README.Rmd

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```{r, echo = FALSE}
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```


# CCAMLRGIS R package

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This package was developed to simplify the production of maps in the CAMLR Convention Area. It provides two main categories of functions: load functions and create functions. Load functions are used to import spatial layers from the online [CCAMLR GIS](https://gis.ccamlr.org/) such as the ASD boundaries. Create functions are used to create layers from user data such as polygons and grids.

## Installation

You can install the CCAMLRGIS R package from CRAN with:

```{r, eval = F}
install.packages("CCAMLRGIS")
```

## Documentation

```{r, echo = FALSE, message = FALSE}
set.seed(1234)
```

<center>
### A package to load and create spatial data, including layers and tools that are relevant to CCAMLR activities.
</center>

------------------------------------------------------------------------

<center>
### Table of contents
</center>

------------------------------------------------------------------------

1.  [Basemaps](#1-basemaps)
2.  [Create functions](#2-create-functions)

-   2.1. [Points](#create-points), [lines](#create-lines), [polygons](#create-polygons) and [grids](#create-grids)
-   2.2. [Create Stations](#22-create-stations)
-   2.3. [Create Pies](#23-create-pies)
-   2.4. [Create Arrow](#24-create-arrow)
-   2.5. [Create Hashes](#25-create-hashes)
-   2.6. [Create Ellipse](#26-create-ellipse)
-   2.7. [Create Circular Arrow](#27-create-circular-arrow)

3.  [Load functions](#3-load-functions)

-   3.1. Online use
-   3.2. Offline use

4.  Other functions

-   4.1. [get_depths](#41-get_depths)
-   4.2. [seabed_area](#42-seabed_area)
-   4.3. [assign_areas](#43-assign_areas)
-   4.4. [project_data](#44-project_data)
-   4.5. [get_C\_intersection](#45-get_c_intersection)
-   4.6. [get_iso_polys](#46-get_iso_polys)
-   4.7. [Rotate_obj](#47-rotate_obj)

5.  Adding colors, legends and labels

-   5.1. [Bathymetry colors](#51-bathymetry-colors)
-   5.2. [Adding colors to data](#52-adding-colors-to-data)
-   5.3. [Adding legends](#53-adding-legends)
-   5.4. [Adding labels](#54-adding-labels)
-   5.5. [Using sf](#55-using-sf)

------------------------------------------------------------------------

## Introduction

First, install the package by typing:

```{r eval=F}
install.packages("CCAMLRGIS")
```

Then, load the package by typing:

```{r eval=T, message = FALSE}
library(CCAMLRGIS)
```

In order to plot bathymetry data, you will also need to load [terra](https://CRAN.R-project.org/package=terra):

```{r eval=T, message = FALSE}
library(terra)
```

[geospatial rules]:https://github.com/ccamlr/geospatial_operations#1-geospatial-rules

All spatial manipulations are made using the South Pole Lambert Azimuthal Equal Area projection (type ?CCAMLRp for more details), and follow CCAMLR's [geospatial rules].

```{r message=F,eval=T}
#Map with axes, to illustrate projection
png(filename='ReadMeFigs/ReadMe_Fig0.png',width=2000,height=2000,res=300)

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(1.2,1.3,0.2,0.2),xpd=TRUE)
#plot entire Coastline
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',lwd=0.1)
#Add reference grid
add_RefGrid(bb=st_bbox(Coast[Coast$ID=='All',]),ResLat=10,ResLon=20,LabLon=-40,fontsize=0.8,lwd=0.5)
#add axes and labels
axis(1,pos=0,at=seq(-4000000,4000000,by=1000000),tcl=-0.15,labels=F,lwd=0.8,lwd.ticks=0.8,col='blue')
axis(2,pos=0,at=seq(-4000000,4000000,by=1000000),tcl=-0.15,labels=F,lwd=0.8,lwd.ticks=0.8,col='blue')
text(seq(1000000,4000000,by=1000000),0,seq(1,4,by=1),cex=0.75,col='blue',adj=c(0.5,1.75))
text(seq(-4000000,-1000000,by=1000000),0,seq(-4,-1,by=1),cex=0.75,col='blue',adj=c(0.5,1.75))
text(0,seq(1000000,4000000,by=1000000),seq(1,4,by=1),cex=0.75,col='blue',adj=c(1.75,0.5))
text(0,seq(-4000000,-1000000,by=1000000),seq(-4,-1,by=1),cex=0.75,col='blue',adj=c(1.75,0.5))
text(0,0,0,cex=0.75,col='blue',adj=c(-0.5,-0.5))
text(4400000,0,expression('x ('*10^6~'m)'),cex=0.75,col='blue')
text(0,4200000,expression('y ('*10^6~'m)'),cex=0.75,col='blue')

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig0.png")
```

<center>
#### The South Pole Lambert Azimuthal Equal Area projection converts Latitudes and Longitudes into locations on a disk with x/y axes and units of meters. The South Pole is at x=0m ; y=0m. The tip of the Peninsula, for example, is around x=-2,500,000m ; y=2,000,000m.
</center>

<br>

## 1. Basemaps

[here]:https://github.com/ccamlr/CCAMLRGIS/blob/master/Basemaps/Basemaps.md

Additional basemaps are available [here].

#### Bathymetry:

Prior to detailing the package's capabilities, a set of basic commands are shown here to display a few core mapping elements. All scripts use the low-resolution bathymetry raster included in the package ('SmallBathy'). In order to obtain higher resolution bathymetry data, use the *Load_Bathy()* function:

```{r message=F,eval=T}
#Load_Bathy() example:
Bathy=load_Bathy(LocalFile = FALSE,Res=5000)

png(filename='ReadMeFigs/ReadMe_Fig1.1.png',width=2000,height=2000,res=300,bg="transparent")

plot(Bathy, breaks=Depth_cuts,col=Depth_cols,axes=FALSE,legend=FALSE,mar=c(0,0,0,0))

dev.off()

#Please refer to ?load_Bathy for more details, including how to save the bathymetry data so that you
#do not have to re-download it every time you need it.
```


```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig1.1.png")
```


```{r, echo = FALSE, message = FALSE}
#Delete GEBCO file
Fs=list.files()
Fs=Fs[grep("GEBCO",Fs)]
a=file.remove(Fs)
```

