ccamlr · sthanassekos · Oct 15, 2024 · Oct 15, 2024
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 4.1.0
-Date: 2024-05-06 23:31:49 UTC
-SHA: 8168f4bb1350977e417dda478e6a991d57bfe89d
+Version: 4.1.1
+Date: 2024-05-28 01:04:04 UTC
+SHA: 29503e531bd21aff581f5595526b8d8a5c821734
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: CCAMLRGIS
 Title: Antarctic Spatial Data Manipulation
-Version: 4.1.1
-Date: 2024-05-28
+Version: 4.2.0
+Date: 2024-10-15
 Authors@R:
     c(person("Stephane","Thanassekos",role = c("aut", "cre"), email = "[email protected]"),
     person("Keith", "Reid", role = "aut"),
@@ -26,10 +26,10 @@ Imports:
     graphics,
     grDevices,
     magrittr,
-    stars,
+    isoband,
     bezier,
     lwgeom
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,8 @@ export(add_col)
 export(add_labels)
 export(assign_areas)
 export(create_Arrow)
+export(create_CircularArrow)
+export(create_Ellipse)
 export(create_Hashes)
 export(create_Lines)
 export(create_Pies)
@@ -55,19 +57,21 @@ importFrom(graphics,plot)
 importFrom(graphics,rect)
 importFrom(graphics,segments)
 importFrom(graphics,text)
+importFrom(isoband,iso_to_sfg)
+importFrom(isoband,isobands)
 importFrom(lwgeom,st_linesubstring)
 importFrom(lwgeom,st_transform_proj)
 importFrom(magrittr,"%>%")
-importFrom(stars,st_as_stars)
-importFrom(stars,st_contour)
 importFrom(stats,median)
 importFrom(stats,quantile)
 importFrom(stats,sd)
+importFrom(terra,as.matrix)
 importFrom(terra,as.polygons)
 importFrom(terra,clamp)
 importFrom(terra,classify)
 importFrom(terra,click)
 importFrom(terra,crop)
+importFrom(terra,crs)
 importFrom(terra,expanse)
 importFrom(terra,ext)
 importFrom(terra,extend)
@@ -77,10 +81,13 @@ importFrom(terra,plot)
 importFrom(terra,project)
 importFrom(terra,rast)
 importFrom(terra,vect)
+importFrom(terra,xFromCol)
+importFrom(terra,yFromRow)
 importFrom(utils,download.file)
 importFrom(utils,edit)
 importFrom(utils,globalVariables)
 importFrom(utils,menu)
 importFrom(utils,read.csv)
 importFrom(utils,setTxtProgressBar)
+importFrom(utils,tail)
 importFrom(utils,txtProgressBar)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+# CCAMLRGIS 4.2.0
+
+Added create_Ellipse() function,
+Added create_CircularArrow() function,
+Increased timeout in download within load_Bathy(),
+Moved from stars to isoband in get_iso_polys() as the former wouldn't work with large rasters (Thanks to M. D. Sumner),
+Updated bathymetry to GEBCO 2024 grid,
+Added ellipses in add_Legend(),
+Added custom path example in create_Arrow().
+
 # CCAMLRGIS 4.1.1
 
 Optimized create_Arrow() which should now be faster and less prone to errors,

diff --git a/R/CCAMLRGIS-package.R b/R/CCAMLRGIS-package.R
@@ -53,10 +53,10 @@ utils::globalVariables(c('CCAMLRp','Coast','Depth_cols','Depth_cuts','Depth_cols
 #' @importFrom grDevices colorRampPalette recordPlot replayPlot chull col2rgb rgb
 #' @importFrom graphics abline legend lines par plot rect segments text  
 #' @importFrom stats median quantile sd
-#' @importFrom terra as.polygons clamp classify click crop expanse ext extend extract mask plot project rast vect
-#' @importFrom utils download.file edit globalVariables menu read.csv setTxtProgressBar txtProgressBar   
+#' @importFrom terra as.matrix as.polygons clamp classify click crop crs expanse ext extend extract mask plot project rast vect xFromCol yFromRow
+#' @importFrom utils download.file edit globalVariables menu read.csv setTxtProgressBar tail txtProgressBar   
 #' @importFrom magrittr %>%
-#' @importFrom stars st_as_stars st_contour
+#' @importFrom isoband isobands iso_to_sfg
 #' @importFrom bezier bezier
 #' @importFrom lwgeom st_transform_proj st_linesubstring
 ## usethis namespace: end

