In ecoquants/bbnj: Biodiversity Beyond National Jurisdiction

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

library(prioritizr) # devtools::load_all("~/github/prioritizr")
#library(bbnj)       # 
devtools::load_all() # devtools::install_local(force=T)
library(raster)
library(sf)
library(dplyr)
library(stringr)
library(glue)
library(here)
library(fs)
library(knitr)
library(formattable)
area   = raster::area
select = dplyr::select

rmd <- knitr::current_input(dir = T)
#rmd <- file.path(getwd(), "s00a.bio.30pct.gl.mol100km.Rmd")
pfx <- rmd %>% path_ext_remove()

# variables ----
rel_target <- 0.3
prjres     <-  "_mer36km" # View(projections_tbl)

redo = F
P <- projections_tbl %>% filter(prjres==!!prjres)

# planning unit: ----
r_pu_id <- get_d_prjres("r_pu_id", prjres) # plot(r_pu_id)
r_pu <- setValues(r_pu_id, 1) %>% 
  mask(r_pu_id) # plot(r_pu)

# biodiversity: now, not 2100 ----
# devtools::load_all()
s_bio_gmbi <- get_d_prjres("s_bio_gmbi", prjres)
lyrs_bio_now <- names(s_bio_gmbi) %>% 
  setdiff(str_subset(names(s_bio_gmbi), "2100$")) %>% 
  setdiff(c("nspp_all", "nspp_na", "rls_all", "rls_na"))
s_bio_now <- subset(s_bio_gmbi, lyrs_bio_now)

# features ----
s_features <- stack(
  get_d_prjres("r_vgpm", prjres),
  s_bio_now)
  #raster(s_fish_gfw, "mean_scaled_profits_with_subsidies") %>%
  #    gap_fill_raster() %>%
  #    rescale_raster(inverse=T),
  #raster(s_fish_ubc, "mcp_2004"),
  #s_phys_seamounts,
  #r_phys_vents,
  #s_phys_scapes)
names(s_features) <- c(
  "bio_vgpm",
  names(s_bio_now))
  #"fish_profit.subs"
  #"fish_mcp.2004",
  #sprintf("phys_seamounts_%sm", c("0to200","gt200to800","gt800")),
  #"phys_vents",
  #glue("phys_scape.{1:11}"))

# problem ----
p <- problem(r_pu, s_features) %>%
  add_min_set_objective() %>% 
  add_relative_targets(rel_target)

# solve ----
tif <- solve_log(p, pfx, redo=redo)