Global bare soil, photosynthetic and non-photosynthetic vegetation fraction annual at 500 m resolution

Annual mean and std for (1) bare soil fraction, and (2) photosynthetic and (3) non-photosynthetic vegetation annual at 500 m resolution for 2001–2023. The dataset was obtained from: https://thredds.nci.org.au/thredds/catalog/tc43/modis-fc/v310/tiles/monthly/cover/catalog.html (monthly values; 320GB in total). Mean and std was derived using terra package in R using functions "mean" and "std" from 12 monthly values; missing values were ignored during derivation.

Note: the Global Vegetation Fractional Cover Product (GVFCP) v3.1 (Hill and Guerschman, 2022) is derived from spectral unmixing of all seven optical bands from the 500 m MODIS (Moderate Resolution Imaging Spectroradiometer) Nadir BRDF (Bidirectional Reflectance Distribution Function)-adjusted Reflectance Product (NBAR, MCD43A4 Collection 6). A similar dataset has been produced by Sun et al., (2024), covering period 2001–2022. Below is the sample code explaining how were the mean, max and std derived.

## Download from: https://thredds.nci.org.au/thredds/catalog/tc43/modis-fc/v310/tiles/monthly/cover/catalog.html
## wget -e robots=off -nH --cut-dirs 4 -nc -r -l5 -A '*.nc' -R 'catalog*' -I /thredds/fileServer/,/thredds/catalog/ 'https://thredds.nci.org.au/thredds/catalog/tc43/modis-fc/v310/tiles/monthly/cover/catalog.html'
## 6857 tiles
library(terra)
modis.tiles = list.files("/mnt/lacus/raw/modis-fc/v310/tiles/monthly/cover/", pattern = glob2rx("*.nc"))
mod.lst = unique(sapply(modis.tiles, function(i){strsplit(i, "\\.")[[1]][4]}))
str(mod.lst)
## 272

## aggregate per year per tile
nc_tile <- function(i, year, dir.x="/mnt/lacus/raw/modis-fc/v310/tiles/monthly/cover/", mc.cores=parallel::detectCores()){
   require(terra)
   if(year == 2023 | year == 2024){
      in.filename = paste0(dir.x, "FC_Monthly_Medoid.v310.MCD43A4.", i, ".", year, ".061.nc")
   } else {
      in.filename = paste0(dir.x, "FC_Monthly_Medoid.v310.MCD43A4.", i, ".", year, ".006.nc")
   }
   bs.filenames = paste0("./modis-fc/bs_", c("mean", "max", "std"), "/FC_Monthly_Medoid.v310.MCD43A4.", i, ".", year, ".006.tif")
   dg = terra::rast(in.filename)
   if(any(!file.exists(bs.filenames))){
      bs = dg["bare_soil"] ## 12 months
      dg.m = app(bs, fun=mean, na.rm=TRUE, 
                 filename=bs.filenames[1], 
                 wopt=list(gdal=c("COMPRESS=DEFLATE"), datatype='INT1S'), 
                 overwrite=TRUE, cores = mc.cores)
      dg.x = app(bs, fun=max, na.rm=TRUE, 
                 filename=bs.filenames[2], 
                 wopt=list(gdal=c("COMPRESS=DEFLATE"), datatype='INT1S'), 
                 overwrite=TRUE, cores = mc.cores)
      dg.s = app(bs, fun=sd, na.rm=TRUE, 
                 filename=bs.filenames[3], 
                 wopt=list(gdal=c("COMPRESS=DEFLATE"), datatype='INT1S'), 
                 overwrite=TRUE, cores = mc.cores)
   }
}
## run in parallel
for(year in 2001:2024){
   x = parallel::mclapply(sample(mod.lst), function(i){try( nc_tile(i, year=year, mc.cores = 2) )}, mc.cores = 40)
   tmpFiles(remove=TRUE)
}