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() # setwd(here()); devtools::install_local(force=T) 
# devtools::install_github("ecoquants/bbnj")
library(raster)
library(sf)
library(dplyr)
library(readr)
library(stringr)
library(glue)
library(here)
library(fs)
library(knitr)
library(formattable)
area   = raster::area
select = dplyr::select

#message("library done")

if (interactive()){
  wd <- file.path(here::here(), "inst/app/www/scenarios/")
  setwd(wd) # getwd()
  if (!exists("rmd")){
    #rmd <- file.path(getwd(), "s00a.bio.30pct.gl.mol50km.Rmd")
    rmd <- file.choose()
  }
} else {
  rmd <- knitr::current_input(dir = T)  
}

pfx <- rmd %>% path_ext_remove()
tif <- glue("{pfx}_sol.tif")

# variables ----
rel_target <- 0.3
prjres     <- "_mol50km" # prjres in: View(projections_tbl)
redo       <- F

# problem & solution ----
P <- projections_tbl %>% filter(prjres == !!prjres)
if (!file.exists(tif) | redo){

  # 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)
  #groups01: 1st taxonomic grouping
  s_bio_all_now <- get_gmbi_grpsmdl_prjres("groups00", "_mol50km")%>% 
     subset(,subset="groups00_nspp_all")

  s_bio_all_future <- get_gmbi_grpsmdl_prjres("groups00_2100", "_mol50km")%>% 
     subset(,subset="groups00_2100_nspp_all")
    #add red list sum for all species as separate layer
  # rls_all <- get_d_prjres("s_bio_gmbi", prjres) %>% 
  #   subset(,subset="rls_all")

  # features ----
  s_features <- stack(
 #   get_d_prjres("r_vgpm", prjres),
    s_bio_all_now,
    s_bio_all_future)
 #   rls_all,
    #raster(s_fish_gfw, "mean_scaled_profits_with_subsidies") %>%
    #    gap_fill_raster() %>%
    #    rescale_raster(inverse=T),
    #raster(s_fish_ubc, "mcp_2004"),
 #   get_d_prjres("s_phys_seamounts",prjres),
  #  get_d_prjres("r_phys_vents",prjres),
 #   get_d_prjres("r_phys_scapes_hetero",prjres))

  names(s_features) <- c(
 #   "bio_vgpm",
   "s_bio_all_now",
    "s_bio_all_future")
  #  "rls_all",
    #"fish_profit.subs"
    #"fish_mcp.2004",
  #  sprintf("phys_seamounts_%sm", c("0to200","gt200to800","gt800")),
  #  "phys_vents",
  #  "scapes_hetero")

  # problem ----
  p <- problem(r_pu, s_features) %>%
    add_min_set_objective() %>% 
    add_relative_targets(rel_target) %>% 
    add_boundary_penalties(penalty = 0.00000001)

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

r basename(pfx)

• Projection: r P$name (r P$res resolution)

• Planning unit cost: set to 1

• Objective function:

  • add_min_set_objective(): Minimize the cost of the solution whilst ensuring that all targets are met

• Feature targets:

  • r rel_target*100% of each input feature amount
  • Biodiversity:
    • nspp_all: number of species by 22 taxonomic group from AquaMaps [now & future]

• Regionalization:

  • none, ie global

• Boundary Penalty

  • boundary penalty = 0.00000001

report_solution(tif, redo=redo)

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