Package 'CCAMLRGIS'

Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources. Provides two categories of functions: load functions and create functions. Load functions are used to import existing spatial layers from the online CCAMLR GIS such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.
Authors: Stephane Thanassekos [aut, cre], Keith Reid [aut], Lucy Robinson [aut], Michael D. Sumner [ctb], Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <[email protected]>
License: GPL-3
Version: 4.2.1
Built: 2025-02-16 23:19:47 UTC
Source: https://github.com/ccamlr/ccamlrgis

Help Index

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

var

numeric vector of the variable to be colorized. Either all values (in which case all values will be assigned to a color) or only two values (in which case these are considered to be the range of values).
cuts

numeric, controls color classes. Either one value (in which case n=cuts equally spaced color classes are generated) or a vector (in which case irregular color classes are generated e.g.: c(-10,0,100,2000)).
cols

character vector of colors (see R standard color names here). cols are interpolated along cuts. Color codes as those generated, for example, by rgb may also be used.

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 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

pos

character, fraction indicating the vertical position of the color scale (which, by default, is on the right side of plots). if pos="1/1", the color scale will be centered. if pos="1/2", the color scale will be centered on the top half of the plotting region. if pos="2/2", the color scale will be centered on the bottom half of the plotting region.
title

character, title of the color scale.
width

numeric, width of the color scale box, expressed in % of the width of the plotting region.
height

numeric, height of the color scale box, expressed in % of the height of the plotting region.
cuts

numeric, vector of color classes. May be generated via add_col.
cols

character, vector of color names. May be generated via add_col.
minVal

numeric, if desired, the color scale may be generated starting from the value minVal. See examples.
maxVal

numeric, if desired, the color scale may be generated up to the value maxVal. See examples.
fontsize

numeric, size of the text in the color scale.
offset

numeric, controls the horizontal position of the color scale.
lwd

numeric, thickness of lines.
Titlefontsize

numeric, size of the title text.
TitleVAdj

numeric, vertical adjustment of the title.
BoxAdj

numeric vector of 4 values to adjust the sides of the box, given as c(bottom,left,top,right).
BoxCol

Color of the legend box frame.
BoxBG

Color of the legend box background.
Clwd

numeric, thickness of lines of cells.
Ccol

character, color of lines of cells, set to NA for no border.
Cwdth

numeric, positive factor to adjust the width of cells.
TckL

numeric, positive factor to adjust the length of tick lines.
Tcklwd

numeric, thickness of tick lines.
Tdist

numeric, horizontal adjustment of labels text.
mode

character, if 'Cscale', the default, the function builds a color scale. if 'Legend', the function gives you the location of a legend, arguments pos, offset and height may be used for adjustments. See examples.

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 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

mode

character, either 'auto', 'manual' or 'input'. See Description above.
layer

character, in 'auto' mode, single or vector of characters, may only be one, some or all of: c("ASDs","SSRUs","RBs","SSMUs","MAs","MPAs","EEZs").
fontsize

numeric, in 'auto' mode, size of the text.
fonttype

numeric, in 'auto' mode, type of the text (1 to 4), where 1 corresponds to plain text, 2 to bold face, 3 to italic and 4 to bold italic.
angle

numeric, in 'auto' mode, rotation of the text in degrees.
col

character, in 'auto' mode, color of the text.
LabelTable

in 'input' mode, name of the label table that was generated in 'manual' mode.

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)

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

bb

bounding box of your plot area. for example, bb=st_bbox(SmallBathy()) or bb=st_bbox(MyPolys).
LegOpt

list of general legend options. for example:

LegOpt=list(Title="Speed",Subtitle="(km/h)").
Items

list, or list of lists containing options for each item to be displayed in the legend. for example:

item1=list(Text="one",Shape="rectangle")

item2=list(Text="two",Shape="circle")

Items=list(item1,item2)

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:

