Merge pull request #287 from mapme-initiative/dev

GDAL based backend (#240)

DESCRIPTION

@@ -23,22 +23,22 @@ URL: https://mapme-initiative.github.io/mapme.biodiversity/index.html,
     https://github.com/mapme-initiative/mapme.biodiversity/
 BugReports: https://github.com/mapme-initiative/mapme.biodiversity/issues
 Depends: R (>= 3.5.0)
-SystemRequirements: GDAL (>= 3.0.0), PROJ (>= 4.8.0)
-Imports: dplyr, furrr, httr, magrittr, purrr, R.utils, sf, terra, tibble, tidyr
+SystemRequirements: GDAL (>= 3.7.0), PROJ (>= 4.8.0)
+Imports: dplyr, furrr, httr, jsonlite, magrittr, purrr, sf, terra, tibble, 
+  tidyr
 Suggests: exactextractr, future, knitr, landscapemetrics, progressr, rmarkdown, 
   rstac, rvest, testthat (>= 3.0.0)
 VignetteBuilder: knitr
-Config/Needs/website: DiagrammeR, ggplot2, lubridate, manipulateWidget, rgl, spatstat, 
-    wdpar
+Config/Needs/website: DiagrammeR
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Collate: 
     'register.R'
-    'calc_active_fire_counts.R'
     'calc_biome.R'
+    'calc_burned_area.R'
     'calc_deforestation_drivers.R'
     'calc_drought_indicator.R'
     'calc_ecoregion.R'
@@ -73,7 +73,7 @@ Collate:
     'get_gfw_treecover.R'
     'get_gmw.R'
     'get_gsw.R'
-    'get_nasa_firms.R'
+    'get_mcd64A1.R'
     'get_nasa_grace.R'
     'get_nasa_srtm.R'
     'get_nelson_et_al.R'
@@ -84,4 +84,5 @@ Collate:
     'get_worldpop.R'
     'mapme.biodiversity-pkg.R'
     'portfolio.R'
+    'spatial-utils.R'
     'utils.R'

NAMESPACE

@@ -2,8 +2,8 @@
 
 export(available_indicators)
 export(available_resources)
-export(calc_active_fire_counts)
 export(calc_biome)
+export(calc_burned_area)
 export(calc_deforestation_drivers)
 export(calc_drought_indicator)
 export(calc_ecoregion)
@@ -32,7 +32,6 @@ export(check_available_years)
 export(check_engine)
 export(check_namespace)
 export(check_stats)
-export(download_or_skip)
 export(get_chirps)
 export(get_esalandcover)
 export(get_fritz_et_al)
@@ -45,7 +44,7 @@ export(get_global_surface_water_recurrence)
 export(get_global_surface_water_seasonality)
 export(get_global_surface_water_transitions)
 export(get_gmw)
-export(get_nasa_firms)
+export(get_mcd64a1)
 export(get_nasa_grace)
 export(get_nasa_srtm)
 export(get_nelson_et_al)
@@ -57,6 +56,7 @@ export(get_worldclim_max_temperature)
 export(get_worldclim_min_temperature)
 export(get_worldclim_precipitation)
 export(get_worldpop)
+export(make_footprints)
 export(make_global_grid)
 export(mapme_options)
 export(portfolio_long)
@@ -65,17 +65,15 @@ export(prep_resources)
 export(register_indicator)
 export(register_resource)
 export(select_engine)
-export(unzip_and_remove)
+export(spds_exists)
 export(write_portfolio)
 import(sf)
 import(terra)
 importFrom(httr,http_error)
 importFrom(magrittr,"%>%")
-importFrom(purrr,walk)
 importFrom(stats,sd)
 importFrom(stats,var)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(utils,download.file)
-importFrom(utils,read.csv)
 importFrom(utils,unzip)

NEWS.md

@@ -4,6 +4,25 @@
 
 - updates `gfw_lossyear` resource to `v20240402` which entails emission data
   between 2000 - 2023
+- removes the `nasa_firms` resource and associated `active_fire_counts` indicator
+- adds `mcd64a1` resource and `burned_area` indicator
+- `mapme.biodiveristy` now leverages GDAL for data I/O meaning that all GDAL
+  readable source data sets and writable destinations are now supported
+- `README.md` now includes a section on how to set up cloud-storages to use
+  as a destination for resource data
+- The quickstart vignette now uses GFW data as example data
+- chunking is now applied based on the area of an assets bounding box instead
+  of its own area
+
+## Internal
+
+- exports `make_footprints()` to ease the process of creating footprints
+  for resource functions
+- exports `spds_exists()` for resource function to check if a data source
+  is exists
+- resource functions are now expected to return footprints for all resource elements including opening and creation options as well as standardized filenames
+- in case a user-specified destination is found, the package now uses `gdal_translate` to write data from source to destination
+- tests for long-running examples and tests are skipped on GA and CRAN
 
