Loads and creates spatial data, including layers and tools that are relevant to CCAMLR activities. All operations use the Lambert azimuthal equal-area projection (via EPSG:6932).

Description

This package provides two broad categories of functions: load functions and create functions.

Load functions

Load functions are used to import CCAMLR geo-referenced layers and include:

• load_ASDs

• load_SSRUs

• load_RBs

• load_SSMUs

• load_MAs

• load_Coastline

• load_MPAs

• load_EEZs

• load_Bathy

Create functions

Create functions are used to create geo-referenced layers from user-generated data and include:

• create_Points

• create_Lines

• create_Polys

• create_PolyGrids

• create_Stations

• create_Pies

• create_Arrow

• create_Hashes

Vignette

To learn more about CCAMLRGIS, start with the GitHub ReadMe (see https://github.com/ccamlr/CCAMLRGIS#ccamlrgis-r-package). Some basemaps are given here https://github.com/ccamlr/CCAMLRGIS/blob/master/Basemaps/Basemaps.md

Author(s)

Maintainer: Stephane Thanassekos stephane.thanassekos@ccamlr.org

Authors:

• Keith Reid

• Lucy Robinson

Other contributors:

• Michael D. Sumner [contributor]

• Roger Bivand [contributor]

See Also

The CCAMLRGIS package relies on several other package which users may want to familiarize themselves with, namely sf (https://CRAN.R-project.org/package=sf) and terra (https://CRAN.R-project.org/package=terra).

CCAMLRGIS Projection

Description

The CCAMLRGIS package uses the Lambert azimuthal equal-area projection (see https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection). Source: https://gis.ccamlr.org/. In order to align with recent developments within Geographic Information Software, this projection will be accessed via EPSG code 6932 (see https://epsg.org/crs_6932/WGS-84-NSIDC-EASE-Grid-2-0-South.html).

Usage

data(CCAMLRp)

Format

character string

Value

"+proj=laea +lat_0=-90 +lon_0=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs"

Clip Polygons to a simplified Antarctic coastline

Description

Clip Polygons to the Coast (removes polygon parts that fall on land) and computes the area of the resulting polygon. Uses an sf object as input which may be user-generated or created via buffered points (see create_Points), buffered lines (see create_Lines) or polygons (see create_Polys). N.B.: this function uses a simplified coastline. For more accurate results, load the high resolution coastline (see load_Coastline), and use sf::st_difference().

Usage

Clip2Coast(Input)

Arguments

Value

sf polygon carrying the same data as the Input.

See Also

Coast, create_Points, create_Lines, create_Polys, create_PolyGrids.

Examples

MyPolys=create_Polys(PolyData,Densify=TRUE,Buffer=c(10,-15,120))
plot(st_geometry(MyPolys),col='red')
plot(st_geometry(Coast[Coast$ID=='All',]),add=TRUE)
MyPolysClipped=Clip2Coast(MyPolys)
plot(st_geometry(MyPolysClipped),col='blue',add=TRUE)
#View(MyPolysClipped)

Simplified and subsettable coastline

Description

Coastline polygons generated from load_Coastline and sub-sampled to only contain data that falls within the boundaries of the Convention Area. This spatial object may be subsetted to plot the coastline for selected ASDs or EEZs (see examples). Source: https://gis.ccamlr.org/

Usage

data(Coast)

Format

sf

See Also

Clip2Coast, load_Coastline.

Examples

#Complete coastline:
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey')

#ASD 48.1 coastline:
plot(st_geometry(Coast[Coast$ID=='48.1',]),col='grey')

Bathymetry colors

Description

Set of standard colors to plot bathymetry, to be used in conjunction with Depth_cuts.

Usage

data(Depth_cols)

Format

character vector

See Also

Depth_cols2, add_col, add_Cscale, SmallBathy.

Examples

terra::plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,axes=FALSE)

Bathymetry colors with Fishable Depth range

Description

Set of colors to plot bathymetry and highlight Fishable Depth range (600-1800), to be used in conjunction with Depth_cuts2.

Usage

data(Depth_cols2)

Format

character vector

See Also

Depth_cols, add_col, add_Cscale, SmallBathy.

Examples

terra::plot(SmallBathy(),breaks=Depth_cuts2,col=Depth_cols2,axes=FALSE,box=FALSE)

Bathymetry depth classes

Description

Set of depth classes to plot bathymetry, to be used in conjunction with Depth_cols.

Usage

data(Depth_cuts)

Format

numeric vector

See Also

Depth_cuts2, add_col, add_Cscale, SmallBathy.

Examples

terra::plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,axes=FALSE,box=FALSE)

Bathymetry depth classes with Fishable Depth range

Description

Set of depth classes to plot bathymetry and highlight Fishable Depth range (600-1800), to be used in conjunction with Depth_cols2.

Usage

data(Depth_cuts2)

Format

numeric vector

See Also

Depth_cuts, add_col, add_Cscale, SmallBathy.

Examples

terra::plot(SmallBathy(),breaks=Depth_cuts2,col=Depth_cols2,axes=FALSE,box=FALSE)

Example dataset for create_PolyGrids

Description

To be used in conjunction with create_PolyGrids.

Usage

data(GridData)

Format

data.frame

See Also

create_PolyGrids.

Examples

#View(GridData)

MyGrid=create_PolyGrids(Input=GridData,dlon=2,dlat=1)
plot(st_geometry(MyGrid),col=MyGrid$Col_Catch_sum)

Polygon labels

Description

Labels for the layers obtained via 'load_' functions. Positions correspond to the centroids of polygon parts. Can be used in conjunction with add_labels.

Usage

data(Labels)

Format

data.frame

See Also

add_labels, load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_EEZs, load_MPAs.

Examples

#View(Labels)

ASDs=load_ASDs()
plot(st_geometry(ASDs))
add_labels(mode='auto',layer='ASDs',fontsize=1,fonttype=2)

Example dataset for create_Lines

Description

To be used in conjunction with create_Lines.

Usage

data(LineData)

Format

data.frame

See Also

create_Lines.

Examples

 
#View(LineData)

MyLines=create_Lines(LineData)
plot(st_geometry(MyLines),lwd=2,col=rainbow(5))

Example dataset for create_Pies

Description

To be used in conjunction with create_Pies. Count and catch of species per location.

Usage

data(PieData)

Format

data.frame

See Also

create_Pies.

Examples

#View(PieData)

#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=50
)
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1.6,Boxexp=c(0.5,0.45,0.12,0.45),
              PieTitle="Species")

Example dataset for create_Pies

Description

To be used in conjunction with create_Pies. Count and catch of species per location.

Usage

data(PieData2)

Format

data.frame

See Also

create_Pies.

