R/knn.R

In david-beauchesne/iEat: Functions to apply a machine learning algorithm to predict species trophic interactions

KNN <- function(taxa, matSim, K, minSim) {
  # K nearest neighbour (KNN) majority vote selection to identify most similar taxa
  similar <- matSim[taxa, ] %>%
    .[!names(.) %in% taxa] %>% # removing i from most similar targetSim
    .[order(., decreasing = TRUE)] %>%
    {
      if (.[K + 1] == .[K]) { # if K + 1 == K, randomly sample a most similar taxa and pick K most similar taxa
        c(.[which(. > .[K])], .[sample(which(. == .[K]))])[1:K]
      } else {
        .[1:K]
      }
    } %>%
    .[!. == 0 & . > minSim] # remove all similarities == 0 and similarities below minSim
  return(similar)
}