<br>

#### Statistical Areas, Subareas and Divisions (ASDs):

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig1.2.png',width=2200,height=1800,res=300)
#Load ASDs and EEZs
ASDs=load_ASDs()
EEZs=load_EEZs()
#Plot the bathymetry
plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,legend=F,axes=F,box=F,mar=c(0,0,0,5))
#Add reference grid
add_RefGrid(bb=st_bbox(SmallBathy()),ResLat=10,ResLon=20,LabLon=0,fontsize=0.75,lwd=0.75,offset = 4)
#Add color scale
add_Cscale(height=70,fontsize=0.75,offset=-50,width=14,maxVal=-1,lwd=0.5)
#Add ASD and EEZ boundaries
plot(st_geometry(ASDs),add=T,lwd=0.75,border='red',xpd=T)
plot(st_geometry(EEZs),add=T,lwd=0.75,border='red',xpd=T)
#Add coastline (for all ASDs)
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',lwd=0.01,add=T,xpd=T)
#Add ASD labels
add_labels(mode='auto',layer='ASDs',fontsize=0.6,col='red')
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig1.2.png")
```

<br>

#### Local map (*e.g.*, Subarea 48.6):

Additional local maps are available [here].

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig1.3.png',width=2000,height=1400,res=300)
#Load ASDs
ASDs=load_ASDs()
#Sub-sample ASDs to only keep Subarea 48.6
S486=ASDs[ASDs$GAR_Short_Label=='486',]
#Crop bathymetry to match the extent of S486
B486=crop(SmallBathy(),ext(S486))
#Plot the bathymetry
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=F,axes=F,mar=c(1.0,2,1.0,6))
#Add color scale
add_Cscale(height=80,fontsize=0.7,offset=250,width=15,lwd=0.5,maxVal=-1)
#Add coastline (for Subarea 48.6 only)
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T,xpd=T)
#Add reference grid
add_RefGrid(bb=st_bbox(B486),ResLat=5,ResLon=10,fontsize=0.75,lwd=0.75,offset = 50000)
#Add Subarea 48.6 boundaries
plot(st_geometry(S486),add=T,lwd=1,border='red',xpd=T)
#Add a -2000m contour
contour(B486,levels=-2000,add=T,lwd=0.5,labcex=0.3,xpd=T)
#Add single label at the centre of the polygon (see ?Labels)
text(Labels$x[Labels$t=='48.6'],Labels$y[Labels$t=='48.6'],labels='48.6',col='red',cex=1.5)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig1.3.png")
```

## 2. Create functions

### 2.1. Points, lines, polygons and grids

These functions are used to transform user data into spatial layers with the appropriate projection. User data should be provided as a dataframe containing Latitudes and Longitudes in decimal degrees. Depending on the function used, some other variables may be required (see help).

#### Create points:

For details, type:

```{r eval=F}
?create_Points
```

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.1.png',width=2000,height=1400,res=300)

#Prepare layout for 4 sub-plots
par(mfrow=c(2,2),mai=c(0.01,0.01,0.2,0.01))

#Example 1: Simple points with labels
MyPoints=create_Points(PointData)
plot(st_geometry(MyPoints),main='Example 1',cex.main=0.75,cex=0.5,lwd=0.5)
text(MyPoints$x,MyPoints$y,MyPoints$name,adj=c(0.5,-0.5),xpd=T,cex=0.75)
box()

#Example 2: Simple points with labels, highlighting one group of points with the same name
MyPoints=create_Points(PointData)
plot(st_geometry(MyPoints),main='Example 2',cex.main=0.75,cex=0.5,lwd=0.5)
text(MyPoints$x,MyPoints$y,MyPoints$name,adj=c(0.5,-0.5),xpd=T,cex=0.75)
plot(st_geometry(MyPoints[MyPoints$name=='four',]),bg='red',pch=21,cex=1,add=T)
box()

#Example 3: Buffered points with radius proportional to catch
MyPoints=create_Points(PointData,Buffer=1*PointData$Catch)
plot(st_geometry(MyPoints),col='green',main='Example 3',cex.main=0.75,cex=0.5,lwd=0.5)
text(MyPoints$x,MyPoints$y,MyPoints$name,adj=c(0.5,0.5),xpd=T,cex=0.75)
box()

#Example 4: Buffered points with radius proportional to catch and clipped to the Coast
MyPoints=create_Points(PointData,Buffer=2*PointData$Catch,Clip=T)
plot(st_geometry(MyPoints),col='cyan',main='Example 4',cex.main=0.75,cex=0.75,lwd=0.5)
plot(st_geometry(Coast[Coast$ID=='All',]),add=T,col='grey',lwd=0.5)
box()

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.1.png")
```

<br>

#### Create lines:

For details, type:

```{r eval=F}
?create_Lines
```

```{r eval=F}
#If your data contains line end locations in separate columns, you may reformat it as follows:

#Original data:
MyData=data.frame(
  Line=c(1,2),
  Lat_Start=c(-60,-65),
  Lon_Start=c(-10,5),
  Lat_End=c(-61,-66),
  Lon_End=c(-2,2)
)

#Reformat data to use as input in create_Lines as:
Input=data.frame(
  Line=c(MyData$Line,MyData$Line),
  Lat=c(MyData$Lat_Start,MyData$Lat_End),
  Lon=c(MyData$Lon_Start,MyData$Lon_End)
)
```

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.2.png',width=2000,height=1000,res=300)

#Prepare layout for 3 sub-plots
par(mai=c(0.01,0.01,0.2,0.01),mfrow=c(1,3))

#Example 1: Simple and non-densified lines
MyLines=create_Lines(LineData)
plot(st_geometry(MyLines),col=rainbow(nrow(MyLines)),main='Example 1',cex.main=0.75,lwd=2)
box()

#Example 2: Simple and densified lines (note the curvature of the lines)
MyLines=create_Lines(LineData,Densify=T)
plot(st_geometry(MyLines),col=rainbow(nrow(MyLines)),main='Example 2',cex.main=0.75,lwd=2)
box()

#Example 3: Densified, buffered and clipped lines
MyLines=create_Lines(LineData,Densify=T,Buffer=c(10,40,50,80,100),Clip=T)
plot(st_geometry(MyLines[5:1,]),col=rainbow(nrow(MyLines)),main='Example 3',cex.main=0.75,lwd=1)
plot(Coast[Coast$ID=='All',],col='grey',add=T,lwd=0.5)
box()

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.2.png")
```

<br>

Adding a buffer with the argument *SeparateBuf* set to FALSE results in a single polygon which may be viewed as a footprint:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.3.png',width=2000,height=1000,res=300)

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0.01,0.01,0.01,0.01))

#Buffer merged lines
MyLines=create_Lines(LineData,Buffer=10,SeparateBuf=F)
#The resulting polygon has an area of:
MyLines$Buffered_AreaKm2

plot(st_geometry(MyLines),col='green',lwd=1)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.3.png")
```

<br>

#### Create polygons:

For details, type:

```{r eval=F}
?create_Polys
```

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.4.png',width=2000,height=1200,res=300)

#Prepare layout for 3 sub-plots
par(mfrow=c(1,3),mai=c(0.01,0.01,0.2,0.01))

#Example 1: Simple and non-densified polygons
MyPolys=create_Polys(PolyData,Densify=F)
plot(st_geometry(MyPolys),col='blue',main='Example 1',cex.main=0.75,lwd=0.5)
text(MyPolys$Labx,MyPolys$Laby,MyPolys$ID,col='white',cex=0.75)
box()

#Example 2: Simple and densified polygons (note the curvature of lines)
MyPolys=create_Polys(PolyData)
plot(st_geometry(MyPolys),col='red',main='Example 2',cex.main=0.75,lwd=0.5)
text(MyPolys$Labx,MyPolys$Laby,MyPolys$ID,col='white',cex=0.75)
box()

#Example 3: Buffered and clipped polygons
MyPolysBefore=create_Polys(PolyData,Buffer=c(10,-15,120))
MyPolysAfter=create_Polys(PolyData,Buffer=c(10,-15,120),Clip=T)
plot(st_geometry(MyPolysBefore),col='green',main='Example 3',cex.main=0.75,lwd=0.5)
plot(st_geometry(Coast[Coast$ID=='All',]),add=T,lwd=0.5)
plot(st_geometry(MyPolysAfter),col='orange',add=T,lwd=0.5)
text(MyPolysAfter$Labx,MyPolysAfter$Laby,MyPolysAfter$ID,col='white',cex=0.75)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.4.png")
```

<br>

```{r message=F,eval=T}
#Convention area
#The locations of vertices are given clockwise, starting from the northwest corner of 48.3
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)
)

png(filename='ReadMeFigs/ReadMe_Fig2.5.png',width=2000,height=1200,res=300)


#Prepare layout for 2 sub-plots
par(mfrow=c(1,2),mai=c(0,0,0.2,0))

#Example 4: Convention area contour
MyPoly=create_Polys(CA)
plot(st_geometry(MyPoly),col='blue',border='green',main='Example 4',cex.main=0.75,lwd=2)
box()

#Example 5: Convention area contour, coastline clipped
MyPoly=create_Polys(CA,Clip = TRUE)
plot(st_geometry(MyPoly),col='blue',border='green',main='Example 5',cex.main=0.75,lwd=2)
box()

dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.5.png")
```

<br>

#### Create grids:

[tutorial]:https://github.com/ccamlr/CCAMLRGIS/blob/master/Advanced_Grids/Advanced_Grids.md

An advanced demo is given in this [tutorial].