diff --git a/R/CCAMLRGIS_DataDescription.R b/R/CCAMLRGIS_DataDescription.R
@@ -1,7 +1,7 @@
 #' CCAMLRGIS Projection
 #'
 #' The CCAMLRGIS package uses the Lambert azimuthal equal-area projection (see \url{https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection}).
-#' Source: \url{http://gis.ccamlr.org/}.
+#' Source: \url{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 \url{https://epsg.org/crs_6932/WGS-84-NSIDC-EASE-Grid-2-0-South.html}).
 #' 
@@ -16,7 +16,7 @@ NULL
 #'
 #' Coastline polygons generated from \link{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: \url{http://gis.ccamlr.org/}
+#' ASDs or EEZs (see examples). Source: \url{https://gis.ccamlr.org/}
 #'
 #' @docType data
 #' @usage data(Coast)

diff --git a/R/add_Legend.R b/R/add_Legend.R
@@ -48,7 +48,7 @@
 #' 
 #' \itemize{
 #'   \item Text: character, text of the item.
-#'   \item Shape: character, shape description, one of "rectangle", "circle", "line", 
+#'   \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.
 #'   \item ShpFill: character, fill color of shape, set to NA for no fill.
 #'   \item ShpBord: character, border color of shape, set to NA for no border.
@@ -70,6 +70,9 @@
 #'   \item RectW: numeric, width of rectangle shape.
 #'   \item RectH: numeric, height of rectangle shape.
 #'   \item CircD: numeric, diameter of circle shape.
+#'   \item EllW: numeric, width of ellipse shape.
+#'   \item EllH: numeric, height of ellipse shape.
+#'   \item EllA: numeric, angle of ellipse shape.
 #'   \item LineTyp: numeric, type of line shape (0=blank, 1=solid, 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash).
 #'   \item LineL: numeric, length of the line shape.
 #'   \item ArrL: numeric, length of the arrow shape.
@@ -91,8 +94,8 @@
 #' 
 #' 
 #' @seealso 
-#' \code{\link{create_Hashes}}, \code{\link{create_Arrow}}, \code{\link{add_labels}},
-#'  \code{\link{add_Cscale}}, \code{\link{add_PieLegend}}.
+#' \code{\link{create_Hashes}}, \code{\link{create_Arrow}}, \code{\link{create_Ellipse}},
+#' \code{\link{add_labels}}, \code{\link{add_Cscale}}, \code{\link{add_PieLegend}}.
 #'  
 #'  
 #' @examples
@@ -107,7 +110,7 @@
 #' Subtitle="(Subtitle)",
 #' Pos = "bottomright",
 #' BoxW= 80,
-#' BoxH= 140,
+#' BoxH= 170,
 #' Boxexp = c(5,-2,-4,-4),
 #' Titlefontsize = 2
 #' )
@@ -172,6 +175,37 @@
 #'   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",
@@ -268,7 +302,8 @@
 #' 
 #' #Combine all items into a single list:
 #' 
-#' Items=list(Rectangle1,Rectangle2,Circle1,Circle2,Line1,Line2,Arrow1,Arrow2,Arrow3,Arrow4,None)
+#' 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())):
 #' 
@@ -287,7 +322,7 @@ add_Legend=function(bb,LegOpt,Items){
 
   if(inherits(bb,"bbox")==FALSE){stop("bb is not an sf bounding box, use st_bbox() to create bb.")}
   dx=as.numeric(bb['xmax']-bb['xmin']) #x scaler
-  dy=as.numeric(bb['ymax']-bb['ymin']) #x scaler
+  dy=as.numeric(bb['ymax']-bb['ymin']) #y scaler
   d=min(c(round(dx/200),round(dy/200)))
 
   #Set defaults
@@ -502,7 +537,7 @@ add_Legend=function(bb,LegOpt,Items){
   #Loop over items and add them
   for(i in seq(1,length(Items))){
     item=Items[[i]]
-    if(!item$Shape%in%c("rectangle","circle","line","arrow","none")){stop(paste0("Argument 'Shape' mis-specified in add_Legend() for item ",i))}
+    if(!item$Shape%in%c("rectangle","circle","ellipse","line","arrow","none")){stop(paste0("Argument 'Shape' mis-specified in add_Legend() for item ",i))}
 