Examples

#View(PieData2)

MyPies=create_Pies(Input=PieData2,
                  NamesIn=c("Lat","Lon","Sp","N"),
                  Size=5,
                  GridKm=250
)
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.8,PosY=-0.3,Boxexp=c(0.5,0.45,0.12,0.45),
             PieTitle="Species")

Example dataset for create_Points

Description

To be used in conjunction with create_Points.

Usage

data(PointData)

Format

data.frame

See Also

create_Points.

Examples

#View(PointData)

MyPoints=create_Points(PointData)
plot(st_geometry(MyPoints))
text(MyPoints$x,MyPoints$y,MyPoints$name,adj=c(0.5,-0.5),xpd=TRUE)
plot(st_geometry(MyPoints[MyPoints$name=='four',]),bg='red',pch=21,cex=1.5,add=TRUE)

Example dataset for create_Polys

Description

To be used in conjunction with create_Polys.

Usage

data(PolyData)

Format

data.frame

See Also

create_Polys.

Examples

#View(PolyData)

MyPolys=create_Polys(PolyData,Densify=TRUE)
plot(st_geometry(MyPolys),col='green')
text(MyPolys$Labx,MyPolys$Laby,MyPolys$ID)
plot(st_geometry(MyPolys[MyPolys$ID=='three',]),border='red',lwd=3,add=TRUE)

Rotate object

Description

Rotate a spatial object by setting the longitude that should point up.

Usage

Rotate_obj(Input, Lon0 = NULL)

Arguments

Value

Spatial object in your environment to only be used for plotting, not for analysis.

See Also

create_Points, create_Lines, create_Polys, create_PolyGrids, create_Stations, create_Pies, create_Arrow.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#47-rotate_obj
# and:
# https://github.com/ccamlr/CCAMLRGIS/blob/master/Basemaps/Basemaps.md

RotB=Rotate_obj(SmallBathy(),Lon0=-180)
terra::plot(RotB,breaks=Depth_cuts,col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE)
add_RefGrid(bb=st_bbox(RotB),ResLat=10,ResLon=20,LabLon = -180,offset = 3)

Small bathymetry dataset

Description

Bathymetry dataset derived from the GEBCO 2024 (see https://www.gebco.net/) dataset. Subsampled at a 10,000m resolution. Projected using the CCAMLR standard projection (CCAMLRp). To highlight the Fishable Depth range, use Depth_cols2 and Depth_cuts2. To be only used for large scale illustrative purposes. Please refer to load_Bathy to get higher resolution data.

Usage

SmallBathy()

Format

raster

References

GEBCO Compilation Group (2024) GEBCO 2024 Grid (doi:10.5285/1c44ce99-0a0d-5f4f-e063-7086abc0ea0f)

See Also

load_Bathy, add_col, add_Cscale, Depth_cols, Depth_cuts, Depth_cols2, Depth_cuts2, get_depths, create_Stations.

Examples

terra::plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,axes=FALSE,box=FALSE)

Add a color scale

Description

Adds a color scale to plots. Default behavior set for bathymetry. May also be used to place a legend.

Usage

add_Cscale(
  pos = "1/1",
  title = "Depth (m)",
  width = 18,
  height = 70,
  cuts = Depth_cuts,
  cols = Depth_cols,
  minVal = NA,
  maxVal = NA,
  fontsize = 1,
  offset = 100,
  lwd = 1,
  Titlefontsize = 1.2 * fontsize,
  TitleVAdj = 0,
  BoxAdj = c(0, 0, 0, 0),
  BoxCol = "black",
  BoxBG = "white",
  Clwd = 0,
  Ccol = "black",
  Cwdth = 1,
  TckL = 1,
  Tcklwd = 1,
  Tdist = 1,
  mode = "Cscale"
)

Arguments

See Also

load_Bathy, SmallBathy, Depth_cuts, Depth_cols, Depth_cuts2, Depth_cols2, add_col, add_Legend, R colors, legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#5-adding-colors-legends-and-labels

library(terra)

#Example 1: Adding two color scales

plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,box=FALSE)
add_Cscale(pos='1/2',height=45,maxVal=0,minVal=-4000,fontsize=0.8)
#Some gridded data
MyGrid=create_PolyGrids(GridData,dlon=2,dlat=1)
Gridcol=add_col(MyGrid$Catch_sum,cuts=10)
plot(st_geometry(MyGrid),col=Gridcol$varcol,add=TRUE)
#Add color scale using cuts and cols generated by add_col, note the use of 'round'
add_Cscale(pos='2/2',height=45,title='Catch (t)',
           cuts=round(Gridcol$cuts,1),cols=Gridcol$cols,fontsize=0.8)

#Example 2: Adding a color scale and a legend

#Create some point data
MyPoints=create_Points(PointData)

#Crop the bathymetry to match the extent of MyPoints 

BathyCr=crop(SmallBathy(),extend(ext(MyPoints),100000))
plot(BathyCr,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(0,0,0,7))
add_Cscale(pos='1/2',height=45,maxVal=0,minVal=-4000,fontsize=0.8)

#Plot points with different symbols and colors (see ?points)
Psymbols=c(21,22,23,24)
Pcolors=c('red','green','blue','yellow')
plot(st_geometry(MyPoints[MyPoints$name=='one',]),pch=Psymbols[1],bg=Pcolors[1],add=TRUE)
plot(st_geometry(MyPoints[MyPoints$name=='two',]),pch=Psymbols[2],bg=Pcolors[2],add=TRUE)
plot(st_geometry(MyPoints[MyPoints$name=='three',]),pch=Psymbols[3],bg=Pcolors[3],add=TRUE)
plot(st_geometry(MyPoints[MyPoints$name=='four',]),pch=Psymbols[4],bg=Pcolors[4],add=TRUE)

#Add legend with position determined by add_Cscale
Loc=add_Cscale(pos='2/2',height=45,mode='Legend')
legend(Loc,legend=c('one','two','three','four'),title='Vessel',pch=Psymbols,
pt.bg=Pcolors,xpd=TRUE)

Add Legend

Description

Add a legend to you map. Give the bounding box of your plot and lists of parameters as inputs.

Usage

add_Legend(bb, LegOpt, Items)

Arguments

Value

Legend added to current plot.

LegOpt options

• Title: character, title of the legend, set to NULL for no title.

• Subtitle: character, subtitle of the legend, set to NULL for no subtitle.

• Pos: character, general position of the legend. One of "bottomright" (default), "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" or "center".

• BoxW: numeric, legend box width (see figure below).

• BoxH: numeric, legend box height (see figure below).

• PosX: numeric, horizontal adjustment of legend (see figure below).

• PosY: numeric, vertical adjustment of legend (see figure below).