For details, type:

```{r eval=F}
?create_PolyGrids
```

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.6.png',width=2000,height=800,res=300)

#Prepare layout for 3 sub-plots
par(mfrow=c(1,3),mai=c(0.01,0.01,0.2,0.01))

#Example 1: Simple grid, using automatic colors
MyGrid=create_PolyGrids(GridData,dlon=2,dlat=1)
plot(st_geometry(MyGrid),col=MyGrid$Col_Catch_sum,main='Example 1',cex.main=0.75,lwd=0.1)
box()

#Example 2: Equal area grid, using automatic colors
MyGrid=create_PolyGrids(GridData,Area=10000)
plot(st_geometry(MyGrid),col=MyGrid$Col_Catch_sum,main='Example 2',cex.main=0.75,lwd=0.1)
box()

#Example 3: Equal area grid, using custom cuts and colors
MyGrid=create_PolyGrids(GridData,Area=10000,cuts=c(0,50,100,500,2000,3500),cols=c('blue','red'))
plot(st_geometry(MyGrid),col=MyGrid$Col_Catch_sum,main='Example 3',cex.main=0.75,lwd=0.1)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.6.png")
```

<br>

Customizing a grid and adding a color scale:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.7.png',width=2000,height=1500,res=300)

#Prepare layout for 2 sub-plots
par(mfrow=c(2,1),mai=c(0.2,0.05,0.1,1.3))

#Step 1: Generate your grid
MyGrid=create_PolyGrids(GridData,Area=10000)

#Step 2: Inspect your gridded data (e.g. sum of Catch) to determine whether irregular cuts are required
hist(MyGrid$Catch_sum,100,cex=0.75,main='Frequency distribution of data',
     cex.main=0.5,col='grey',axes=F)
axis(1,pos=0,tcl=-0.15,lwd=0.8,lwd.ticks=0.8,labels=F)
text(seq(0,2500,by=500),-1.5,seq(0,2500,by=500),cex=0.75,xpd=T)

#In this case (heterogeneously distributed data) irregular cuts would be preferable
#Such as:
MyCuts=c(0,50,100,500,2000,2500)
abline(v=MyCuts,col='green',lwd=1,lty=2) #Add classes to histogram as green dashed lines

#Step 3: Generate colors according to the desired classes (MyCuts)
Gridcol=add_col(MyGrid$Catch_sum,cuts=MyCuts,cols=c('yellow','purple'))

#Step 4: Plot result and add color scale
#Use the colors generated by add_col
plot(st_geometry(MyGrid),col=Gridcol$varcol,lwd=0.1) 
#Add color scale using cuts and cols generated by add_col
add_Cscale(title='Sum of Catch (t)',cuts=Gridcol$cuts,cols=Gridcol$cols,width=18,
     fontsize=0.6,lwd=0.5,height = 100) 
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.7.png")
```

<br>

### 2.2. Create Stations

This function was designed to create random point locations inside a polygon and within bathymetry strata constraints. A distance constraint between stations may also be used if desired. The examples below use the 'SmallBathy' data for illustrative purposes; users should use a higher resolution bathymetry dataset instead, as obtained via the *load_Bathy()* function.

For details, type:

```{r eval=F}
?create_Stations
```

First, create a polygon within which stations will be created:

```{r message=F,eval=T}
#Create polygons
MyPoly=create_Polys(
        data.frame(Name="mypol",
             Latitude=c(-75,-75,-70,-70),
             Longitude=c(-170,-180,-180,-170))
        ,Densify=T)


png(filename='ReadMeFigs/ReadMe_Fig2.8.png',width=2000,height=1000,res=300,bg="transparent")
par(mai=c(0,0,0,0))
plot(st_geometry(Coast[Coast$ID=='88.1',]),col='grey')
plot(st_geometry(MyPoly),col='green',add=T)
text(MyPoly$Labx,MyPoly$Laby,MyPoly$ID)
box()
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.8.png")
```

<br>

Example 1. Set numbers of stations, no distance constraint:

```{r message=F,eval=T}

#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))

png(filename='ReadMeFigs/ReadMe_Fig2.9.png',width=2000,height=1500,res=300)

#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=F,axes=F,main="Example 1")
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=T,border='red',lwd=2,xpd=T)
plot(st_geometry(MyStations),add=T,col='orange',cex=0.75,lwd=1.5,pch=3)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.9.png")
```

<br>

Example 2. Set numbers of stations, with distance constraint:

```{r message=F,eval=T}

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

png(filename='ReadMeFigs/ReadMe_Fig2.10.png',width=2000,height=1500,res=300)

#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=F,axes=F,main="Example 2")
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=T,border='red',lwd=2,xpd=T)
plot(st_geometry(MyStations[MyStations$Stratum=='1000-550',]),pch=21,bg='yellow',add=T,cex=0.75,lwd=0.1)
plot(st_geometry(MyStations[MyStations$Stratum=='1500-1000',]),pch=21,bg='orange',add=T,cex=0.75,lwd=0.1)
plot(st_geometry(MyStations[MyStations$Stratum=='2000-1500',]),pch=21,bg='red',add=T,cex=0.75,lwd=0.1)
dev.off()

```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.10.png")
```

<br>

Example 3. Automatic numbers of stations, with distance constraint:

```{r message=F,eval=T}

#Create Stations
MyStations=create_Stations(MyPoly,BathyCroped,Depths=c(-2000,-1500,-1000,-550),Nauto=30,dist=10)

png(filename='ReadMeFigs/ReadMe_Fig2.11.png',width=2000,height=1500,res=300)

#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=F,axes=F,main="Example 3")
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=T,border='red',lwd=2,xpd=T)
plot(st_geometry(MyStations[MyStations$Stratum=='1000-550',]),pch=21,bg='yellow',add=T,cex=0.75,lwd=0.1)
plot(st_geometry(MyStations[MyStations$Stratum=='1500-1000',]),pch=21,bg='orange',add=T,cex=0.75,lwd=0.1)
plot(st_geometry(MyStations[MyStations$Stratum=='2000-1500',]),pch=21,bg='red',add=T,cex=0.75,lwd=0.1)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.11.png")
```

<br>

### 2.3. Create pies

The function *create_Pies()* 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 pie pieces for each class, and the size of each pie 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* (see Examples 6-8). Once pie charts have been created, the function *add_PieLegend()* may be used to add a legend to the figure.

For details, type:

