[R-sig-Geo] Issue with st_warp, gdal and NAs

[Julian M. Burgos]

Dear list,

My apologies for posting this again.  I am not sure if it went through the first time.

I am having a bit of trouble using st_warp() to aggregate star objects with the option "use_gdal = TRUE".  I am using the "average" method, and I want cells with NA values to be ignored when computing the averages.  To demonstrate, I will make a small raster for testing, and will include cells with NA values:

#-------------------------------------------------
  
library(raster)

# Create raster for testing
myfile <- "~/myraster.tif"
myraster <- raster(xmn = 0, ymn = 0, xmx = 10, ymx = 10, resolution = 0.1,
                   crs = 4326, vals = sample(1:20, size = 10000, replace = TRUE))
myraster[sample(1:10000, 200)] <- NA
writeRaster(myraster, filename = myfile, overwrite = TRUE)

#-------------------------------------------------

With the raster package, I can aggregate the cells ignoring the NA values like this:


r1 <- raster(myfile)
ag1 <- raster::aggregate(x = raster(myfile), fact = 10,
                         fun = mean, na.rm = TRUE)

...which is what I want.  I can also aggregate the cells including the NAs, like this:
                                                                                   
ag2 <- raster::aggregate(x = raster(myfile), fact = 10,
                         fun = mean, na.rm = FALSE)

.... which produces a raster with a lots of gaps.  Now, to do a similar aggregation with the stars package I can do this:

s1 <-  read_stars(myfile)

ag3 <- st_warp(src = s1,
              dest = st_as_stars(st_bbox(s1), dx = 1, dy = 1),
              use_gdal = TRUE,
              method = "average")

The resulting raster (ag3) has gaps like ag2, which means that the NAs are not being ignored when computing the averages.  With use_gdal_TRUE and method="average" we are using gdalwarp with the average resampling method, which according to the documentation "computes the weighted average of all non-NODATA contributing pixels.".  So I guess the problem is that the NAs are not being recognized as NODATA pixels.

Does anybody know how to solve this?

Many thanks,

Julian

-- 
Julian Mariano Burgos, PhD
Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/
Marine and Freshwater Research Institute
Botnsjávarsviðs / Demersal Division
  Fornubúðir 5, IS-220 Hafnarfjörður, Iceland
www.hafogvatn.is
Sími/Telephone : +354-5752037
Netfang/Email: julian.burgos using hafogvatn.is