

trans.mat takes also advantage of the function geoCorrection from package gdistance (van Etten, 2012. https://CRAN.R-project.org/package=gdistance) to take into account map distortions over large areas.

Value

A transition object.

Warning

Please be aware that the use of trans.mat can be time consumming for large bathymetric datasets. The function takes about one minute to compute a transition matrix for the hawaii bathymetric data (bathymetric data of class bathy with 599 rows and 419 columns, see hawaii) on a MacBook Pro with a 2.66 GHz Intel Core i7 processor and 4 Go of RAM.

Author(s)

Benoit Simon-Bouhet

References

Jacob van Etten (2011). gdistance: distances and routes on geographical grids. R package version 1.1-2. https://CRAN.R-project.org/package=gdistance Robert J. Hijmans & Jacob van Etten (2012). raster: Geographic analysis and modeling with raster data. R package version 1.9-92. https://CRAN.R-project.org/package=raster

See Also

lc.dist, hawaii

Examples

# Load and plot bathymetry
data(hawaii)
summary(hawaii)
plot(hawaii)

## Not run: 
# Compute transition object with no depth constraint
trans1 <- trans.mat(hawaii)

# Compute transition object with minimum depth constraint: 
# path impossible in waters shallower than -200 meters depth
trans2 <- trans.mat(hawaii,min.depth=-200)

# Visualizing results
par(mfrow=c(1,2))
plot(raster(trans1), main="No depth constraint")
plot(raster(trans2), main="Constraint in shallow waters")

## End(Not run)