```{r eval=F}
?create_Pies
?add_PieLegend
#The examples below use the following example datasets:
View(PieData)
View(PieData2)
```

<br>

Example 1. Pies of constant size, all classes displayed:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.12.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(5.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=50
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#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")
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.12.png")
```

<br>

Example 2. Pies of constant size, selected classes displayed:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.13.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(5.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=50,
                   Classes=c("TOP","TOA","ANI")
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1.6,Boxexp=c(0.6,0.6,0.12,0.55),
              PieTitle="Selected species")
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.13.png")
```

<br>

Example 3. Pies of constant size, proportions below 25% are grouped in a 'Other' class (*N.B.*: unlike Example 2, the 'Other' class may contain classes that are displayed in the legend. Please compare Example 1 and Example 3):

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.14.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(5.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=50,
                   Other=25
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1.6,Boxexp=c(0.55,0.55,0.12,0.45),
              PieTitle="Other (%) class")
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.14.png")
```

<br>

Example 4. Pies of variable size (here, their area is proportional to 'Catch'), all classes displayed, horizontal legend:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.15.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(5.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=18,
                   SizeVar="Catch"
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=-0.1,PosY=-1.6,Boxexp=c(0.16,0.1,0.1,0.4),
              PieTitle="Species",SizeTitle="Catch (t.)")
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.15.png")
```

<br>

Example 5. Pies of variable size (here, their area is proportional to 'Catch'), all classes displayed, vertical legend:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.16.png',width=2000,height=1200,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(0,0.2,0,8.5))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=18,
                   SizeVar="Catch"
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=2.32,PosY=0.1,Boxexp=c(0.35,0.32,0.02,0.15),
              PieTitle="Species",SizeTitle="Catch (t.)",Horiz=FALSE,LegSp=0.6)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.16.png")
```

<br>

Example 6. Pies of constant size, all classes displayed. Too many pies (see next example for solution):

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.17.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(5.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData2,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=5
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=0.4,PosY=-1.5,Boxexp=c(0.6,0.5,0.14,0.5),
              PieTitle="Species")
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.17.png")
```

<br>

Example 7. Pies of constant size, all classes displayed. Gridded locations (in which case numerical variables in the *Input* are summed for each grid point):

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.18.png',width=2000,height=1400,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(4.5,0,0.1,0))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData2,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=5,
                   GridKm=250
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=0.4,PosY=-1.3,Boxexp=c(0.5,0.45,0.12,0.45),
              PieTitle="Species")
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.18.png")
```

<br>

Example 8. Pies of variable size (here, their area is proportional to 'Catch'), all classes displayed, vertical legend, gridded locations (in which case numerical variables in the *Input* are summed for each grid point):

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.19.png',width=2000,height=1200,res=300,bg="transparent")

#Plot the bathymetry (See section 'Local map' where B486 was created)
plot(B486,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=c(0,0.1,0,8.5))
#Add coastline
plot(Coast[Coast$ID=='48.6',],col='grey',lwd=0.01,add=T)
#Create pies
MyPies=create_Pies(Input=PieData2,
                   NamesIn=c("Lat","Lon","Sp","N"),
                   Size=3,
                   GridKm=250,
                   SizeVar='Catch'
                   )
#Plot Pies
plot(st_geometry(MyPies),col=MyPies$col,add=TRUE)
#Add Pies legend
add_PieLegend(Pies=MyPies,PosX=2.8,PosY=0.15,Boxexp=c(0.38,0.32,0.08,0.18),
              PieTitle="Species",Horiz=FALSE,SizeTitle="Catch (t.)",
              SizeTitleVadj=0.8,nSizes=2)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.19.png")
```

<br>

### 2.4. Create Arrow

This function creates an arrow, which can be curved and/or segmented. Input is a dataframe with columns Latitude, Longitude, Weight (optional). First row is start, last row is end (where the arrow will point to), and intermediate rows are points towards which the arrow's path will bend. A weight can be added to the intermediate points to make the arrow's path bend more towards them. The arrow's path is a curve along *Np* points, if it appears too segmented, increase *Np*. The arrow's path width is controlled by *Pwidth*. The arrow's head length and width are controlled by *Hlength* and *Hwidth* respectively. Two types of arrows (*Atype*) can be created: '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*.

For details, type:

```{r eval=F}
?create_Arrow
```

Examples 1-4:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.20.png',width=2000,height=1400,res=300)

ASDs=load_ASDs()
ASDs=ASDs[ASDs$GAR_Short_Label%in%c("481","482","483"),]

# Example 1: straight green arrow.
myInput=data.frame(lat=c(-61,-52),
                 lon=c(-60,-40))

Arrow=create_Arrow(Input=myInput)

par(mai=c(0,0,0.5,0),mfrow=c(2,2))
plot(st_geometry(ASDs),main="Example 1")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE)

# 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(ASDs),main="Example 2")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE)

#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(ASDs),main="Example 3")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE)


#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(ASDs),main="Example 4")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.20.png")
```

<br>

Examples 5-8:

```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig2.21.png',width=2000,height=1400,res=300)

#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)

par(mai=c(0,0,0.5,0),mfrow=c(2,2))
plot(st_geometry(ASDs),main="Example 5")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE,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(ASDs),main="Example 6")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE,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(ASDs),main="Example 7")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE,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(ASDs),main="Example 8")
plot(st_geometry(Coast[Coast$ID%in%c("48.1","48.2","48.3"),]),col="grey",add=TRUE)
plot(st_geometry(Arrow),col=Arrow$col,add=TRUE,border=NA)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.21.png")
```

<br>

Example 9:

```{r message=F,eval=T}
#Example 9
#Prepare mapping elements
ASDs=ASDs[ASDs$GAR_Short_Label=="481",]
bb=st_bbox(st_buffer(ASDs,20000)) #Get bounding box (x/y limits) +20,000m buffer
bx=st_as_sfc(bb) #Build spatial box to plot
coast=load_Coastline()
C481=st_intersection(st_union(coast[coast$surface=="Land",]),bx) #Crop coastline to box limits
B481=crop(SmallBathy(),ext(bb))

#Create arrows

myInput=data.frame(lat=c(-68,-65,-64,-61,-61,-60),
                   lon=c(-75,-70,-65,-60,-55,-50),
                   w=c(1,3,3,3,3,1))
Arrow1=create_Arrow(Input=myInput,Acol="orange",Atrans=0.3,Pwidth=3,Hlength=10,Hwidth=6)

myInput=data.frame(lat=c(-66,-65,-66),
                   lon=c(-71,-70,-67))
Arrow2=create_Arrow(Input=myInput,Acol="orange",Atrans=0.3,Pwidth=1,Hlength=5,Hwidth=2.5)

myInput=data.frame(lat=c(-63.8,-63,-63),
                   lon=c(-65,-62,-60))
Arrow3=create_Arrow(Input=myInput,Acol="orange",Atrans=0.3,Pwidth=1,Hlength=5,Hwidth=2.5)

myInput=data.frame(lat=c(-61,-62,-63,-64.5),
                   lon=c(-55,-52,-53,-55))
Arrow4=create_Arrow(Input=myInput,Acol="orange",Atrans=0.3,Pwidth=1,Hlength=5,Hwidth=2.5)

#Merge arrows 1 to 4
Arrow1_4=suppressWarnings(st_union(Arrow1,Arrow2))
Arrow1_4=suppressWarnings(st_union(Arrow1_4,Arrow3))
Arrow1_4=suppressWarnings(st_union(Arrow1_4,Arrow4))

myInput=data.frame(lat=c(-71,-67,-65),
                   lon=c(-57,-60,-55))
Arrow5=create_Arrow(Input=myInput,Acol=c("white","red"),Atrans = c(1,0),Pwidth=5,
                    Hlength=10,Hwidth=10,Atype = "dashed",Np=100)

myInput=data.frame(lat=c(-59,-60,-62,-63,-65),
                   lon=c(-52,-60,-65,-70,-75))
Arrow6=create_Arrow(Input=myInput,Acol=c("purple","cyan","black"),Pwidth=2,
                    Hlength=10,Hwidth=5,Atype = "dashed",dlength = 1)


png(filename='ReadMeFigs/ReadMe_Fig2.22.png',width=2000,height=1600,res=300)

#Plot the bathymetry
plot(B481,breaks=Depth_cuts,col=Depth_cols,legend=FALSE,axes=FALSE,mar=rep(1.5,4))
text(-2050000,2070000,"Example 9",font=2,xpd=TRUE,cex=2)
#Plot border
plot(bx,border='black',lwd=1,xpd=TRUE,add=TRUE)
#Add coastline (for Subarea 48.6 only)
plot(C481,col="grey",add=TRUE,xpd=T)
#Add reference grid
add_RefGrid(bb=bb,ResLat=2,ResLon=5,fontsize=0.8,lwd=0.75,offset = c(20000,30000))
#Add Subarea 48.1 boundaries
plot(st_geometry(ASDs),add=TRUE,lwd=3,border='black',xpd=T)
#Add Arrows
plot(st_geometry(Arrow1_4),col=Arrow1_4$col,add=TRUE,border="orange",lwd=2,xpd=T)
plot(st_geometry(Arrow5),col=Arrow5$col,add=TRUE,border=NA,xpd=T)
plot(st_geometry(Arrow6),col=Arrow6$col,add=TRUE,border='white',xpd=T)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.22.png")
```