• Boxexp: numeric, vector of length 4 controlling the expansion of the legend box, given as c(xmin,xmax,ymin,ymax), see figure below.

• Boxbd: character, color of the background of the legend box. set to NA for no background.

• Boxcol: character, color of the border of the legend box. Set to NA for no box.

• Boxlwd: numeric, line thickness of the legend box. Set Boxcol to NA for no box.

• Titlefontsize: numeric, size of the legend title.

• Subtitlefontsize: numeric, size of the legend subtitle.

• TitleAdj: numeric vector of length 2, as c(x,y) to adjust title location (see figure below).

• SubtitleAdj: numeric vector of length 2, as c(x,y) to adjust subtitle location.

Items options that are common to all items

• Text: character, text of the item.

• Shape: character, shape description, one of "rectangle", "circle", "ellipse", "line", "arrow" or "none". Using "none" will leave a blank space that can be filled by a user-defined shape.

• ShpFill: character, fill color of shape, set to NA for no fill.

• ShpBord: character, border color of shape, set to NA for no border.

• ShpHash: logical (TRUE/FALSE) to add hashed lines to the shape (see create_Hashes).

• Shplwd: numeric, line thickness of the shape's border, set ShpBord to NA for no border.

• fontsize: numeric, size of the text.

• STSpace: numeric, space between the Shape and its Text (see figure below).

• ShiftX: numeric, shift Shape and Text left or right (see figure below).

• ShiftY: numeric, shift Shape and Text up or down (see figure below).

• Hashcol: character, color of hashes (if ShpHash is TRUE), see create_Hashes for details.

• Hashangle: numeric, angle of hashes (if ShpHash is TRUE), see create_Hashes for details.

• Hashspacing: numeric, spacing between hashes (if ShpHash is TRUE), see create_Hashes for details.

• Hashwidth: numeric, width of hashes (if ShpHash is TRUE), see see create_Hashes for details.

Items options that are specific to the item's Shape

• RectW: numeric, width of rectangle shape.

• RectH: numeric, height of rectangle shape.

• CircD: numeric, diameter of circle shape.

• EllW: numeric, width of ellipse shape.

• EllH: numeric, height of ellipse shape.

• EllA: numeric, angle of ellipse shape.

• LineTyp: numeric, type of line shape (0=blank, 1=solid, 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash).

• LineL: numeric, length of the line shape.

• ArrL: numeric, length of the arrow shape.

• ArrPwidth: numeric, width of arrow's path. see create_Arrow for details.

• ArrHlength: numeric, length of arrow's head. see create_Arrow for details.

• ArrHwidth: numeric, width of arrow's head. see create_Arrow for details.

• Arrdlength: numeric, length of dashes for dashed arrows. see create_Arrow for details.

• Arrtype: character, arrow type either "normal" or "dashed". see create_Arrow for details.

• Arrcol: character, color of the arrow. see create_Arrow for details.

• Arrtrans: numeric, transparency of the arrow. see create_Arrow for details.

The figure below shows some of the options used to customize the legend box and its items. Blue arrows represent location options and black arrows represent sizing options:

See Also

create_Hashes, create_Arrow, create_Ellipse, add_labels, add_Cscale, add_PieLegend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#53-adding-legends

# Set general options:

LegOpt=list( 
Title= "Title",
Subtitle="(Subtitle)",
Pos = "bottomright",
BoxW= 80,
BoxH= 170,
Boxexp = c(5,-2,-4,-4),
Titlefontsize = 2
)


#Create separate items, each with their own options:


Rectangle1=list(
  Text="Rectangle 1", 
  Shape="rectangle",
  ShpFill="cyan",
  ShpBord="blue",
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  RectW=10,
  RectH=7
)

Rectangle2=list(
  Text="Rectangle 2", 
  Shape="rectangle",
  ShpFill="red",
  ShpBord="orange",
  ShpHash=TRUE,
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  RectW=10,
  RectH=7,
  Hashcol="white",
  Hashangle=45,
  Hashspacing=1,
  Hashwidth=1
)

Circle1=list(
  Text="Circle 1", 
  Shape="circle",
  ShpFill="grey",
  ShpBord="yellow",
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  CircD=10
)

Circle2=list(
  Text="Circle 2", 
  Shape="circle",
  ShpFill="white",
  ShpBord="red",
  ShpHash=TRUE,
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  CircD=10,
  Hashcol="black",
  Hashangle=0,
  Hashspacing=2,
  Hashwidth=2
)

Ellipse1=list(
  Text="Ellipse 1", 
  Shape="ellipse",
  ShpFill="white",
  ShpBord="darkblue",
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  EllW=10,
  EllH=6,
  EllA=35
)

Ellipse2=list(
  Text="Ellipse 2", 
  Shape="ellipse",
  ShpFill="red",
  ShpBord="green",
  ShpHash=TRUE,
  Shplwd=2,
  fontsize=1.2,
  STSpace=3,
  EllW=10,
  EllH=7,
  EllA=0,
  Hashcol="black",
  Hashangle=-45,
  Hashspacing=1.5,
  Hashwidth=1.5
)

Line1=list(
  Text="Line 1", 
  Shape="line",
  ShpFill="black",
  Shplwd=5,
  fontsize=1.2,
  STSpace=3,
  LineL=10
)

Line2=list(
  Text="Line 2", 
  Shape="line",
  Shplwd=5,
  ShpFill="green",
  Shplwd=5,
  fontsize=1.2,
  STSpace=3,
  LineTyp=6, 
  LineL=10
)

Arrow1=list(
  Text="Arrow 1", 
  Shape="arrow",
  ShpBord="green",
  Shplwd=1,
  ArrL=10,
  ArrPwidth=5,
  ArrHlength=15, 
  ArrHwidth=10, 
  Arrcol="orange",
  fontsize=1.2,
  STSpace=3
)

Arrow2=list(
  Text="Arrow 2", 
  Shape="arrow",
  ShpBord=NA,
  ArrL=10,
  ArrPwidth=5,
  ArrHlength=15, 
  ArrHwidth=10, 
  Arrdlength=0, 
  Arrtype="dashed",
  Arrcol=c("red","green","blue"),
  fontsize=1.2,
  STSpace=3
)

Arrow3=list(
  Text="Arrow 3", 
  Shape="arrow",
  ShpBord=NA,
  ArrL=10,
  ArrPwidth=5,
  ArrHlength=15, 
  ArrHwidth=10, 
  Arrdlength=5, 
  Arrtype="dashed",
  Arrcol="darkgreen",
  fontsize=1.2,
  STSpace=3
)