Addlegenddetails.png

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

Pies

Spatial object created using create_Pies.
bb

Spatial object, sf bounding box created with st_bbox(). If provided, the legend will be centered in that bb. Otherwise it is centered on the min(Latitudes) and median(Longitudes) of coordinates found in the input Pies.
PosX

numeric, horizontal adjustment of legend.
PosY

numeric, vertical adjustment of legend.
Size

numeric, controls the size of pies.
lwd

numeric, line thickness of pies.
Boxexp

numeric, vector of length 4 controls the expansion of the legend box, given as c(xmin,xmax,ymin,ymax).
Boxbd

character, color of the background of the legend box.
Boxlwd

numeric, line thickness of the legend box. Set to zero if no box is desired.
Labexp

numeric, controls the distance of the pie labels to the center of the pie.
fontsize

numeric, size of the legend font.
LegSp

numeric, spacing between the pie and the size chart (only used if SizeVar was specified in create_Pies).
Horiz

logical. Set to FALSE for vertical layout (only used if SizeVar was specified in create_Pies).
PieTitle

character, title of the pie chart.
SizeTitle

character, title of the size chart (only used if SizeVar was specified in create_Pies).
PieTitleVadj

numeric, vertical adjustment of the title of the pie chart.
SizeTitleVadj

numeric, vertical adjustment of the title of the size chart (only used if SizeVar was specified in create_Pies).
nSizes

integer, number of size classes to display in the size chart. Minimum and maximum sizes are displayed by default. (only used if SizeVar was specified in create_Pies).
SizeClasses

numeric, vector (e.g. c(1,10,100)) of size classes to display in the size chart (only used if SizeVar was specified in create_Pies). If set, overrides nSizes.

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

bb

bounding box of the first plotted object. for example, bb=st_bbox(SmallBathy()) or bb=st_bbox(MyPolys).
ResLat

numeric, latitude resolution in decimal degrees.
ResLon

numeric, longitude resolution in decimal degrees.
LabLon

numeric, longitude at which Latitude labels should appear. if set, the resulting Reference grid will be circumpolar.
LatR

numeric, range of latitudes of circumpolar grid.
lwd

numeric, line thickness of the Reference grid.
lcol

character, line color of the Reference grid.
fontsize

numeric, font size of the Reference grid's labels.
fontcol

character, font color of the Reference grid's labels.
offset

numeric, offset of the Reference grid's labels (distance to plot border).

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)

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

Input

dataframe containing - at the minimum - Latitudes and Longitudes to be assigned to polygons.

If NamesIn is not provided, the columns in the Input must be in the following order: Latitude, Longitude, Variable 1, Variable 2, ... Variable x..
Polys

character vector of polygon names (e.g., Polys=c('ASDs','RBs')).

Must be matching the names of the pre-loaded spatial objects (loaded via e.g., ASDs=load_ASDs()).
AreaNameFormat

dependent on the polygons loaded. For the Secretariat's spatial objects loaded via 'load_' functions, we have the following:

'GAR_Name' e.g., 'Subarea 88.2'

'GAR_Short_Label' e.g., '882'

'GAR_Long_Label' (default) e.g., '88.2'

Several values may be entered if several Polys are used, e.g.:

c('GAR_Short_Label','GAR_Name'), in which case AreaNameFormat must be given in the same order as Polys.
Buffer

numeric, distance in nautical miles to be added around the Polys of interest. Can be specified for each of the Polys (e.g., Buffer=c(2,5)). Useful to determine whether locations are within Buffer nautical miles of a polygon.
NamesIn

character vector of length 2 specifying the column names of Latitude and Longitude fields in the Input. Latitudes name must be given first, e.g.:

NamesIn=c('MyLatitudes','MyLongitudes').
NamesOut

character, names of the resulting column names in the output dataframe, with order matching that of Polys (e.g., NamesOut=c('Recapture_ASD','Recapture_RB')). If not provided will be set as equal to Polys.

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

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

Input

sf polygon(s) to be clipped.

