scripts/1_14_bytile_woodyveg.R

In sustainablefarms/linking-data: OBSOLETE: Linking Data Project R Package

# tile region into 1 degree x 1 degree pieces and apply existing scripts
library(sf); library(raster)
devtools::load_all()
locs <- read.csv("private/data/clean/site_locations_cleaned.csv", stringsAsFactors = FALSE)
locs_wgs84 <- st_as_sf(locs, coords = c("MeanLON", "MeanLAT"))
locs_wgs84 <- st_set_crs(locs_wgs84, 4326) #4326 is the epsg code for WGS84, make this default crs I'll return to

# locs_wgs84 %>%
#   filter(StudyCode == "Restoration Study") %>%
#   st_bbox()
# tileswpts <- divide_into_tiles(locs_wgs84, cellsize = 0.05, buffer = 0.01)
tileswpts <- readRDS("./tmpdata/woodyl_tileswpts.rds")
tiles <- lapply(tileswpts, function(x) st_as_sf(x$tile))
tilegrd <- do.call(rbind, tiles)
# plot(tilegrd)

#### read RS rasters ####
# empty gppl object
woodyl <- lapply(tileswpts, function(x) return(NULL))
# woodyl <- readRDS("./tmpdata/woodyl.rds")
uncompleted <- vapply(woodyl, is.null, FUN.VALUE = FALSE)
attempts <- 0

rasterOptions(tmpdir = "/media/kassel/Seagate1TB/tmpdir/")
while(any(uncompleted) && attempts <= 5){
  cat("Attempting:", sum(uncompleted), "tiles.\n")
  woodyl[uncompleted] <- pbapply::pblapply(tileswpts[uncompleted],
                                         FUN = function(x) {
                                           woody <- NULL
                                           try(woody <- woody_vals_buffer(x$tile, x$pts, 2000:2018, 500))
                                           gc()
                                           return(woody)
                                         })
  uncompleted <- vapply(woodyl, is.null, FUN.VALUE = FALSE)
  attempts <- attempts + 1
}
saveRDS(woodyl, "./tmpdata/woodyl.rds")
woodyl_wsitecode <- lapply(1:length(woodyl),
                           function(id){
                             woodyvals <- woodyl[[id]]
                             pts <- tileswpts[[id]]$pts
                             woodyvals$SiteCode <- pts$SiteCode
                             return(woodyvals)
                           })
woody <- do.call(rbind, woodyl_wsitecode)
saveRDS(woody, "./tmpdata/woody.rds")

saveRDS(woody, "./private/data/remote_sensed/woody500.rds")