<br>

Example 10 (path along isobath):

```{r message=F,eval=T}
#Example 10 
#Prepare mapping elements
Iso=st_as_sf(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

#Create arrows
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)


png(filename='ReadMeFigs/ReadMe_Fig2.22b.png',width=2000,height=1600,res=300)
#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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 10")
plot(st_geometry(Arr1),col="darkred",add=T)
plot(st_geometry(Arr2),col="darkred",add=T)
plot(st_geometry(Arr3),col="darkred",add=T)
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=T)

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.22b.png")
```

<br>

### 2.5. Create Hashes

This function creates hashed lines to fill a polygon. Its output is a spatial object in your environment, to be added to your plot.

For details, type:

```{r eval=F}
?create_Hashes
```

Example:

```{r message=F,eval=T}

#load ASDs
ASDs=load_ASDs()
#Generate colors, angles, spacings and widths of hashes, one per ASD
Colors=rainbow(nrow(ASDs))
angles=seq(10,355,length.out=nrow(ASDs))
spacings=seq(3,10,length.out=nrow(ASDs))
widths=seq(3,10,length.out=nrow(ASDs))

png(filename='ReadMeFigs/ReadMe_Fig2.23.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

plot(st_geometry(ASDs),col="white")
for(i in seq(1,nrow(ASDs))){
  H=create_Hashes(pol=ASDs[i,],angle=angles[i],spacing=spacings[i],width=widths[i])
  plot(st_geometry(H),col=Colors[i],add=T)

}
plot(st_geometry(ASDs),lwd=2,add=T)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.23.png")
```

<br>


### 2.6. Create Ellipse

This function creates an ellipse. Its output is a spatial object in your environment, to be added to your plot.

For details, type:

```{r eval=F}
?create_Ellipse
```

Example:

```{r message=F,eval=T}

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)

png(filename='ReadMeFigs/ReadMe_Fig2.24.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.24.png")
```

<br>

### 2.7. Create Circular Arrow

This function creates circular arrows. Its output is a spatial object in your environment, to be added to your plot.

For details, type:

```{r eval=F}
?create_CircularArrow
```

Example 1:

```{r message=F,eval=T}

Arr=create_CircularArrow()

png(filename='ReadMeFigs/ReadMe_Fig2.25.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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",col.main='grey')
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.25.png")
```

<br>

Example 2:

```{r message=F,eval=T}

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

png(filename='ReadMeFigs/ReadMe_Fig2.26.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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",col.main='grey')
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.26.png")
```

<br>

Example 3:

```{r message=F,eval=T}

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

png(filename='ReadMeFigs/ReadMe_Fig2.27.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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",col.main='grey')
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.27.png")
```

<br>

Example 4:

```{r message=F,eval=T}

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

png(filename='ReadMeFigs/ReadMe_Fig2.28.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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",col.main='grey')
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.28.png")
```

<br>

Example 5 (path around two ellipses):

```{r message=F,eval=T}
#Create elipses
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)

png(filename='ReadMeFigs/ReadMe_Fig2.29.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))

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",col.main='grey')
plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.29.png")
```

<br>

Example 6 (path along isobath):

```{r message=F,eval=T}

Iso=st_as_sf(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=st_polygon(list(Iso[seq(1,nrow(Iso),length.out=200),])) #Subsample

Arr=create_CircularArrow(Narr=20,Spc=1,Input=Iso,
                         Pwidth=10,Hlength=30,Hwidth=20)

png(filename='ReadMeFigs/ReadMe_Fig2.30.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0.5,0.5,0.5,0.5))

plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',main="Example 6",
     xlim=c(-2.5e6,2.5e6),ylim=c(-2.5e6,2.5e6),col.main='grey')
plot(st_geometry(Arr),col=rainbow(nrow(Arr)),add=TRUE,xpd=TRUE)
dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig2.30.png")
```

<br>

Example 7 (Weddell Sea animation):

```{r message=F,eval=T}

library(gifski)
gif_file = "ReadMeFigs/Woooo.gif" #Path for repo

save_gif(
  for(Stp in seq(1,0,length.out=10)){
    Arr=create_CircularArrow(Narr=8,Spc=-2,Npa=200,Acol=c("red","orange","green"),
                             Atrans = c(0,0.9,0),Atype = "dashed",Stp=Stp)
    Arr2=create_CircularArrow(Lmaj=600,Lmin=300,dir="ccw",Spc=50,Stp=1-Stp,
                              Pwidth=2.5,Hlength=10,Hwidth=7,Acol="cyan")
    plot(SmallBathy(),xlim=c(-3e6,0),ylim=c(0,3e6),breaks=Depth_cuts,
                col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,main="Example 7")
    plot(st_geometry(Coast[Coast$ID=='All',]),col='grey',add=TRUE)
    plot(st_geometry(Arr),col=Arr$col,border=NA,add=TRUE)
    plot(st_geometry(Arr2),col=Arr2$col,border=NA,add=TRUE)
  }
  , gif_file, 800, 800, res = 150,delay = 0.1,progress = FALSE)

```


<img src="https://github.com/ccamlr/CCAMLRGIS/blob/master/ReadMeFigs/Woooo.gif" width="800" height="800" />

<br>


## 3. Load functions

### 3.1. Online use

Download the up-to-date spatial layers from the online CCAMLR GIS and load them to your environment.