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')

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

Input

input dataframe with at least two columns (Latitudes then Longitudes) and an optional third column for weights. First row is the location of the start of the arrow, Last row is the location of the end of the arrow (where the arrow will point to). Optional intermediate rows are the locations of points towards which the arrow's path will bend. Weights (third column) can be added to the intermediate points to make the arrow's path bend more towards them. Projected coordinates may be used (Y then X) instead of Latitudes and Longitudes by setting yx to TRUE. Coordinates may be extracted from a spatial object and used as input (see Example 9 below).
Np

integer, number of additional points generated to create a curved path. If the arrow's path appears too segmented, increase Np.
Pwidth

numeric, width of the arrow's path.
Hlength

numeric, length of the arrow's head.
Hwidth

numeric, width of the arrow's head.
dlength

numeric, length of dashes for dashed arrows.
Atype

character, arrow type either "normal" or "dashed". A normal arrow is a single polygon, with a single color (set by Acol) and transparency (set by Atrans). A dashed arrow is a series of polygons which can be colored separately by setting two or more values as Acol=c("color start","color end") and two or more transparency values as Atrans=c("transparency start","transparency end"). The length of dashes is controlled by dlength.
Acol

Color of the arrow, see Atype above.
Atrans

Numeric, transparency of the arrow, see Atype above.
yx

Logical, if set to TRUE the input coordinates are projected. Give Y in the first column, X in the second.

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

Latc

numeric, latitude of the ellipse centre in decimal degrees, or Y projected coordinate if yx is set to TRUE.
Lonc

numeric, longitude of the ellipse centre in decimal degrees, or X projected coordinate if yx is set to TRUE.
Lmaj

numeric, length of major axis.
Lmin

numeric, length of minor axis.
Ang

numeric, angle of rotation (0-360).
Npe

integer, number of points on the ellipse.
dir

character, direction along the ellipse, either "cw" (clockwise) or "ccw" (counterclockwise).
Narr

integer, number of arrows.
Spc

integer, spacing between arrows, or length of single arrow.
Stp

numeric, starting point of an arrow on the ellipse (0 to 1).
Npa

integer, number of points to build the path of the arrow.
Pwidth

numeric, width of the arrow's path.
Hlength

numeric, length of the arrow's head.
Hwidth

numeric, width of the arrow's head.
dlength

numeric, length of dashes for dashed arrows.
Atype

character, arrow type either "normal" or "dashed". A normal arrow is a single polygon, with a single color (set by Acol) and transparency (set by Atrans). A dashed arrow is a series of polygons which can be colored separately by setting two or more values as Acol=c("color start","color end") and two or more transparency values as Atrans=c("transparency start","transparency end"). The length of dashes is controlled by dlength.
Acol

Color of the arrow, see Atype above.
Atrans

Numeric, transparency of the arrow, see Atype above.
yx

Logical, if set to TRUE the input coordinates are projected. Give Y in the first column, X in the second.
Input

Either NULL, or a projected spatial object to control the arrow's path (see examples).

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

Latc

numeric, latitude of the ellipse centre in decimal degrees, or Y projected coordinate if yx is set to TRUE.
Lonc

numeric, longitude of the ellipse centre in decimal degrees, or X projected coordinate if yx is set to TRUE.
Lmaj

numeric, length of major axis.
Lmin

numeric, length of minor axis.
Ang

numeric, angle of rotation (0-360).
Np

integer, number of points on the ellipse.
dir

character, either "cw" (clockwise) or "ccw" (counterclockwise). Sets the order of points, only matters for create_CircularArrow.
yx

Logical, if set to TRUE the input coordinates are projected. Give Y as Latc and X as Lonc.

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

pol

single polygon inside which hashed lines will be created. May be created using create_Polys or by subsetting an object obtained using one of the load_ functions.
angle

numeric, angle of the hashed lines in degrees (0-360), noting that the function might struggle with angles 0, 180, -180 or 360.
spacing

numeric, spacing between hashed lines.
width

numeric, width of hashed lines.

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

Input

input dataframe.

If NamesIn is not provided, the columns in the Input must be in the following order:

Line name, Latitude, Longitude.

If a given line is made of more than two points, the locations of points must be given in order, from one end of the line to the other.
NamesIn

character vector of length 3 specifying the column names of line identifier, Latitude and Longitude fields in the Input.

