R/min_dist.R

In rNeighborQTL: Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

#' Calculating the minimum distance
#'
#' A function to calculate a Euclidian distance including at least one neighbor for all individuals.
#' @param smap A matrix showing a spatial map. The first and second column include spatial points along a x-axis and y-axis, respectively.
#' @param grouping A integer vector assigning each individual to a group. This argument can be useful when a "smap" contains different experimental replicates. Default setting means that all individuals are belong to a single group.
#' @return Return a scalar of the minimum Euclidian distance that allows all individuals to have at least one neighbor.
#' @author Yasuhiro Sato (\email{sato.yasuhiro.36c@kyoto-u.jp})
#' @export
min_dist = function(smap, grouping = rep(1,nrow(smap))) {
  min_d_i <- c()
  for(i in 1:nrow(smap)) {
    id <- c(1:nrow(smap))[grouping==grouping[i]]
    d_i <- mapply(function(x) { return(sqrt((smap[x,1]-smap[i,1])^2 + (smap[x,2]-smap[i,2])^2)) },id)
    min_d_i <- c(min_d_i, min(d_i[d_i!=0]))
  }
  return(max(min_d_i)[1])
}