For details, type:

```{r eval=F}
?load_ASDs
?load_Bathy
```

```{r message=F,eval=T}

#Load ASDs, EEZs, and Coastline
ASDs=load_ASDs()
EEZs=load_EEZs()
Coastline=load_Coastline()
Coastline=Coastline[Coastline$surface=="Land",]

png(filename='ReadMeFigs/ReadMe_Fig3.1.png',width=2000,height=2000,res=300,bg="transparent")

#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))
#Plot
plot(st_geometry(ASDs),col='green',border='blue')
plot(st_geometry(EEZs),col='orange',border='purple',add=T)
plot(st_geometry(Coastline),col='grey',add=T)
add_labels(mode='auto',layer='ASDs',fontsize=0.75,col='red')
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig3.1.png")
```

<br>

### 3.2. Offline use

Since the '*load\_*' functions require an internet connection, users may desire to save layers on their hard drive for offline use. This may be done, at the risk of not having the most up-to-date layers, as follows:

```{r eval=F}

#Load all layers
ASDs=load_ASDs()
EEZs=load_EEZs()
Coastline=load_Coastline()
SSRUs=load_SSRUs()
RBs=load_RBs()
SSMUs=load_SSMUs()
MAs=load_MAs()
MPAs=load_MPAs()

#Save as .RData file (here in the temp directory, but users might want to chose their own directory)
save(list=c('ASDs','EEZs','Coastline','SSRUs','RBs','SSMUs','MAs','MPAs'),
     file = file.path(tempdir(), "CCAMLRLayers.RData"), compress='xz')

#Later, when offline load layers:
load(file.path(tempdir(), "CCAMLRLayers.RData"))
```

The *load_Bathy()* function may also be used to download and store bathymetry data for later use, see ?load_Bathy for details.

## 4. Other functions

### 4.1. get_depths

Given a bathymetry raster and an input dataframe of latitudes/longitudes, this function computes the depths at these locations. The examples below use the 'SmallBathy' data for illustrative purposes; users should use a higher resolution bathymetry dataset instead, as obtained via the *load_Bathy()* function.

For details, type:

```{r eval=F}
?get_depths
```

```{r message=F,eval=T}

#Generate a dataframe
MyData=data.frame(Lat=PointData$Lat,
                  Lon=PointData$Lon,
                  Catch=PointData$Catch)
#The input data looks like this:
head(MyData)

#Get depths of locations
MyDataD=get_depths(Input=MyData,Bathy=SmallBathy())
#The resulting data looks like this (where 'd' is the depth):
head(MyDataD)

png(filename='ReadMeFigs/ReadMe_Fig4.1.png',width=2000,height=1400,res=300,bg="white")

#Plot Catch vs Depth
plot(MyDataD$d,MyDataD$Catch,xlab='Depth',ylab='Catch',pch=21,bg='red')

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig4.1.png")
```

<br>

### 4.2. seabed_area

Function to calculate planimetric seabed area within polygons and depth strata in square kilometers. Its accuracy depends on the input bathymetry raster. The examples below use the 'SmallBathy' data for illustrative purposes; users should use a higher resolution bathymetry dataset instead, as obtained via the *load_Bathy()* function. Higher accuracy will be obtained with raw, unprojected bathymetry data.

For details, type:

```{r eval=F}
?seabed_area
```

```{r message=F,eval=T}
#create some polygons
MyPolys=create_Polys(PolyData,Densify=T)
#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')
head(FishDepth)
```

### 4.3. assign_areas

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 ASD the given fishing locations occurred.

For details, type:

```{r eval=F}
?assign_areas
```

```{r message=F,eval=T}
#Generate a dataframe with random locations
MyData=data.frame(Lat=runif(100,min=-65,max=-50),
                  Lon=runif(100,min=20,max=40))
#The input data looks like this:
head(MyData)

#load ASDs and SSRUs
ASDs=load_ASDs()
SSRUs=load_SSRUs()

#Assign ASDs and SSRUs to these locations 
MyData=assign_areas(MyData,Polys=c('ASDs','SSRUs'),NamesOut=c('MyASDs','MySSRUs'))
#The output data looks like this:
head(MyData)

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

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

```

### 4.4. project_data

A simple function to project user-supplied locations. Input must be a dataframe, outputs may be appended to the dataframe.

For details, type:

```{r eval=F}
?project_data
```

```{r message=FALSE,eval=TRUE}

#The input data looks like this:
head(PointData)
#Generate a dataframe with random locations
MyData=project_data(Input=PointData,NamesIn=c('Lat','Lon'),
                    NamesOut=c('Projected_Y','Projected_X'),append=TRUE)
#The output data looks like this:
head(MyData)
```

### 4.5. get_C\_intersection

Get Cartesian coordinates of lines intersection in Euclidean space. This may have several uses, including when creating polygons with shared boundaries. Uses the coordinates of line extremities as input.

For details, type:

```{r eval=F}
?get_C_intersection
```


```{r message=F,eval=T}

png(filename='ReadMeFigs/ReadMe_Fig4.2.png',width=2000,height=1800,res=300,bg="white")

#Prepare layout for 4 sub-plots
par(mfrow=c(2,2),mai=c(0.7,0.7,0.25,0.07))

#Example 1 (Intersection beyond the range of segments)
get_C_intersection(Line1=c(-30,-55,-29,-50),Line2=c(-50,-60,-40,-60))
text(-40,-42,"Example 1",xpd=T)
box()
#Example 2 (Intersection on one of the segments)
get_C_intersection(Line1=c(-30,-65,-29,-50),Line2=c(-50,-60,-40,-60))
text(-40,-41,"Example 2",xpd=T)
box()
#Example 3 (Crossed segments)
get_C_intersection(Line1=c(-30,-65,-29,-50),Line2=c(-50,-60,-25,-60))
text(-38,-41,"Example 3",xpd=T)
box()
#Example 4 (Antimeridian crossed)
get_C_intersection(Line1=c(-179,-60,-150,-50),Line2=c(-120,-60,-130,-62))
text(-180,-37,"Example 4",xpd=T)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig4.2.png")
```

<br>

### 4.6. get_iso_polys

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). if *Grp* is 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 (see example 2 below).

For details, type:

```{r eval=F}
?get_iso_polys
```


```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig4.3.png',width=2000,height=1200,res=300,bg="white")

#Prepare layout for 3 sub-plots
par(mfrow=c(1,3),mai=c(0,0.01,0.2,0.01))

#Example 1 - Whole Convention Area 
IsoPols=get_iso_polys(Rast=SmallBathy(),Cuts=c(-10000,-4000,-2000,0),Cols=c("blue","white","red"))

plot(st_geometry(IsoPols),col=IsoPols$c,main="Example 1")
box()

#Example 2 - SSRU 882H seamounts
SSRUs=load_SSRUs()
Poly=SSRUs[SSRUs$GAR_Short_Label=="882H",]
IsoPols=get_iso_polys(Rast=SmallBathy(),Poly=Poly,Cuts=c(-2500,-1800,-600),Cols=c("cyan","green"),Grp=TRUE)

plot(st_geometry(IsoPols),col=IsoPols$c,main="Example 2")
text(IsoPols$Labx,IsoPols$Laby,IsoPols$Grp,col="red",font=2,xpd=TRUE,cex=1.25, adj=c(-.5,-.5))
box()

#Example 3 - Custom polygon
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),main="Example 3")
plot(st_geometry(IsoPols),col=IsoPols$c,add=TRUE)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig4.3.png")
```

