Question

I have a spatial dataframe with about 3000 points. I want to generate a matrix that provides the k (in this case 30) nearest neighbors for each point.

I can do it using a loop but i feel that there should be an elegant and optimal way for spatial points dataframe class that i do not know of.

Answer 1

Probably the fastest is to use RANN package – assuming you have x and y:

library(RANN)
m <- as.matrix(nn(data.frame(x=x, y=y, z=rep(0,length(x))), p=30)$nn.idx)

gives you a 3000 x 30 matrix of closest neighbors. It is several orders of magnitude faster than a naive quadratic search.

Edit: Just for completeness, it doesn’t matter which ANN frontend you pick, with FNN (suggested by Spacedman) this would be

library(FNN)
m <- get.knn(data.frame(x=x, y=y), 30)$nn.index