Arrow4=list(
  Text="Arrow 4", 
  Shape="arrow",
  ShpBord="black",
  Shplwd=0.1,
  ArrL=10,
  ArrPwidth=5,
  ArrHlength=15, 
  ArrHwidth=10, 
  Arrcol="pink",
  ShpHash=TRUE,
  Hashcol="blue",
  Hashangle=-45,
  Hashspacing=1,
  Hashwidth=1,
  fontsize=1.2,
  STSpace=3
)

None=list(
  Text="None", 
  Shape="none",
  fontsize=1.2,
  STSpace=3,
  ShiftX=10
)


#Combine all items into a single list:

Items=list(Rectangle1,Rectangle2,Circle1,Circle2,
Ellipse1,Ellipse2,Line1,Line2,Arrow1,Arrow2,Arrow3,Arrow4,None)

#manually build a bounding box (same as st_bbox(load_ASDs())):

bb=st_bbox(c(xmin=-3348556,xmax=4815055,ymax=4371127,ymin=-3329339),
           crs = st_crs(6932))
bx=st_as_sfc(bb) #Convert to polygon to plot it

#Plot and add legend

plot(bx,col="grey")
add_Legend(bb,LegOpt,Items)

Add a legend to Pies

Description

Adds a legend to pies created using create_Pies.

Usage

add_PieLegend(
  Pies = NULL,
  bb = NULL,
  PosX = 0,
  PosY = 0,
  Size = 25,
  lwd = 1,
  Boxexp = c(0.2, 0.2, 0.12, 0.3),
  Boxbd = "white",
  Boxlwd = 1,
  Labexp = 0.3,
  fontsize = 1,
  LegSp = 0.5,
  Horiz = TRUE,
  PieTitle = "Pie chart",
  SizeTitle = "Size chart",
  PieTitleVadj = 0.5,
  SizeTitleVadj = 0.3,
  nSizes = 3,
  SizeClasses = NULL
)

Arguments

Value

Adds a legend to a pre-existing pie plot.

See Also

create_Pies, PieData, PieData2.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#23-create-pies

#Pies of constant size, all classes displayed:
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=50
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1,Boxexp=c(0.5,0.45,0.12,0.45),
             PieTitle="Species")

Add a Reference grid

Description

Add a Latitude/Longitude reference grid to maps.

Usage

add_RefGrid(
  bb,
  ResLat = 1,
  ResLon = 2,
  LabLon = NA,
  LatR = c(-80, -45),
  lwd = 1,
  lcol = "black",
  fontsize = 1,
  fontcol = "black",
  offset = NA
)

Arguments

See Also

load_Bathy, SmallBathy, add_Legend.

Examples

library(terra)

#Example 1: Circumpolar grid with Latitude labels at Longitude 0

plot(SmallBathy(),breaks=Depth_cuts, col=Depth_cols, legend=FALSE,axes=FALSE,box=FALSE)
add_RefGrid(bb=st_bbox(SmallBathy()),ResLat=10,ResLon=20,LabLon = 0)

#Example 2: Local grid around created polygons

MyPolys=create_Polys(PolyData,Densify=TRUE)
BathyC=crop(SmallBathy(),ext(MyPolys))#crop the bathymetry to match the extent of MyPolys
Mypar=par(mai=c(0.5,0.5,0.5,0.5)) #Figure margins as c(bottom, left, top, right)
par(Mypar)
plot(BathyC,breaks=Depth_cuts, col=Depth_cols, legend=FALSE,axes=FALSE,box=FALSE)
add_RefGrid(bb=st_bbox(BathyC),ResLat=2,ResLon=6)
plot(st_geometry(MyPolys),add=TRUE,col='orange',border='brown',lwd=2)

Add colors

Description

Given an input variable, generates either a continuous color gradient or color classes. To be used in conjunction with add_Cscale.

Usage

add_col(var, cuts = 100, cols = c("green", "yellow", "red"))

Arguments

Value

list containing the colors for the variable var (given as $varcol in the output) as well as the single cols and cuts, to be used as inputs in add_Cscale.

See Also

add_Cscale, create_PolyGrids, add_Legend, R colors.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#52-adding-colors-to-data

MyPoints=create_Points(PointData)
MyCols=add_col(MyPoints$Nfishes)
plot(st_geometry(MyPoints),pch=21,bg=MyCols$varcol,cex=2)

Add labels

Description

Adds labels to plots. Three modes are available: In 'auto' mode, labels are placed at the centres of polygon parts of spatial objects loaded via the load_ functions. Internally used in conjunction with Labels. In 'manual' mode, users may click on their plot to position labels. An editable label table is generated to allow fine-tuning of labels appearance, and may be saved for external use. To edit the label table, double-click inside one of its cells, edit the value, then close the table. In 'input' mode, a label table that was generated in 'manual' mode is re-used.

Usage

add_labels(
  mode = NULL,
  layer = NULL,
  fontsize = 1,
  fonttype = 1,
  angle = 0,
  col = "black",
  LabelTable = NULL
)

Arguments

Value

Adds labels to plot. To save a label table generated in 'manual' mode, use: MyLabelTable=add_labels(mode='auto'). To re-use that label table, use: add_labels(mode='input',LabelTable=MyLabelTable).

See Also

Labels, load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_EEZs, load_MPAs, add_Legend, R colors.

Examples

#Example 1: 'auto' mode
#label ASDs in bold and red
ASDs=load_ASDs()
plot(st_geometry(ASDs))
add_labels(mode='auto',layer='ASDs',fontsize=1,fonttype=2,col='red')
#add EEZs and their labels in large, green and vertical text
EEZs=load_EEZs()
plot(st_geometry(EEZs),add=TRUE,border='green')
add_labels(mode='auto',layer='EEZs',fontsize=2,col='green',angle=90)


#Example 2: 'manual' mode (you will have to do it yourself)
#Examples 2 and 3 below are commented (remove the # to test)
#library(terra)
#plot(SmallBathy())
#ASDs=load_ASDs()
#plot(st_geometry(ASDs),add=TRUE)
#MyLabels=add_labels(mode='manual')


#Example 3: Re-use the label table generated in Example 2
#plot(SmallBathy())
#plot(st_geometry(ASDs),add=TRUE)
#add_labels(mode='input',LabelTable=MyLabels)

Assign point locations to polygons

Description

Given a set of polygons and a set of point locations (given in decimal degrees), finds in which polygon those locations fall. Finds, for example, in which Subarea the given fishing locations occurred.

Usage

assign_areas(
  Input,
  Polys,
  AreaNameFormat = "GAR_Long_Label",
  Buffer = 0,
  NamesIn = NULL,
  NamesOut = NULL
)

Arguments

Value

dataframe with the same structure as the Input, with additional columns corresponding to the Polys used and named after NamesOut.

See Also

load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_MPAs, load_EEZs.

