I don't have the TB so can't do anything directly, but... I don't suppose there's anything like pdist2 available? I didn't see anything in the 'See Also' section but the TB doc's are often lacking in the detail the main product gets it seems...
All that comes to mind is that distance is vectorized internally to accept vectors for its inputs. If you built the the complete list of points and passed it instead of the explicit loop you could take advantage of that altho depending upon how it is implemented it may just be the loop anyways...but, that would bypass the overhead of calling the function so many times and that ought to be observable, at least. Whether it would be a sizable fraction of the overall time I suspect is unlikely, but "ya never know!".
Sometimes taking time is the price of trying to deal with large datasets...
The one thing that isn't shown in your above code snippet that could help measurably even with the loop is if you have not preallocated dist so you're doing dynamic reallocation. With array of this size, that would definitely be a noticeable hit.
dist=zeros(height(A),height(B)); % preallocate output array
for i=1:height(A)
for j=1:height(B)
dist(i,j) = distance(A.Lat(i),A.Lon(i),B.Lat(j),B.Lon(j));
end
end
dist=dist/180*pi*6378.137;
Also you can move the scaling calculation to the end and do it with vectorized operation that might make a tic quicker...
