Matrix Indices Computation

mat_dist.R

# Matrix of presence-absence
m = structure(c(1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1), .Dim = c(4L, 
4L), .Dimnames = list(c("a", "b", "c", "d"), c("site1", "site2", 
"site3", "site4")))


# Distance matrix
dist = structure(c(0, 0.2, 0.7, 0.33, 0.2, 0, 0.5, 0.15, 0.7, 0.5, 0, 
0.23, 0.33, 0.15, 0.23, 0), .Dim = c(4L, 4L), .Dimnames = list(
    c("a", "b", "c", "d"), c("a", "b", "c", "d")))


di_mat = do.call(cbind, 
  tapply(m, col(m), function(x) {
      # 'x' is a column vector of m
      # Select sub distance matrix
      sub_dist = dist[which(x != 0), which(x != 0)]
      # sums all distances for all species
      di = colSums(sub_dist)
      di = di/(length(di) -1)
      # Returns given vector value if non zero
      ifelse(x != 0, di, x)
  })
)

# Copy dimensions names
dimnames(di_mat) = dimnames(m)