Examples

#Generate a dataframe
MyData=data.frame(Lat=runif(100,min=-65,max=-50),
                  Lon=runif(100,min=20,max=40))

#Assign ASDs and SSRUs to these locations (first load ASDs and SSRUs)
ASDs=load_ASDs()
SSRUs=load_SSRUs()

MyData=assign_areas(Input=MyData,Polys=c('ASDs','SSRUs'),NamesOut=c('MyASDs','MySSRUs'))

#View(MyData)
table(MyData$MyASDs) #count of locations per ASD
table(MyData$MySSRUs) #count of locations per SSRU

Create Arrow

Description

Create an arrow which can be curved and/or segmented.

Usage

create_Arrow(
  Input,
  Np = 50,
  Pwidth = 5,
  Hlength = 15,
  Hwidth = 10,
  dlength = 0,
  Atype = "normal",
  Acol = "green",
  Atrans = 0,
  yx = FALSE
)

Arguments

Value

Spatial object in your environment with colors included in the dataframe (see examples).

See Also

create_CircularArrow, create_Ellipse,add_Legend, create_Points, create_Lines, create_Polys, create_PolyGrids, create_Stations, create_Pies.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#24-create-arrow

#Example 1: straight green arrow
myInput=data.frame(lat=c(-61,-52),
                   lon=c(-60,-40))
Arrow=create_Arrow(Input=myInput)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 1")


#Example 2: blue arrow with one bend
myInput=data.frame(lat=c(-61,-65,-52),
                   lon=c(-60,-45,-40))
Arrow=create_Arrow(Input=myInput,Acol="lightblue")
plot(st_geometry(Arrow),col=Arrow$col,main="Example 2")

#Example 3: blue arrow with two bends
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40))
Arrow=create_Arrow(Input=myInput,Acol="lightblue")
plot(st_geometry(Arrow),col=Arrow$col,main="Example 3")

#Example 4: blue arrow with two bends, with more weight on the second bend
#and a big head
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40),
                   w=c(1,1,2,1))
Arrow=create_Arrow(Input=myInput,Acol="lightblue",Hlength=20,Hwidth=20)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 4")

#Example 5: Dashed arrow, small dashes
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40),
                   w=c(1,1,2,1))
Arrow=create_Arrow(Input=myInput,Acol="blue",Atype = "dashed",dlength = 1)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 5",border=NA)

#Example 6: Dashed arrow, big dashes
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40),
                   w=c(1,1,2,1))
Arrow=create_Arrow(Input=myInput,Acol="blue",Atype = "dashed",dlength = 2)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 6",border=NA)

#Example 7: Dashed arrow, no dashes, 3 colors and transparency gradient
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40),
                   w=c(1,1,2,1))
Arrow=create_Arrow(Input=myInput,Acol=c("red","green","blue"),
Atrans = c(0,0.9,0),Atype = "dashed",dlength = 0)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 7",border=NA)

#Example 8: Same as example 7 but with more points, so smoother
myInput=data.frame(lat=c(-61,-60,-65,-52),
                   lon=c(-60,-50,-45,-40),
                   w=c(1,1,2,1))
Arrow=create_Arrow(Input=myInput,Np=200,Acol=c("red","green","blue"),
                   Atrans = c(0,0.9,0),Atype = "dashed",dlength = 0)
plot(st_geometry(Arrow),col=Arrow$col,main="Example 8",border=NA)

#Example 9 Path along isobath
Iso=st_as_sf(terra::as.contour(SmallBathy(),levels=-1000)) #Take isobath
Iso=suppressWarnings(st_cast(Iso,"LINESTRING")) #convert to individual lines
Iso$L=st_length(Iso) #Get line length
Iso=Iso[Iso$L==max(Iso$L),] #Keep longest line (circumpolar)
Iso=st_coordinates(Iso) #Extract coordinates
Iso=Iso[Iso[,1]>-2.1e6 & Iso[,1]<(-0.1e6) & Iso[,2]>0,] #crop line
Inp=data.frame(Y=Iso[,2],X=Iso[,1])
Inp=Inp[seq(nrow(Inp),1),] #Go westward
Third=nrow(Inp)/3 #Cut in thirds
Arr1=create_Arrow(Input=Inp[1:Third,],yx=TRUE)
Arr2=create_Arrow(Input=Inp[(Third+2):(2*Third),],yx=TRUE)
Arr3=create_Arrow(Input=Inp[(2*Third+2):nrow(Inp),],yx=TRUE)

terra::plot(SmallBathy(),xlim=c(-2.5e6,0.5e6),ylim=c(0.25e6,2.75e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 9")
plot(st_geometry(Arr1),col="darkred",add=TRUE)
plot(st_geometry(Arr2),col="darkred",add=TRUE)
plot(st_geometry(Arr3),col="darkred",add=TRUE)
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)

Create Circular Arrow

Description

Create one or multiple arrows on an elliptical path, or a custom path (using Input). This function uses create_Arrow and create_Ellipse. Defaults are set for a simplified Weddell Sea gyre.

Usage

create_CircularArrow(
  Latc = -67,
  Lonc = -30,
  Lmaj = 800,
  Lmin = 500,
  Ang = 140,
  Npe = 100,
  dir = "cw",
  Narr = 1,
  Spc = 0,
  Stp = 0,
  Npa = 50,
  Pwidth = 5,
  Hlength = 15,
  Hwidth = 10,
  dlength = 0,
  Atype = "normal",
  Acol = "green",
  Atrans = 0,
  yx = FALSE,
  Input = NULL
)

Arguments

Value

Spatial object in your environment.

See Also

create_Ellipse, create_Arrow, create_Polys, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#27-create-circular-arrow

#Example 1
Arr=create_CircularArrow()

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 1")
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)


#Example 2
Arr=create_CircularArrow(Narr=2,Spc=5)

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 2")
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)


#Example 3
Arr=create_CircularArrow(Narr=10,Spc=-4,Hwidth=15,Hlength=20)

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 3")
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)


#Example 4
Arr=create_CircularArrow(Narr=8,Spc=-2,Npa=200,Acol=c("red","orange","green"),
                         Atrans = c(0,0.9,0),Atype = "dashed")

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 4")
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)


#Example 5 Path around two ellipses
El1=create_Ellipse(Latc=-61,Lonc=-50,Lmaj=500,Lmin=250,Ang=120)
El2=create_Ellipse(Latc=-68,Lonc=-57,Lmaj=400,Lmin=200,Ang=35)
#Merge ellipses and take convex hull
El=st_union(st_geometry(El1),st_geometry(El2))
El=st_convex_hull(El)
El=st_segmentize(El,dfMaxLength = 10000)
#Go counterclockwise if desired:
#El=st_coordinates(El)
#El=st_polygon(list(El[nrow(El):1,])) 

Arr=create_CircularArrow(Narr=10,Spc=3,Npa=200,Acol=c("green","darkgreen"),
                         Atype = "dashed",Input=El)

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 5")
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)

Create Ellipse

Description

Create an ellipse.

