ClimateAndMSP/scripts/download_data.R

#!/usr/bin/env Rscript
# Download publicly available data for ClimateAndMSP project
# This script attempts to download OceanAdapt, BCO-DMO, NatCap, and EEZ data

library(data.table)
library(utils)

# Create directory structure
dirs_to_create <- c(
  "dataDL/oceanadapt",
  "dataDL/bco_dmo",
  "dataDL/natcap",
  "dataDL/eez",
  "temp",
  "NatCap_temp"
)

for (d in dirs_to_create) {
  if (!dir.exists(d)) {
    dir.create(d, recursive = TRUE, showWarnings = FALSE)
    cat("Created:", d, "\n")
  }
}

# Set timeout for large files
options(timeout = 600)

# ============================================================================
# 1. OceanAdapt data (Zenodo)
# ============================================================================
cat("\n=== Downloading OceanAdapt data ===\n")

oceanadapt_url <- "https://zenodo.org/record/3890214/files/all-regions-full.rds"
oceanadapt_file <- "dataDL/oceanadapt/all-regions-full.rds"

if (!file.exists(oceanadapt_file)) {
  cat("Downloading OceanAdapt RDS file (~500MB)...\n")
  tryCatch({
    download.file(oceanadapt_url, oceanadapt_file, mode = "wb", quiet = FALSE)
    cat("✓ OceanAdapt data downloaded successfully\n")
  }, error = function(e) {
    cat("✗ Failed to download OceanAdapt:", conditionMessage(e), "\n")
  })
} else {
  cat("✓ OceanAdapt data already exists\n")
}

# ============================================================================
# 2. BCO-DMO Morley et al. species projections
# ============================================================================
cat("\n=== Downloading BCO-DMO Morley species projections ===\n")

# Create a data.frame of BCO-DMO files to download
bco_dmo_files <- data.frame(
  url = c(
    "https://www.bco-dmo.org/sites/default/files/attachment/Morley_2018_projection_OA_pH_5.csv.gz",
    "https://www.bco-dmo.org/sites/default/files/attachment/Morley_2018_projection_O2_5.csv.gz",
    "https://www.bco-dmo.org/sites/default/files/attachment/Morley_2018_projection_SST_5.csv.gz",
    "https://www.bco-dmo.org/sites/default/files/attachment/Morley_2018_projection_MLD_5.csv.gz"
  ),
  filename = c(
    "dataDL/bco_dmo/Morley_2018_projection_OA_pH_5.csv.gz",
    "dataDL/bco_dmo/Morley_2018_projection_O2_5.csv.gz",
    "dataDL/bco_dmo/Morley_2018_projection_SST_5.csv.gz",
    "dataDL/bco_dmo/Morley_2018_projection_MLD_5.csv.gz"
  ),
  stringsAsFactors = FALSE
)

for (i in 1:nrow(bco_dmo_files)) {
  url <- bco_dmo_files$url[i]
  file <- bco_dmo_files$filename[i]
  
  if (!file.exists(file)) {
    cat("Downloading:", basename(file), "\n")
    tryCatch({
      download.file(url, file, mode = "wb", quiet = FALSE)
      cat("✓", basename(file), "downloaded\n")
    }, error = function(e) {
      cat("✗ Failed:", conditionMessage(e), "\n")
    })
  } else {
    cat("✓", basename(file), "already exists\n")
  }
}

# ============================================================================
# 3. EEZ (Exclusive Economic Zones) shapefiles
# ============================================================================
cat("\n=== Downloading EEZ shapefiles ===\n")

eez_url <- "https://www.marineregions.org/download_file.php?name=eez.zip"
eez_zip <- "dataDL/eez/eez.zip"

if (!file.exists(eez_zip)) {
  cat("Downloading EEZ shapefiles (~50MB)...\n")
  tryCatch({
    download.file(eez_url, eez_zip, mode = "wb", quiet = FALSE)
    unzip(eez_zip, exdir = "dataDL/eez")
    cat("✓ EEZ shapefiles extracted\n")
  }, error = function(e) {
    cat("✗ Failed to download EEZ:", conditionMessage(e), "\n")
  })
} else if (!dir.exists("dataDL/eez/eez")) {
  cat("Extracting EEZ shapefiles...\n")
  unzip(eez_zip, exdir = "dataDL/eez")
}

# ============================================================================
# 4. Natural Capital / InVEST reference data (if available)
# ============================================================================
cat("\n=== Checking for NatCap reference data ===\n")

# Create placeholder for NatCap wind/wave energy outputs
# (Note: Full InVEST runs produce these; we'll document expected structure)

natcap_regions <- c("westcoastwind", "eastcoastwind", "gulfwind", "alaskawind",
                    "westcoastwave", "eastcoastwave", "gulfwave")

for (region in natcap_regions) {
  dir_path <- file.path("NatCap_temp", region, "output")
  if (!dir.exists(dir_path)) {
    dir.create(dir_path, recursive = TRUE, showWarnings = FALSE)
    cat("Created:", dir_path, "\n")
  }
}

cat("NatCap_temp directory structure created (actual .tif files require InVEST computation)\n")

# ============================================================================
# 5. WDPA (World Database of Protected Areas) - requires registration
# ============================================================================
cat("\n=== WDPA Protected Areas Database ===\n")
cat("Note: WDPA requires free registration at https://www.protectedplanet.net/\n")
cat("Download 'WDPA_Feb2025_marine_shp.zip' and extract to: dataDL/WDPA_marine/\n")
cat("Instructions:\n")
cat("  1. Visit: https://www.protectedplanet.net/en/thematic-areas/wdpa?tab=data-download\n")
cat("  2. Create free account\n")
cat("  3. Download 'World Database of Protected Areas (WDPA) - February 2025' (marine)\n")
cat("  4. Extract to: dataDL/WDPA_marine/\n\n")

# ============================================================================
# Summary
# ============================================================================
cat("\n=== Download Summary ===\n")
cat("Directory structure created at: dataDL/ and NatCap_temp/\n")
cat("Successfully downloaded:\n")

downloaded_files <- list.files(recursive = TRUE, path = "dataDL", full.names = TRUE)
if (length(downloaded_files) > 0) {
  for (f in downloaded_files) {
    size_mb <- file.size(f) / (1024^2)
    cat(sprintf("  ✓ %s (%.1f MB)\n", f, size_mb))
  }
} else {
  cat("  (No files downloaded yet - check network and URLs)\n")
}

cat("\nNext steps:\n")
cat("  1. Check output above for any failed downloads\n")
cat("  2. Manually download WDPA from ProtectedPlanet (requires registration)\n")
cat("  3. Verify files in dataDL/ and NatCap_temp/ directories\n")
cat("  4. Run: Rscript scripts/validate_inputs.R\n")
cat("  5. Run: Rscript code/0.2_averageSBT.r (first step in pipeline)\n\n")