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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| #' Title | ||
| #' | ||
| #' @param output_dir | ||
| #' @param output_filename | ||
| #' @param raster_template | ||
| #' | ||
| #' @return | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| get_bioclim_data <- function(output_dir, | ||
| output_filename, | ||
| raster_template) { | ||
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| template <- terra::unwrap(raster_template) | ||
| bioclim_data <- geodata::worldclim_global(var = "bio", res = 2.5, path = output_dir) | ||
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| bioclim_data <- transform_raster(bioclim_data, template) | ||
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| bioclim_names <- c( | ||
| "Annual_Mean_Temperature", "Mean_Diurnal_Range", "Isothermality", | ||
| "Temperature_Seasonality", "Max_Temperature_of_Warmest_Month", | ||
| "Min_Temperature_of_Coldest_Month", "Temperature_Annual_Range", | ||
| "Mean_Temperature_of_Wettest_Quarter", "Mean_Temperature_of_Driest_Quarter", | ||
| "Mean_Temperature_of_Warmest_Quarter", "Mean_Temperature_of_Coldest_Quarter", | ||
| "Annual_Precipitation", "Precipitation_of_Wettest_Month", | ||
| "Precipitation_of_Driest_Month", "Precipitation_Seasonality", | ||
| "Precipitation_of_Wettest_Quarter", "Precipitation_of_Driest_Quarter", | ||
| "Precipitation_of_Warmest_Quarter", "Precipitation_of_Coldest_Quarter") | ||
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| # Assign the new names to the layers | ||
| names(bioclim_data) <- bioclim_names | ||
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| filename = paste(output_dir, output_filename, sep = "/") | ||
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| if(grepl("\\.parquet", filename)) { | ||
| # Convert to dataframe | ||
| dat <- as.data.frame(bioclim_data, xy = TRUE) |> as_tibble() | ||
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| # Save as parquet | ||
| arrow::write_parquet(dat, filename, compression = "gzip", compression_level = 5) | ||
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| terra::writeRaster(bioclim_data, filename=gsub("parquet", "tif", filename), overwrite=T, gdal=c("COMPRESS=LZW")) | ||
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| } else { | ||
| terra::writeRaster(bioclim_data, filename=filename, overwrite=T, gdal=c("COMPRESS=LZW")) | ||
| } | ||
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| unlink(paste(output_dir, "climate", sep = "/"), recursive=TRUE) | ||
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| return(filename) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| #' Title | ||
| #' | ||
| #' @param output_dir | ||
| #' @param output_filename | ||
| #' @param raster_template | ||
| #' | ||
| #' @return | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| get_elevation_data <- function(output_dir, | ||
| output_filename, | ||
| raster_template) { | ||
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| # Create directory if it does not yet exist | ||
| dir.create(output_dir, recursive = TRUE, showWarnings = FALSE) | ||
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| template <- terra::unwrap(raster_template) | ||
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| # Create a bounding bounding box template | ||
| elevation_data <- geodata::elevation_global(res = 0.5 , | ||
| path = output_dir) | ||
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| elevation_data <- transform_raster(elevation_data, | ||
| template = template) | ||
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| filename = paste(output_dir, output_filename, sep = "/") | ||
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| if(grepl("\\.parquet", filename)) { | ||
| # Convert to dataframe | ||
| dat <- as.data.frame(elevation_data, xy = TRUE) |> as_tibble() | ||
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| # Save as parquet | ||
| arrow::write_parquet(dat, filename, compression = "gzip", compression_level = 5) | ||
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| terra::writeRaster(elevation_data, filename=gsub("parquet", "tif", filename), overwrite=T, gdal=c("COMPRESS=LZW")) | ||
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| } else { | ||
| terra::writeRaster(elevation_data, filename=filename, overwrite=T, gdal=c("COMPRESS=LZW")) | ||
| } | ||
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| unlink(paste(output_dir, "elevation", sep = "/"), recursive=TRUE) | ||
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| # Return path to compressed raster | ||
| return(filename) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| get_landcover_data <- function(output_dir, | ||
| output_filename, | ||
| raster_template) { | ||
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| template <- terra::unwrap(raster_template) | ||
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| landcover_types <- c("trees", "grassland", "shrubs", "cropland", "built", "bare", "snow", "water", "wetland", "mangroves", "moss") | ||
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| # Fetch each layer, process them and stack them into a single SpatRaster | ||
| # Cleaning up files as we go to save space. | ||
| landcover_data <- map(landcover_types, function(l) { | ||
| landcover <- geodata::landcover(var = l, path = output_dir) | ||
| file <- sources(landcover) | ||
| landcover <- transform_raster(landcover, template) | ||
| unlink(file) | ||
| landcover | ||
| }) | ||
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| landcover_data <- do.call(c, landcover_data) | ||
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| filename = paste(output_dir, output_filename, sep = "/") | ||
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| if(grepl("\\.parquet", filename)) { | ||
| # Convert to dataframe | ||
| dat <- as.data.frame(landcover_data, xy = TRUE) |> as_tibble() | ||
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| # Save as parquet | ||
| arrow::write_parquet(dat, filename, compression = "gzip", compression_level = 5) | ||
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| terra::writeRaster(landcover_data, filename=gsub("parquet", "tif", filename), overwrite=T, gdal=c("COMPRESS=LZW")) | ||
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| } else { | ||
| terra::writeRaster(landcover_data, filename=filename, overwrite=T, gdal=c("COMPRESS=LZW")) | ||
| } | ||
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| unlink(paste(output_dir, "landuse", sep = "/"), recursive=TRUE) | ||
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| return(filename) | ||
| } |
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