 # mapme.biodiversity 0.7.0
 

R/calc_burned_area.R

@@ -0,0 +1,90 @@
+#' Calculate Monthly Burned Area based on MODIS (MCD64A1)
+#'
+#' Calculates Monthly Burned Area based on the Terra and Aqua combined
+#' MCD64A1 Version 6.1. which s a monthly, global gridded 500 meter (m)
+#' product containing per-pixel burned-area information.
+#'
+#' The required resources for this indicator are:
+#'  - [mcd64a1]
+#'
+#' @name burned_area
+#' @param engine The preferred processing functions from either one of "zonal",
+#'   "extract" or "exactextract" as character.
+#' @keywords indicator
+#' @returns A function that returns a tibble with a column for terrain
+#'   ruggedness index statistics (in meters).
+#' @references Giglio, L., C. Justice, L. Boschetti, D. Roy. MODIS/Terra+Aqua
+#'   Burned Area Monthly L3 Global 500m SIN Grid V061. 2021, distributed by
+#'   NASA EOSDIS Land Processes Distributed Active Archive Center.
+#'   \doi{https://doi.org/10.5067/MODIS/MCD64A1.061}
+#' @include register.R
+#' @export
+#' @examples
+#' \dontshow{
+#' mapme.biodiversity:::.copy_resource_dir(file.path(tempdir(), "mapme-data"))
+#' }
+#' \dontrun{
+#' library(sf)
+#' library(mapme.biodiversity)
+#'
+#' outdir <- file.path(tempdir(), "mapme-data")
+#' dir.create(outdir, showWarnings = FALSE)
+#'
+#' mapme_options(
+#'   outdir = outdir,
+#'   verbose = FALSE
+#' )
+#'
+#' aoi <- system.file("extdata", "sierra_de_neiba_478140_2.gpkg",
+#'   package = "mapme.biodiversity"
+#' ) %>%
+#'   read_sf() %>%
+#'   get_resources(get_mcd64a1(years = 2010)) %>%
+#'   calc_indicators(calc_burned_area(engine = "extract")) %>%
+#'   portfolio_long()
+#'
+#' aoi
+#' }
+calc_burned_area <- function(engine = "extract") {
+  engine <- check_engine(engine)
+
+  function(x,
+           mcd64a1 = NULL,
+           name = "burned_area",
+           mode = "asset",
+           aggregation = "sum",
+           verbose = mapme_options()[["verbose"]]) {
+    if (is.null(mcd64a1)) {
+      return(NULL)
+    }
+
+    x_proj <- st_transform(x, st_crs(mcd64a1))
+    mcd64a1 <- terra::mask(mcd64a1, x_proj)
+    mcd64a1 <- terra::subst(mcd64a1, from = c(-2, -1, 0, NA), to = 0, others = 1)
+    arearaster <- cellSize(mcd64a1, mask = FALSE, unit = "ha")
+    mcd64a1 <- mcd64a1 * arearaster
+
+    stats <- select_engine(
+      x = x_proj,
+      raster = mcd64a1,
+      stats = "sum",
+      engine = engine,
+      name = "burned_area",
+      mode = "asset"
+    )
+
+    names(stats) <- "value"
+
+    dates <- gsub("^.*?\\.A([0-9]+)\\..*$", "\\1", names(mcd64a1))
+    stats[["datetime"]] <- as.Date(dates, "%Y%j")
+    stats[["unit"]] <- "ha"
+    stats[["variable"]] <- "burned_area"
+    stats[, c("datetime", "variable", "unit", "value")]
+  }
+}
+
+register_indicator(
+  name = "burned_area",
+  description = "Monthly burned area detected by MODIS satellites",
+  resources = "mcd64a1"
+)

R/calc_fatalities.R

@@ -76,7 +76,8 @@
 #'
 #' mapme_options(
 #'   outdir = outdir,
-#'   verbose = FALSE
+#'   verbose = FALSE,
+#'   chunk_size = 1e8
 #' )
 #'
 #' aoi <- system.file("extdata", "burundi.gpkg",
@@ -117,10 +118,10 @@ calc_fatalities <- function(years = 1989:2023,
     date_prec <- where_prec <- date_start <- type_of_violence <- NULL
     year <- month <- deaths_a <- deaths_b <- event_count <- type_of_death <- NULL
 
-    ucdp_ged <- ucdp_ged[[1]]
-    if (length(ucdp_ged) == 0) {
-      return(NA)
+    if (is.null(ucdp_ged)) {
+      return(NULL)
     }
+    ucdp_ged <- ucdp_ged[[1]]
 
     months_tibble <- tidyr::expand_grid(
       year = as.character(years),