In ecoquants/bbnj: Biodiversity Beyond National Jurisdiction

knitr::opts_chunk$set(echo = TRUE, message = F, warning = F)

For Christopher Costello [e-mail], facilitated by Reniel Cabral [e-mail].

Install bbnj R package

Install the bbnj R package (and devtools if needed).

install.packages(devtools)
devtools::install_github("ecoquants/bbnj")

Get Data

See list of datasets in bbnj reference. Datasets are "lazy-loaded"" with library(bbnj), meaning available in path but not showing up in Environment tab of RStudio.

library(tidyverse)
library(raster)
library(bbnj)

# list bbnj datasets in RStudio:
data(package="bbnj")

# list raster layers within stacks (s_*)
names(s_fish_gfw)
names(s_bio_gmbi)

# get rasters from stacks
profit_fishing <- raster(s_fish_gfw, "mean_scaled_profits_with_subsidies") %>% 
  gap_fill_raster()
nspp_tunas     <- raster(s_bio_gmbi, "nspp_tunas.n.billfishes")
nspp_sharks    <- raster(s_bio_gmbi, "nspp_sharks")

# stack wanted rasters for later cropping
s <- stack(profit_fishing, nspp_tunas, nspp_sharks)
names(s) <- c("profit_fishing", "nspp_tunas", "nspp_sharks")

Get Area of Interest

You'll need to run the raster::drawExtent() function interactively (ie not "knitting") within RStudio, outputting to console.

aoi_rds   <-   "aoi.rds"
s_aoi_rds <- "s_aoi.rds"

if (interactive()){
  # draw your own area of interest
  plot(nspp_tunas)
  aoi <- raster::drawExtent()
  saveRDS(aoi, file = aoi_rds)
} else {
  # load existing
  aoi <- readRDS(aoi_rds) 
}

# show area of interest
aoi

plot(nspp_tunas)
plot(aoi, col = "red", lwd = 2, add = T)

# crop raster
s_aoi <- raster::crop(s, aoi)

# save and plot
saveRDS(s_aoi, file = s_aoi_rds)
plot(s_aoi)

ecoquants/bbnj documentation built on April 4, 2023, 9:08 p.m.