Names must be given in that order, e.g.:

NamesIn=c('Line ID','Line Latitudes','Line Longitudes').
Buffer

numeric, distance in nautical miles by which to expand the lines. Can be specified for each line (as a numeric vector).
Densify

logical, if set to TRUE, additional points between extremities of lines spanning more than 0.1 degree longitude are added at every 0.1 degree of longitude prior to projection (see examples).
Clip

logical, if set to TRUE, polygon parts (from buffered lines) that fall on land are removed (see Clip2Coast).
SeparateBuf

logical, if set to FALSE when adding a Buffer, all spatial objects are merged, resulting in a single spatial object.

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

Input

input dataframe.
NamesIn

character vector of length 4 specifying the column names of Latitude, Longitude, Class and value fields in the Input.

Names must be given in that order, e.g.:

NamesIn=c('Latitude','Longitude','Class','Value').
Classes

character, optional vector of classes to be displayed. If this excludes classes that are in the Input, those excluded classes will be pooled in a 'Other' class.
cols

character, vector of two or more color names to colorize pie pieces.
Size

numeric, value controlling the size of pies.
SizeVar

numeric, optional, name of the field in the Input that should be used to scale the area of pies. Must be unique to locations in the input.
GridKm

numeric, optional, cell size of the grid in kilometers. If provided, locations are pooled by grid cell and values are summed for each class.
Other

numeric, optional, percentage threshold below which classes are pooled in a 'Other' class.
Othercol

character, optional, color of the pie piece for the 'Other' class.

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

Input

input dataframe.

If NamesIn is not provided, the columns in the Input must be in the following order:

Latitude, Longitude, Variable 1, Variable 2, ... Variable x.
NamesIn

character vector of length 2 specifying the column names of Latitude and Longitude fields in the Input. Latitudes name must be given first, e.g.:

NamesIn=c('MyLatitudes','MyLongitudes').
Buffer

numeric, radius in nautical miles by which to expand the points. Can be specified for each point (as a numeric vector).
Clip

logical, if set to TRUE, polygon parts (from buffered points) that fall on land are removed (see Clip2Coast).
SeparateBuf

logical, if set to FALSE when adding a Buffer, all spatial objects are merged, resulting in a single spatial object.

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

Input

input dataframe.

If NamesIn is not provided, the columns in the Input must be in the following order:

Latitude, Longitude, Variable 1, Variable 2 ... Variable x.
NamesIn

character vector of length 2 specifying the column names of Latitude and Longitude fields in the Input. Latitudes name must be given first, e.g.:

NamesIn=c('MyLatitudes','MyLongitudes').
dlon

numeric, width of the grid cells in decimal degrees of longitude.
dlat

numeric, height of the grid cells in decimal degrees of latitude.
Area

numeric, area in square kilometers of the grid cells. The smaller the Area, the longer it will take.
cuts

numeric, number of desired color classes.
cols

character, desired colors. If more that one color is provided, a linear color gradient is generated.

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

Input

input dataframe.

If NamesIn is not provided, the columns in the Input must be in the following order:

Polygon name, Latitude, Longitude.

Latitudes and Longitudes must be given clockwise.
NamesIn

character vector of length 3 specifying the column names of polygon identifier, Latitude and Longitude fields in the Input.

Names must be given in that order, e.g.:

NamesIn=c('Polygon ID','Poly Latitudes','Poly Longitudes').
Buffer

numeric, distance in nautical miles by which to expand the polygons. Can be specified for each polygon (as a numeric vector).
Densify

logical, if set to TRUE, additional points between extremities of lines spanning more than 0.1 degree longitude are added at every 0.1 degree of longitude prior to projection (compare examples 1 and 2 below).
Clip

logical, if set to TRUE, polygon parts that fall on land are removed (see Clip2Coast).
SeparateBuf

logical, if set to FALSE when adding a Buffer, all spatial objects are merged, resulting in a single spatial object.