<br>

### 4.7. Rotate_obj

Rotate an *sf* or *SpatRaster* object by setting the longitude that should point up. The output should **only** be used for plotting, not analysis (as the projection is modified to a non-standard EPSG projection). See also [here] for more examples.

```{r message=F}
library(gifski)
gif_file = "ReadMeFigs/Weeee.gif"

save_gif(
for(Lonzero in c(seq(0,180,by=20),seq(-160,-20,by=20))){
Rot_SmallBathy=Rotate_obj(SmallBathy(),Lon0=Lonzero)
terra::plot(Rot_SmallBathy,breaks=Depth_cuts, col=Depth_cols,
            legend=FALSE,axes=FALSE,box=FALSE,ext=ext(SmallBathy()),
            mar=rep(0,4))
add_RefGrid(bb=st_bbox(Rot_SmallBathy),ResLat=10,ResLon=20,LabLon = Lonzero,offset = 3)
}
, gif_file, 800, 800, res = 150,delay = 0.1,progress = F)
```

<img src="https://github.com/ccamlr/CCAMLRGIS/blob/master/ReadMeFigs/Weeee.gif" width="800" height="800" />

<br>


## 5. Adding colors, legends and labels

### 5.1. Bathymetry colors

Coloring bathymetry requires a vector of depth classes and a vector of colors. Colors are applied between depth classes (so there is one less color than there are depth classes). Two sets of bathymetry colors are included in the package. One simply colors the bathymetry in shades of blue (*Depth_cols* and *Depth_cuts*), the other adds shades of green to highlight the Fishable Depth range (600-1800m; *Depth_cols2* and *Depth_cuts2*). The examples below use the 'SmallBathy' data for illustrative purposes; users should use a higher resolution bathymetry dataset instead, as obtained via the *load_Bathy()* function.

#### Simple set of colors:

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig5.1.png',width=2000,height=1800,res=300,bg="transparent")

#Plot the bathymetry
plot(SmallBathy(),breaks=Depth_cuts,col=Depth_cols,axes=FALSE,box=FALSE,legend=FALSE,mar=c(0,0,0,7))
#Add color scale
add_Cscale(cuts=Depth_cuts,cols=Depth_cols,fontsize=0.75,height=80,offset=0,width=16,maxVal=-1)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.1.png")
```

#### Highlighting the Fishable Depth range:

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig5.2.png',width=2000,height=1800,res=300,bg="transparent")

#Plot the bathymetry
plot(SmallBathy(),breaks=Depth_cuts2,col=Depth_cols2,axes=FALSE,box=FALSE,legend=FALSE,mar=c(0,0,0,7))
#Add color scale
add_Cscale(cuts=Depth_cuts2,cols=Depth_cols2,fontsize=0.75,height=80,offset=0,width=16,maxVal=-1)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.2.png")
```

### 5.2. Adding colors to data

Adding colors to plots revolves around two functions:

```{r eval=F}
?add_col
#and
?add_Cscale
```

*add_col()* generates colors for a variable of interest as well as a set of color classes and colors to be used as inputs to the *add_Cscale()* function. Colors and color classes may be generated automatically or customized, depending on the intended appearance. Knowing the names of colors in R would be useful here (<http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf>).

```{r message=F,eval=T}

#Adding color to points
png(filename='ReadMeFigs/ReadMe_Fig5.3.png',width=2000,height=1800,res=300,bg="white")

#Prepare layout for 3 sub-plots
par(mfrow=c(3,1),mai=c(0.1,0.1,0.1,1))
#Create some points
MyPoints=create_Points(PointData)

#Example 1: Add default cols and cuts
MyCols=add_col(MyPoints$Nfishes) 
plot(st_geometry(MyPoints),pch=21,bg=MyCols$varcol,main='Example 1:',cex.main=0.75,cex=1.5,lwd=0.5)
box()
add_Cscale(title='Number of fishes',
           height=95,fontsize=0.75,width=16,lwd=1,offset=0,
           cuts=MyCols$cuts,cols=MyCols$cols)

#Example 2: Given the look of example 1, reduce the number of cuts and round their values (in add_Cscale)
MyCols=add_col(MyPoints$Nfishes,cuts=10) 
plot(st_geometry(MyPoints),pch=21,bg=MyCols$varcol,main='Example 2:',cex.main=0.75,cex=1.5,lwd=0.5)
box()
add_Cscale(title='Number of fishes',
           height=95,fontsize=0.75,width=16,lwd=1,offset=0,
           cuts=round(MyCols$cuts,1),cols=MyCols$cols)

#Example 3: same as example 2 but with custom colors
MyCols=add_col(MyPoints$Nfishes,cuts=10,cols=c('black','yellow','purple','cyan')) 
plot(st_geometry(MyPoints),pch=21,bg=MyCols$varcol,main='Example 3:',cex.main=0.75,cex=1.5,lwd=0.5)
add_Cscale(title='Number of fishes',
           height=95,fontsize=0.75,width=16,lwd=1,offset=0,
           cuts=round(MyCols$cuts,1),cols=MyCols$cols)
box()
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.3.png")
```

<br>

```{r message=F,eval=T}

#Adding colors to a grid with custom cuts (see also the last example in section 2.1.)

#Step 1: Generate your grid
MyGrid=create_PolyGrids(GridData,Area=10000)

#Step 2: Inspect your gridded data (e.g. hist(MyGrid$Catch_sum,100))
#to determine whether irregular cuts are required.
#In this case (heterogeneously distributed data) irregular cuts 
#would be preferable, such as:
MyCuts=c(0,50,100,500,2000,2500)

#Step 3: Generate colors according to the desired classes (MyCuts)
Gridcol=add_col(MyGrid$Catch_sum,cuts=MyCuts,cols=c('blue','white','red'))

png(filename='ReadMeFigs/ReadMe_Fig5.4.png',width=2000,height=1200,res=300,bg="transparent")

#Step 4: Plot result and add color scale
par(mai=c(0,0,0,1.5)) #set plot margins as c(bottom, left, top, right)
#Use the colors generated by add_col
plot(st_geometry(MyGrid),col=Gridcol$varcol,lwd=0.1) 
#Add color scale using cuts and cols generated by add_col
add_Cscale(title='Sum of Catch (t)',cuts=Gridcol$cuts,cols=Gridcol$cols,width=24,
     fontsize=0.75,lwd=1) 
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.4.png")
```

<br>

### 5.3. Adding legends

A simple way to quickly add a legend, is by using the base *legend()* function:

```{r eval=F}
?legend
```

To position the legend, the *add_Cscale()* function can generate legend coordinates which correspond to the top-left corner of the legend box. These may be adjusted using the 'pos', 'height' and 'offset' arguments within *add_Cscale()*, *e.g.*:

```{r eval=F}
Legend_Coordinates=add_Cscale(pos='2/3',offset=1000,height=40,mode="Legend")
```

```{r message=F,eval=T}
#Adding a color scale and a legend

#Create some point data
MyPoints=create_Points(PointData)

#Crop the bathymetry to match the extent of MyPoints (extended extent)
BathyCr=crop(SmallBathy(),extend(ext(MyPoints),100000))

png(filename='ReadMeFigs/ReadMe_Fig5.5.png',width=2000,height=1200,res=300,bg="transparent")

#Plot the bathymetry
plot(BathyCr,breaks=Depth_cuts,col=Depth_cols,legend=F,axes=F,mar=c(0,0.1,0,6))
#Add a color scale
add_Cscale(pos='3/8',height=50,maxVal=-1,minVal=-4000,fontsize=0.75,lwd=1,width=16)

#Plot points with different symbols and colors (see ?points)
par(xpd=T)
Psymbols=c(21,22,23,24)
Pcolors=c('red','green','blue','yellow')
plot(st_geometry(MyPoints[MyPoints$name=='one',]),pch=Psymbols[1],bg=Pcolors[1],add=T)
plot(st_geometry(MyPoints[MyPoints$name=='two',]),pch=Psymbols[2],bg=Pcolors[2],add=T)
plot(st_geometry(MyPoints[MyPoints$name=='three',]),pch=Psymbols[3],bg=Pcolors[3],add=T)
plot(st_geometry(MyPoints[MyPoints$name=='four',]),pch=Psymbols[4],bg=Pcolors[4],add=T)

#Add legend with position determined by add_Cscale
Loc=add_Cscale(pos='8/8',mode='Legend')
legend(Loc,legend=c('one','two','three','four'),
       title='Vessel',pch=Psymbols,pt.bg=Pcolors,xpd=T,
       box.lwd=1,cex=0.75,pt.cex=1,y.intersp=0.7,bg="white")
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.5.png")
```