Usage

create_Ellipse(
  Latc,
  Lonc,
  Lmaj,
  Lmin,
  Ang = 0,
  Np = 100,
  dir = "cw",
  yx = FALSE
)

Arguments

Value

Spatial object in your environment.

See Also

create_Arrow, create_CircularArrow, create_Polys, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#26-create-ellipse

El1=create_Ellipse(Latc=-61,Lonc=-50,Lmaj=500,Lmin=250,Ang=120)
El2=create_Ellipse(Latc=-72,Lonc=-30,Lmaj=500,Lmin=500)
Hash=create_Hashes(El2,spacing=2,width=2)
El3=create_Ellipse(Latc=-68,Lonc=-55,Lmaj=400,Lmin=100,Ang=35)

terra::plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
            col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE)
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(El1),col=rgb(0,1,0.5,alpha=0.5),add=TRUE,lwd=2)
plot(st_geometry(El3),col=rgb(0,0.5,0.5,alpha=0.5),add=TRUE,border="orange",lwd=2)
plot(st_geometry(Hash),add=TRUE,col="red",border=NA)

Create Hashes

Description

Create hashed lines to fill a polygon.

Usage

create_Hashes(pol, angle = 45, spacing = 1, width = 1)

Arguments

Value

Spatial object in your environment, to be added to your plot.

See Also

create_Polys, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#25-create-hashes

#Create some polygons
MyPolys=create_Polys(Input=PolyData)
#Create hashes for each polygon
H1=create_Hashes(pol=MyPolys[1,],angle=45,spacing=1,width=1)
H2=create_Hashes(pol=MyPolys[2,],angle=90,spacing=2,width=2)
H3=create_Hashes(pol=MyPolys[3,],angle=0,spacing=3,width=3)

plot(st_geometry(MyPolys),col='cyan')
plot(st_geometry(H1),col='red',add=TRUE)
plot(st_geometry(H2),col='green',add=TRUE)
plot(st_geometry(H3),col='blue',add=TRUE)

Create Lines

Description

Create lines to display, for example, fishing line locations or tagging data.

Usage

create_Lines(
  Input,
  NamesIn = NULL,
  Buffer = 0,
  Densify = FALSE,
  Clip = FALSE,
  SeparateBuf = TRUE
)

Arguments

Value

Spatial object in your environment. Data within the resulting spatial object contains the data provided in the Input plus additional "LengthKm" and "LengthNm" columns which corresponds to the lines lengths, in kilometers and nautical miles respectively. If additional data was included in the Input, any numerical values are summarized for each line (min, max, mean, median, sum, count and sd).

To see the data contained in your spatial object, type: View(MyLines).

See Also

create_Points, create_Polys, create_PolyGrids, create_Stations, create_Pies, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#create-lines

#Densified lines (note the curvature of the lines)

MyLines=create_Lines(Input=LineData,Densify=TRUE)
plot(st_geometry(MyLines),lwd=2,col=rainbow(nrow(MyLines)))

Create Pies

Description

Generates pie charts that can be overlaid on maps. The Input data must be a dataframe with, at least, columns for latitude, longitude, class and value. For each location, a pie is created with pieces for each class, and the size of each piece depends on the proportion of each class (the value of each class divided by the sum of values). Optionally, the area of each pie can be proportional to a chosen variable (if that variable is different than the value mentioned above, the Input data must have a fifth column and that variable must be unique to each location). If the Input data contains locations that are too close together, the data can be gridded by setting GridKm. Once pie charts have been created, the function add_PieLegend may be used to add a legend to the figure.

Usage

create_Pies(
  Input,
  NamesIn = NULL,
  Classes = NULL,
  cols = c("green", "red"),
  Size = 50,
  SizeVar = NULL,
  GridKm = NULL,
  Other = 0,
  Othercol = "grey"
)

Arguments

Value

Spatial object in your environment, ready to be plotted.

See Also

add_PieLegend, PieData, PieData2.

Examples

 
# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#23-create-pies
  
#Pies of constant size, all classes displayed:
#Create pies
MyPies=create_Pies(Input=PieData,NamesIn=c("Lat","Lon","Sp","N"),Size=50)
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1,Boxexp=c(0.5,0.45,0.12,0.45),
             PieTitle="Species")

Create Points

Description

Create Points to display point locations. Buffering points may be used to produce bubble charts.

Usage

create_Points(
  Input,
  NamesIn = NULL,
  Buffer = 0,
  Clip = FALSE,
  SeparateBuf = TRUE
)

Arguments

Value

Spatial object in your environment. Data within the resulting spatial object contains the data provided in the Input plus additional "x" and "y" columns which corresponds to the projected points locations and may be used to label points (see examples).

To see the data contained in your spatial object, type: View(MyPoints).

See Also

create_Lines, create_Polys, create_PolyGrids, create_Stations, create_Pies, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#create-points

#Simple points with labels

MyPoints=create_Points(Input=PointData)
plot(st_geometry(MyPoints))
text(MyPoints$x,MyPoints$y,MyPoints$name,adj=c(0.5,-0.5),xpd=TRUE)

Create a Polygon Grid

Description

Create a polygon grid to spatially aggregate data in cells of chosen size. Cell size may be specified in degrees or as a desired area in square kilometers (in which case cells are of equal area).

Usage

create_PolyGrids(
  Input,
  NamesIn = NULL,
  dlon = NA,
  dlat = NA,
  Area = NA,
  cuts = 100,
  cols = c("green", "yellow", "red")
)

Arguments

Value

Spatial object in your environment. Data within the resulting spatial object contains the data provided in the Input after aggregation within cells. For each Variable, the minimum, maximum, mean, sum, count, standard deviation, and, median of values in each cell is returned. In addition, for each cell, its area (AreaKm2), projected centroid (Centrex, Centrey) and unprojected centroid (Centrelon, Centrelat) is given.

To see the data contained in your spatial object, type: View(MyGrid).

Also, colors are generated for each aggregated values according to the chosen cuts and cols.

To generate a custom color scale after the grid creation, refer to add_col and add_Cscale. See Example 4 below.

See Also

create_Points, create_Lines, create_Polys, create_Stations, create_Pies, add_col, add_Cscale, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#create-grids
# And:
# https://github.com/ccamlr/CCAMLRGIS/blob/master/Advanced_Grids/Advanced_Grids.md

#Simple grid, using automatic colors

MyGrid=create_PolyGrids(Input=GridData,dlon=2,dlat=1)
#View(MyGrid)
plot(st_geometry(MyGrid),col=MyGrid$Col_Catch_sum)

Create Polygons

Description

Create Polygons such as proposed Research Blocks or Marine Protected Areas.

