Find K nearest neighbors, starting from a distance matrix

Question

I\'m looking for a well-optimized function that accepts an n X n distance matrix and returns an n X k matrix with the indices of the k

Answer 1

Try to use FastKNN CRAN package (although it is not well documented). It offers k.nearest.neighbors function where an arbitrary distance matrix can be given. Below you have an example that computes the matrix you need.

# arbitrary data
train <- matrix(sample(c("a","b","c"),12,replace=TRUE), ncol=2) # n x 2
n = dim(train)[1]
distMatrix <- matrix(runif(n^2,0,1),ncol=n) # n x n

# matrix of neighbours
k=3
nn = matrix(0,n,k) # n x k
for (i in 1:n)
   nn[i,] = k.nearest.neighbors(i, distMatrix, k = k)

Notice: You can always check Cran packages list for Ctrl+F='knn' related functions: https://cran.r-project.org/web/packages/available_packages_by_name.html