R/tanimoto.r

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

tanimoto <- function(taxon1, taxon2) {
  # Tanimoto similarity measure, which compares two vectors x and y with n = |x| = |y| elements, and is defined as the size of the intersection (∩) of two sets divided by their union (∪):
  # The order of vectors taxon1 or taxon2 has no importance, as long as elements in vectors are unique
  if (length(taxon1) == 0 || length(taxon2) == 0) { # If either length of taxon1 or taxon2 == 0, similarity == 0
    return(0.0)
  } else if (taxon1 == "" || taxon2 == "") { # "" or NAs, to verify
    return(0.0)
  } else {
    inter <- length(taxon2[match(taxon1, taxon2, nomatch = 0)])
    return(inter / ((length(taxon1) + length(taxon2)) - inter))
  } # if
} # end tanimoto function