minor changes in plots and tables.

07_figures/plots_argo.R

@@ -214,13 +214,18 @@ ggsave(p_png, p, width=25, height=14, units="cm", dpi=300)
 # Plot 7: Coldspots
 #------------------------------------------------
 
-p <- plotrasterDis(r = coldspots, land = land.prj, box = box,
-                   colors = c("1" = "#08519c"),
-                   breaks = 1, legend.position = "none")
-
-# Save as png file
+# set output file and open device
 p_png <- paste(fig_dir,"argo","coldspot.png", sep="/")
-ggsave(p_png, p, width=25, height=14, units="cm", dpi=300)
+png(p_png , width=25, height=14, units="cm", res=300)
+
+# plot
+plot(coldspots, col=c("#4393c3") , axes=FALSE, box=FALSE, legend=FALSE)
+plot(coldspots_shp, col= "transparent", border= "grey40", lwd=0.01, add=TRUE) #border=NA
+plot(land.prj, col= "grey80", border= "grey40", lwd=0.01, add=TRUE) #border=NA
+plot(box, border= "grey70", add=TRUE)
+
+# close device
+dev.off()
 
 
 #------------------------------------------------

07_figures/plots_eoo.R

@@ -10,6 +10,7 @@ library(raster)
 library(rgdal)
 library(ggplot2)
 library(Hmisc)
+library(data.table)
 source("R/utils.R")
 source("R/data_paths.R")
 
@@ -28,7 +29,8 @@ class <- unique(match$group)  # get group classes
 # Fig 1. Density maps of species subject to telemetry by taxonomic group.
 #-------------------------------------------------------------------------
 # Plot of number of species per taxa.
-
+# Normalized from 0 to 1 in order to use the same color palette
+range_list <- list()
 for (i in 1:length(class)){
 
   print(i)
@@ -37,14 +39,20 @@ for (i in 1:length(class)){
   ncfile <- list.files(eoo_dir, pattern=paste0(class[i], ".nc"), full.names=TRUE)
   nc <- raster(ncfile)
 
+  # Get min and max values per class
+  nc <- setMinMax(nc)
+  lim = data.frame(class=class[i], min=minValue(nc), max=maxValue(nc))
+  range_list[[i]] <- lim
+
   # Plot
-  p <- plotraster(r = nc, land = land.prj, box = box, legendTitle = "No. species")
+  p <- plotraster(r = nc, land = land.prj, box = box, legendTitle = "")
 
   # Save as png file
   p_png = paste0(fig_dir, "/eoo/", class[i],".png")
   ggsave(p_png, p, width=25, height=14, units="cm", dpi=300)
 }
-
+range <- rbindlist(range_list)
+write.csv(range, paste0(fig_dir, "/eoo/", "ranges_per_taxa.csv"), row.names=FALSE)
 
 #-------------------------------------------------------------------------
 # Fig 2. Density maps of species subject to telemetry (all taxa)
@@ -66,16 +74,16 @@ for (i in 1:length(class)){
   ## Normalize from zero to one
   nc <- setMinMax(nc)
   norm <- (nc - minValue(nc)) / (maxValue(nc) - minValue(nc))
+  if (minValue(nc) == maxValue(nc)) norm <- nc  # this exception applies for sirenians with max values = 1
   rnorm <- stack(rnorm, norm)
 }
 
 ## Average across taxa
 allnorm <- mean(rnorm, na.rm=TRUE)
-allnorm[allnorm == 0] <- NA
 
 ## Plot
-legend <- paste0("All taxa \n (normalized)")
-p <- plotraster(r = allnorm, land = land.prj, box = box, legendTitle = legend)
+legend <- paste0("All taxa\n(normalized)\n")
+p <- plotraster(r = allnorm, land = land.prj, box = box, lim=c(0,1), legendTitle = legend, legend.position = "bottom")
 
 # Save as png file
 p_png = paste0(fig_dir, "/eoo/", "alltaxa_normalized",".png")

07_figures/plots_overlap.R

@@ -46,7 +46,7 @@ for (i in 1:length(class)){
   ## Normalize number of species from zero to one
   nc <- setMinMax(nc)
   norm <- (nc - minValue(nc)) / (maxValue(nc) - minValue(nc))
-  if (minValue(nc) == maxValue(nc)) norm <- nc
+  if (minValue(nc) == maxValue(nc)) norm <- nc # this exception applies for sirenians with max values = 1
 
   ## Mask with coldspots
   ov <- norm * coldspots  # Mask for Argo undersampled areas

07_figures/plots_telemetry.R

@@ -30,8 +30,8 @@ pin <- raster(pin_dens)
 #-------------------------------------------------------------------------
 
 # Create plot
-p <- plotraster(r = log10(chelo), land = land.prj, box = box,
-                legendTitle = expression(log[10]~(records / km^2)))
+p <- plotraster(r = log10(chelo), land = land.prj, box = box, legend.position="bottom",
+                legendTitle = expression(log[10]~(observations / km^2)))
 
 # Save as png file
 p_png <- paste(fig_dir,"telemetry","turtle_telemetry_density.png", sep="/")

08_tables/tbl_taxonomic_groups.R

@@ -22,6 +22,8 @@ spp <- merge(match, eoo_overlap, by="taxonid")
 df <- spp %>%
   group_by (group_name) %>% #ISO_Ter1, Sovereign1
   summarise (
+    # no. species
+    n = n(),
     # exntent
     meanExtent_km2 = mean(range_km2, na.rm=TRUE),
     sdExtent_km2 = sd(range_km2, na.rm=TRUE),