<br>

For a more complete and customizable approach, use the *add_Legend()* function. It uses the bounding box of your plot and lists of parameters as inputs. The help given in the R package contains all the details:

```{r eval=F}
?add_Legend
```

Below is an example showing its capabilities:


```{r message=F,eval=T}
#load ASDs to get their bounding box
ASDs=load_ASDs()
bb=st_bbox(ASDs) #Get bounding box
bx=st_as_sfc(bb) #Convert to polygon to plot it

# 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 legend 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)

png(filename='ReadMeFigs/ReadMe_Fig5.6.png',width=2000,height=1600,res=300,bg="transparent")
#Set the figure margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))
#Plot and add legend
plot(bx,col="grey")
plot(st_geometry(ASDs),add=TRUE)
add_Legend(bb,LegOpt,Items)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.6.png")
```

<br>

### 5.4. Adding labels

To add labels, use the *add_labels()* function:

```{r eval=F}
?add_labels
```

Three modes are available within the *add_labels()* function:

-   In 'auto' mode, labels are placed at the centres of polygon parts of spatial objects loaded via the *load\_* functions.
-   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 later 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.

```{r message=F,eval=T}
#Example 1: 'auto' mode
#label ASDs in bold and red
ASDs=load_ASDs()

png(filename='ReadMeFigs/ReadMe_Fig5.7.png',width=2000,height=1600,res=300,bg="white")
#set plot margins as c(bottom, left, top, right)
par(mai=c(0,0,0,0))
plot(st_geometry(ASDs))
add_labels(mode='auto',layer='ASDs',fontsize=0.75,fonttype=2,col='red')
#add MPAs and EEZs and their labels in large, green and vertical text
MPAs=load_MPAs()
EEZs=load_EEZs()
plot(st_geometry(MPAs),add=TRUE,border='green')
plot(st_geometry(EEZs),add=TRUE,border='green')
add_labels(mode='auto',layer=c('EEZs','MPAs'),fontsize=1,col='green',angle=90)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.7.png")
```


```{r eval=F}
#Example 2: 'auto' and 'input' modes
#This example is not executed here because it needs user interaction.
#Please copy and paste it in the Console to see how it works.

#Prepare a basemap
plot(SmallBathy())
ASDs=load_ASDs()
plot(st_geometry(ASDs),add=T)

#Build your labels
MyLabels=add_labels(mode='manual') 

#Re-use the label table generated (if desired)
plot(SmallBathy())
plot(st_geometry(ASDs),add=T)
add_labels(mode='input',LabelTable=MyLabels)
```

### 5.5. Using sf

Due to the retirement of some packages that the CCAMLRGIS package used to rely on, since CCAMLRGIS V4.0.0 the package relies on the [sf package](https://CRAN.R-project.org/package=sf), users may need to familiarize themselves with it. Using *sf* objects has advantages such as the ability to use [Tidyverse methods](https://r-spatial.github.io/sf/reference/tidyverse.html). Further, additional [plotting methods](https://r-spatial.github.io/sf/articles/sf5.html) are available, some of which are described in this section.

Depending on the function used, the CCAMLRGIS package computes data summaries and includes them in the resulting spatial object. For example, *create_Polys* takes any numerical values included in the *Input* data frame and computes, for each polygon, the minimum, maximum, mean, median, sum, count and standard deviation of values associated with each polygon. The *sf* package has some useful plotting methods, some of which are shown below.

```{r message=F,eval=T}

#First, let's create some example polygons
MyPolys=create_Polys(PolyData)

#MyPolys is an sf object; it is a data frame that includes a column named 'geometry':
kableExtra::kable(MyPolys,row.names = F)

```

The 'geometry' column contains the locations of each point of a given polygon (each row), and can be plotted using *plot(st_geometry(MyPolys))*, as shown previously in this document. Alternatively, one can use *plot(MyPolys)* directly:


```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig5.8.png',width=2000,height=1600,res=300,bg="white")

plot(MyPolys)

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.8.png")
```

This results in a warning *Warning: plotting the first 9 out of 25 attributes...* and a 9-panel plot as shown above, with each panel corresponding to each column present in *MyPolys* and automatic colors generated according to the values in each column. In order to plot only one variable, it must be named in the plotting command:

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig5.9.png',width=2000,height=1000,res=300,bg="white")

plot(MyPolys["Catch_mean"])

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.9.png")
```

There are several available options, for example:

```{r message=F,eval=T}
png(filename='ReadMeFigs/ReadMe_Fig5.10.png',width=2000,height=1000,res=300,bg="white")

Gr=st_graticule(MyPolys,lon=seq(-180,180,by=5),lat=seq(-80,0,by=2.5))
plot(MyPolys["Catch_mean"],
     graticule=Gr,axes=T,key.pos=1,key.width=0.2,key.length=0.8,breaks=seq(50,65,by=2.5))

dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.10.png")
```

Where:

- *key.pos* controls the color legend position as 1=below, 2=left, 3=above and 4=right,

- *key.width* and *key.length* control the size of the color legend,

- *breaks* controls the classes,

- The function *st_graticule* generates a Lat/Lon grid.


Additionally, *sf* objects can be plotted using *ggplot2*. For example:

```{r message=F,eval=T}
library(ggplot2)
png(filename='ReadMeFigs/ReadMe_Fig5.11.png',width=2000,height=1000,res=300,bg="white")

ggplot() + 
  geom_sf(data = MyPolys, aes(fill = Catch_mean))

dev.off()
```
```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.11.png")
```

Using *ggplot2* and *gridExtra*, multi-panel plots can be drawn:

```{r message=F,eval=T}
library(gridExtra)
png(filename='ReadMeFigs/ReadMe_Fig5.12.png',width=2000,height=1400,res=300,bg="white")

map1 <- ggplot() +
  geom_sf(data = MyPolys, aes(fill = Catch_mean)) + 
  labs(title="Mean catch")

map2 <- ggplot() +
  geom_sf(data = MyPolys, aes(fill = Catch_sd)) + 
  labs(title="S.D. of catch")

map3 <- ggplot() +
  geom_sf(data = MyPolys, aes(fill = AreaKm2)) + 
  labs(title="Polygon area")

grid.arrange(map1, map2, map3, ncol=2)
dev.off()
```

```{r fig.align="center",out.width="100%",message=F,dpi=300,echo=F}
include_graphics("ReadMeFigs/ReadMe_Fig5.12.png")
```