     #Set defaults
     if(is.null(item$ShpFill)){item$ShpFill="white"}
@@ -520,6 +555,9 @@ add_Legend=function(bb,LegOpt,Items){
     if(is.null(item$RectW)){item$RectW=10}
     if(is.null(item$RectH)){item$RectH=7}
     if(is.null(item$CircD)){item$CircD=10}
+    if(is.null(item$EllW)){item$EllW=10}
+    if(is.null(item$EllH)){item$EllH=7}
+    if(is.null(item$EllA)){item$EllA=0}
     if(is.null(item$LineTyp)){item$LineTyp=1}
     if(is.null(item$LineL)){item$LineL=10}
     if(is.null(item$ArrL)){item$ArrL=10}
@@ -574,6 +612,27 @@ add_Legend=function(bb,LegOpt,Items){
       text(X+item$CircD*d+item$STSpace*d+item$ShiftX*d,Y,item$Text,cex=item$fontsize,adj=c(0,0.5),xpd=TRUE)
     }
 
+    #Circle
+    if(item$Shape=="ellipse"){
+      #Get radius
+      R=item$EllW*d/2
+      #Get center
+      Cx=X+R+item$ShiftX*d
+      Cy=Y
+      #build shape
+      sh=create_Ellipse(Latc=Cy,Lonc=Cx,Lmaj=item$EllW*20,Lmin=item$EllH*20,Ang=item$EllA,yx=TRUE)
+      #plot shape
+      plot(st_geometry(sh),add=TRUE,lwd=item$Shplwd,col=item$ShpFill,border=item$ShpBord,xpd=TRUE)
+      #Hashed?
+      if(item$ShpHash==TRUE){
+        Hh=create_Hashes(pol=sh,angle=item$Hashangle,spacing=item$Hashspacing,width=item$Hashwidth)
+        plot(Hh,add=TRUE,col=item$Hashcol,xpd=TRUE,border=NA)
+        plot(st_geometry(sh),add=TRUE,lwd=item$Shplwd,border=item$ShpBord,xpd=TRUE)
+      }
+      #Add text
+      text(X+item$EllW*d+item$STSpace*d+item$ShiftX*d,Y,item$Text,cex=item$fontsize,adj=c(0,0.5),xpd=TRUE)
+    }
+
     #Line
     if(item$Shape=="line"){
       #Build shape

diff --git a/R/create.R b/R/create.R
@@ -39,20 +39,24 @@
 #' \code{\link{create_Stations}}, \code{\link{add_RefGrid}}, \code{\link{add_Legend}}.
 #' 
 #' @examples
-#' \donttest{
 #' 
 #' # 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)
 #' 
-#' }
 #' 
 #' @export
 

diff --git a/R/create_Arrow.R b/R/create_Arrow.R
@@ -8,7 +8,8 @@
 #' 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 \code{yx} to \code{TRUE}.
+#' and Longitudes by setting \code{yx} to \code{TRUE}. Coordinates may be extracted from a
+#' spatial object and used as input (see Example 9 below).
 #' 
 #' @param Np integer, number of additional points generated to create a curved path. If the 
 #' arrow's path appears too segmented, increase \code{Np}.
@@ -38,9 +39,10 @@
 #' @return Spatial object in your environment with colors included in the dataframe (see examples).
 #' 
 #' @seealso 
+#' \code{\link{create_CircularArrow}}, \code{\link{create_Ellipse}},\code{\link{add_Legend}},
 #' \code{\link{create_Points}}, \code{\link{create_Lines}}, \code{\link{create_Polys}},
-#' \code{\link{create_PolyGrids}}, \code{\link{create_Stations}}, \code{\link{create_Pies}}, 
-#' \code{\link{add_Legend}}.
+#' \code{\link{create_PolyGrids}}, \code{\link{create_Stations}}, \code{\link{create_Pies}}.
+#' 
 #' 
 #' @examples
 #' 
@@ -104,6 +106,27 @@
 #'                    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)
+#' 
 #' @export
 
 create_Arrow=function(Input,Np=50,Pwidth=5,Hlength=15,Hwidth=10,dlength=0,Atype="normal",Acol="green",Atrans=0,yx=FALSE){