Usage

create_Polys(
  Input,
  NamesIn = NULL,
  Buffer = 0,
  Densify = TRUE,
  Clip = FALSE,
  SeparateBuf = TRUE
)

Arguments

Value

Spatial object in your environment. Data within the resulting spatial object contains the data provided in the Input after aggregation within polygons. For each numeric variable, the minimum, maximum, mean, sum, count, standard deviation, and, median of values in each polygon is returned. In addition, for each polygon, its area (AreaKm2) and projected centroid (Labx, Laby) are given (which may be used to add labels to polygons).

To see the data contained in your spatial object, type: View(MyPolygons).

See Also

create_Points, create_Lines, create_PolyGrids, create_Stations, add_RefGrid, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#create-polygons


#Densified polygons (note the curvature of lines)
MyPolys=create_Polys(Input=PolyData)
plot(st_geometry(MyPolys),col='red')
text(MyPolys$Labx,MyPolys$Laby,MyPolys$ID,col='white')

#Convention Area outline
CA=data.frame(Name="CA",
              Lat=c(-50,-50,-45,-45,-55,-55,-60,-60),
              Lon=c(-50,30,30,80,80,150,150,-50))

MyPoly=create_Polys(CA)
plot(st_geometry(MyPoly),col='blue',border='green',lwd=2)

Create Stations

Description

Create random point locations inside a polygon and within bathymetry strata constraints. A distance constraint between stations may also be used if desired.

Usage

create_Stations(
  Poly,
  Bathy,
  Depths,
  N = NA,
  Nauto = NA,
  dist = NA,
  Buf = 1000,
  ShowProgress = FALSE
)

Arguments

Value

Spatial object in your environment. Data within the resulting object contains the strata and stations locations in both projected space ("x" and "y") and decimal degrees of Latitude/Longitude.

To see the data contained in your spatial object, type: View(MyStations).

See Also

create_Polys, SmallBathy, add_Legend.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#22-create-stations

#First, create a polygon within which stations will be created
MyPoly=create_Polys(
 data.frame(Name="mypol",
            Latitude=c(-75,-75,-70,-70),
            Longitude=c(-170,-180,-180,-170))
 ,Densify=TRUE)

par(mai=c(0,0,0,0))
plot(st_geometry(Coast[Coast$ID=='88.1',]),col='grey')
plot(st_geometry(MyPoly),col='green',add=TRUE)
text(MyPoly$Labx,MyPoly$Laby,MyPoly$ID)

#Create a set numbers of stations, without distance constraint:
library(terra)
#optional: crop your bathymetry raster to match the extent of your polygon
BathyCroped=crop(SmallBathy(),ext(MyPoly))

#Create stations
MyStations=create_Stations(MyPoly,BathyCroped,Depths=c(-2000,-1500,-1000,-550),N=c(20,15,10))

#add custom colors to the bathymetry to indicate the strata of interest
MyCols=add_col(var=c(-10000,10000),cuts=c(-2000,-1500,-1000,-550),cols=c('blue','cyan'))
plot(BathyCroped,breaks=MyCols$cuts,col=MyCols$cols,legend=FALSE,axes=FALSE)
add_Cscale(height=90,fontsize=0.75,width=16,lwd=0.5,
offset=-130,cuts=MyCols$cuts,cols=MyCols$cols)
plot(st_geometry(MyPoly),add=TRUE,border='red',lwd=2,xpd=TRUE)
plot(st_geometry(MyStations),add=TRUE,col='orange',cex=0.75,lwd=1.5,pch=3)

Get Cartesian coordinates of lines intersection in Euclidean space

Description

Given two lines defined by the Latitudes/Longitudes of their extremities, finds the location of their intersection, in Euclidean space, using this approach: https://en.wikipedia.org/wiki/Line-line_intersection.

Usage

get_C_intersection(Line1, Line2, Plot = TRUE)

Arguments

Examples

#Example 1 (Intersection beyond the range of segments)
get_C_intersection(Line1=c(-30,-55,-29,-50),Line2=c(-50,-60,-40,-60))

#Example 2 (Intersection on one of the segments)
get_C_intersection(Line1=c(-30,-65,-29,-50),Line2=c(-50,-60,-40,-60))

#Example 3 (Crossed segments)
get_C_intersection(Line1=c(-30,-65,-29,-50),Line2=c(-50,-60,-25,-60))

#Example 4 (Antimeridian crossed)
get_C_intersection(Line1=c(-179,-60,-150,-50),Line2=c(-120,-60,-130,-62))

#Example 5 (Parallel lines - uncomment to test as it will return an error)
#get_C_intersection(Line1=c(0,-60,10,-60),Line2=c(-10,-60,10,-60))

Get depths of locations from a bathymetry raster

Description

Given a bathymetry raster and an input dataframe of point locations (given in decimal degrees), computes the depths at these locations (values for the cell each point falls in). The accuracy is dependent on the resolution of the bathymetry raster (see load_Bathy to get high resolution data).

Usage

get_depths(Input, Bathy, NamesIn = NULL)

Arguments

Value

dataframe with the same structure as the Input with an additional depth column 'd'.

See Also

load_Bathy, create_Points, create_Stations, get_iso_polys.

Examples

#Generate a dataframe
MyData=data.frame(Lat=PointData$Lat,
Lon=PointData$Lon,
Catch=PointData$Catch)

#get depths of locations
MyDataD=get_depths(Input=MyData,Bathy=SmallBathy())
#View(MyDataD)
plot(MyDataD$d,MyDataD$Catch,xlab='Depth',ylab='Catch',pch=21,bg='blue')

Generate contour polygons from raster

Description

From an input raster and chosen cuts (classes), turns areas between contours into polygons. An input polygon may optionally be given to constrain boundaries. The accuracy is dependent on the resolution of the raster (e.g., see load_Bathy to get high resolution bathymetry).

Usage

get_iso_polys(
  Rast,
  Poly = NULL,
  Cuts,
  Cols = c("green", "yellow", "red"),
  Grp = FALSE,
  strict = TRUE
)

Arguments

Value

Spatial object in your environment. Data within the resulting object contains a polygon in each row. Columns are as follows: ID is a unique polygon identifier; Iso is a contour polygon identifier; Min and Max are the range of contour values; c is the color of each contour polygon; if Grp was set to TRUE, additional columns are: Grp is a group identifier (e.g., a seamount constituted of several isobaths); AreaKm2 is the polygon area in square kilometers; Labx and Laby can be used to label groups (see GitHub example).