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

Poly

single polygon inside which stations will be generated. May be created using create_Polys.
Bathy

bathymetry raster with the appropriate projection, such as this one.
Depths

numeric, vector of depths. For example, if the depth strata required are 600 to 1000 and 1000 to 2000, Depths=c(-600,-1000,-2000).
N

numeric, vector of number of stations required in each depth strata, therefore length(N) must equal length(Depths)-1.
Nauto

numeric, instead of specifying N, a number of stations proportional to the areas of the depth strata may be created. Nauto is the maximum number of stations required in any depth stratum.
dist

numeric, if desired, a distance constraint in nautical miles may be applied. For example, if dist=2, stations will be at least 2 nautical miles apart.
Buf

numeric, distance in meters from isobaths. Useful to avoid stations falling on strata boundaries.
ShowProgress

logical, if set to TRUE, a progress bar is shown (create_Stations may take a while).

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)

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)

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

Line1

Vector of 4 coordinates, given in decimal degrees as:

c(Longitude_start,Latitude_start,Longitude_end,Latitude_end).
Line2

Same as Line1.
Plot

logical, if set to TRUE, plots a schematic of calculations.

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

Input

dataframe with, at least, Latitudes and Longitudes. If NamesIn is not provided, the columns in the Input must be in the following order:

Latitude, Longitude, Variable 1, Variable 2, ... Variable x.
Bathy

bathymetry raster with the appropriate projection, such as this one. It is highly recommended to use a raster of higher resolution than SmallBathy (see load_Bathy).
NamesIn

character vector of length 2 specifying the column names of Latitude and Longitude fields in the Input. Latitudes name must be given first, e.g.:

NamesIn=c('MyLatitudes','MyLongitudes').

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

Rast

raster with the appropriate projection, such as SmallBathy. It is recommended to use a raster of higher resolution (see load_Bathy).
Poly

optional, single polygon inside which contour polygons will be generated. May be created using create_Polys or by subsetting an object obtained using one of the load_ functions.
Cuts

numeric, vector of desired contours. For example, Cuts=c(-2000,-1000,-500).
Cols

character, vector of desired colors (see add_col).
Grp

logical (TRUE/FALSE), if set to TRUE (slower), contour polygons that touch each other are identified and grouped (a Grp column is added to the object). This can be used, for example, to identify seamounts that are constituted of several isobaths.
strict

logical (TRUE/FALSE), if set to TRUE (default) polygons are created only between the chosen Cuts. If set to FALSE, extra polygons are created beyond the bounds of Cuts.

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)

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))

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

LocalFile

To download the data, set to FALSE. To re-use a downloaded file, set to the full path of the file (e.g., LocalFile="C:/Desktop/GEBCO2024_5000.tif").
Res

Desired resolution in meters. May only be one of: 500, 1000, 2500 or 5000.

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

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)

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

Input

dataframe containing - at the minimum - Latitudes and Longitudes to be projected (or Y and X to be back-projected).
NamesIn

character vector of length 2 specifying the column names of Latitude and Longitude fields in the Input. Latitudes (or Y) name must be given first, e.g.:

NamesIn=c('MyLatitudes','MyLongitudes').
NamesOut

character vector of length 2, optional. Names of the resulting columns in the output dataframe, with order matching that of NamesIn (e.g., NamesOut=c('Y','X')).
append

logical (T/F). Should the projected locations be appended to the Input?
inv

logical (T/F). Should a back-projection be performed? In such case, locations must be given in meters and have been projected using a Lambert azimuthal equal-area projection (CCAMLRp).

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)

Rotate object

Description

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

Usage

Rotate_obj(Input, Lon0 = NULL)

Arguments

Input

Spatial object of class sf, sfc or SpatRaster (terra).
Lon0

numeric, longitude that will point up in the resulting map.

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)

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

Bathy

bathymetry raster with the appropriate projection. It is highly recommended to use a raster of higher resolution than SmallBathy, see load_Bathy.
Poly

polygon(s) within which the areas of depth strata are computed.
PolyNames

character, column name (from the polygon object) to be used in the output.
depth_classes

numeric vector of strata depths. for example, depth_classes=c(-600,-1000,-2000). If the values -600,-1800 are given within depth_classes, the computed area will be labelled as 'Fishable_area'.

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)

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)