Spatially Manipulating NetCDF Files

I ended up getting a bunch of climate NetCDF files from a colleague for each combination of climate model, climate change scenario and variable. So, what I have is a list of 3-D files consisting of observations/predictions of a given weather variable over latitude, longitude and time (you can picture them as cubes, if you like). I will need to spatially adjust the files, and then subset the data.

ncpdq -a lat,lon in.nc out.nc

I need to…

• keep only the extent within a shape file we’re using
• figure out how to summarize it by the polygons in the shape file
  • average?
  • keep only the center point?

Some of my closest colleagues, Brooke Bateman and Andy Allstadt, had some good advice for how to work with the netCDF files in R once I get them:

• ncdf4 package
• raster package: can open netCDF either as…
  • single layer (with the raster function)
  • the entire thing (brick function)
• SDMTools
  • sample x,y points from raster using extract data function
  • convert the raster to ASCII

You can load those libraries, and then do a few things to take a look.

library(<span class="pl-smi">raster</span>)
print(raster(<span class="pl-s"><span class="pl-pds">"</span>afile.nc<span class="pl-pds">"</span></span>))  <span class="pl-c">## same as 'ncdump -h afile.nc</span>
b <- brick(<span class="pl-s"><span class="pl-pds">"</span>afile.nc<span class="pl-pds">"</span></span>, <span class="pl-v">varname</span> <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>pr<span class="pl-pds">"</span></span>) #this is the variable name internal to the file