See Also

load_Bathy, create_Polys, get_depths.

Examples

# For more examples, see:
# https://github.com/ccamlr/CCAMLRGIS#46-get_iso_polys

Poly=create_Polys(Input=data.frame(ID=1,Lat=c(-55,-55,-61,-61),Lon=c(-30,-25,-25,-30)))
IsoPols=get_iso_polys(Rast=SmallBathy(),Poly=Poly,Cuts=seq(-8000,0,length.out=10),Cols=rainbow(9))

plot(st_geometry(Poly))
plot(st_geometry(IsoPols),col=IsoPols$c,add=TRUE) 

Load CCAMLR statistical Areas, Subareas and Divisions

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_ASDs()

See Also

load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_Coastline, load_MPAs, load_EEZs.

Examples

 


#When online:
ASDs=load_ASDs()
plot(st_geometry(ASDs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load Bathymetry data

Description

Download the up-to-date projected GEBCO data from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. This functions can be used in two steps, to first download the data and then use it. If you keep the downloaded data, you can then re-use it in all your scripts.

Usage

load_Bathy(LocalFile, Res = 5000)

Arguments

Details

To download the data, you must either have set your working directory using setwd, or be working within an Rproject. In any case, your file will be downloaded to the folder path given by getwd.

It is strongly recommended to first download the lowest resolution data (set Res=5000) to ensure it is working as expected.

To re-use the downloaded data, you must provide the full path to that file, for example:

LocalFile="C:/Desktop/GEBCO2024_5000.tif".

This data was reprojected from the original GEBCO Grid after cropping at 40 degrees South. Projection was made using the Lambert azimuthal equal-area projection (CCAMLRp), and the data was aggregated at several resolutions.

Value

Bathymetry raster.

References

GEBCO Compilation Group (2024) GEBCO 2024 Grid (doi:10.5285/1c44ce99-0a0d-5f4f-e063-7086abc0ea0f)

See Also

add_col, add_Cscale, Depth_cols, Depth_cuts, Depth_cols2, Depth_cuts2, get_depths, create_Stations, get_iso_polys, SmallBathy.

Examples

 


#The examples below are commented. To test, remove the '#'.

##Download the data. It will go in the folder given by getwd():
#Bathy=load_Bathy(LocalFile = FALSE,Res=5000)
#plot(Bathy, breaks=Depth_cuts,col=Depth_cols,axes=FALSE)

##Re-use the downloaded data (provided it's here: "C:/Desktop/GEBCO2024_5000.tif"):
#Bathy=load_Bathy(LocalFile = "C:/Desktop/GEBCO2024_5000.tif")
#plot(Bathy, breaks=Depth_cuts,col=Depth_cols,axes=FALSE)

Load the full CCAMLR Coastline

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp). Note that this coastline expands further north than Coast. Sources: UK Polar Data Centre/BAS and Natural Earth. Projection: EPSG 6932. More details here: https://github.com/ccamlr/geospatial_operations

Usage

load_Coastline()

References

UK Polar Data Centre/BAS and Natural Earth.

See Also

load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_MPAs, load_EEZs.

Examples

 


#When online:
Coastline=load_Coastline()
plot(st_geometry(Coastline))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load Exclusive Economic Zones

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_EEZs()

See Also

load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_Coastline, load_MPAs.

Examples

 


#When online:
EEZs=load_EEZs()
plot(st_geometry(EEZs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load CCAMLR Management Areas

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_MAs()

See Also

load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_Coastline, load_MPAs, load_EEZs.

Examples

 


#When online:
MAs=load_MAs()
plot(st_geometry(MAs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load CCAMLR Marine Protected Areas

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_MPAs()

See Also

load_ASDs, load_SSRUs, load_RBs, load_SSMUs, load_MAs, load_Coastline, load_EEZs.

Examples

 


#When online:
MPAs=load_MPAs()
plot(st_geometry(MPAs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load CCAMLR Research Blocks

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_RBs()

See Also

load_ASDs, load_SSRUs, load_SSMUs, load_MAs, load_Coastline, load_MPAs, load_EEZs.

Examples

 


#When online:
RBs=load_RBs()
plot(st_geometry(RBs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load CCAMLR Small Scale Management Units

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_SSMUs()

See Also

load_ASDs, load_SSRUs, load_RBs, load_MAs, load_Coastline, load_MPAs, load_EEZs.

Examples

 


#When online:
SSMUs=load_SSMUs()
plot(st_geometry(SSMUs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Load CCAMLR Small Scale Research Units

Description

Download the up-to-date spatial layer from the online CCAMLRGIS (https://gis.ccamlr.org/) and load it to your environment. See examples for offline use. All layers use the Lambert azimuthal equal-area projection (CCAMLRp)

Usage

load_SSRUs()

See Also

load_ASDs, load_RBs, load_SSMUs, load_MAs, load_Coastline, load_MPAs, load_EEZs.

Examples

 


#When online:
SSRUs=load_SSRUs()
plot(st_geometry(SSRUs))

#For offline use, see:
#https://github.com/ccamlr/CCAMLRGIS#32-offline-use

Project user-supplied locations

Description

Given an input dataframe containing locations given in decimal degrees or meters (if projected), projects these locations and, if desired, appends them to the input dataframe. May also be used to back-project to Latitudes/Longitudes provided the input was projected using a Lambert azimuthal equal-area projection (CCAMLRp).

Usage

project_data(
  Input,
  NamesIn = NULL,
  NamesOut = NULL,
  append = TRUE,
  inv = FALSE
)

Arguments

See Also

assign_areas.

Examples

#Generate a dataframe
MyData=data.frame(Lat=runif(100,min=-65,max=-50),
                  Lon=runif(100,min=20,max=40))

#Project data using a Lambert azimuthal equal-area projection
MyData=project_data(Input=MyData,NamesIn=c("Lat","Lon"))
#View(MyData)

Calculate planimetric seabed area

Description

Calculate planimetric seabed area within polygons and depth strata in square kilometers.

Usage

seabed_area(Bathy, Poly, PolyNames = NULL, depth_classes = c(-600, -1800))

Arguments

Value

dataframe with the name of polygons in the first column and the area for each strata in the following columns.

See Also

load_Bathy, SmallBathy, create_Polys, load_RBs.

Examples

#create some polygons
MyPolys=create_Polys(PolyData,Densify=TRUE)
#compute the seabed areas
FishDepth=seabed_area(SmallBathy(),MyPolys,PolyNames="ID",
depth_classes=c(0,-200,-600,-1800,-3000,-5000))
#Result looks like this (note that the 600-1800 stratum is renamed 'Fishable_area')
#View(FishDepth)