Extract values from raster into points: data loss using extract function from raster package

Question

I am trying to extract values of raster cells on points using extract from raster package in R (similar to 'Extract Values to Points' in ArcGIS-10.2). After doing so in order to check integrity, I computed the total value of all the raster cells (i.e. sum) ~66,000 and total extracted values on points ~49,000. We have tried both techniques simple and bilinear interpolation techniques. Data loss gets only slightly reduced with bilinear technique, i.e. ~50,000 points are extracted. There is a huge data loss, if anyone can provide a way forward or has experienced the same.

Answer 1

You might want to give a try to the GMT tool grdtrack. You can start by reconverting to your raster to a NetCDF file using gdal_translate:

gdal_translate -of NetCDF myraster.tif myraster.grd

and then put your x,y locations in a text file:

x1, y1
x2, y2
.., ..

then call grdtrack on that NetCDF grid based on your table of locations:

grdtrack mylocations.xy -Gmyraster.grd > myvalues.txt

You will get a new table with the sampled points. This procedure should work well and it is relatively fast. Good luck!

Answer 2

You said:

I am trying to extract values of raster cells on points using extract from raster package in R (similar to 'Extract Values to Points' in ArcGIS-10.2).

Lets set up a test raster:

require(raster)
r = raster(ncol=100,nrow=100,xmn=0,xmx=1,ymn=0,ymx=1)
r[]=runif(100*100)

You said:

After doing so in order to check integrity, I computed the total value of all the raster cells (i.e. sum) ~66,000 and total extracted values on points ~49,000.

Okay, lets do that:

pts = cbind(runif(100),runif(100))
vr = extract(r,pts)
sum(vr)
[1] 55.41762
sum(values(r))
[1] 5003.098

Obviously the sum of 100 points sampled at random across that raster is going to be approximately 0.5*100 = 50. The sum of the whole raster is 0.5*100*100 because there's 100*100 cells with an average value of 0.5.

You said:

We have tried both techniques simple and bilinear interpolation techniques. Data loss gets only slightly reduced with bilinear technique, i.e. ~50,000 points are extracted. There is a huge data loss, if anyone can provide a way forward or has experienced the same.

I do not understand why you think this is a good idea for some kind of "integrity test" unless I misunderstand what you are doing. If this answer doesn't help please clarify your question with some sample code like mine. Otherwise this question is unclear.