R/simulate_pairwise_distances_cheap.R

In sams25/rcombinator_old: Tools to Simulate the Evolution of Genetic Sequences

# Gets pairwise distances from the sequence data of a simulation
simulate_pairwise_distances_cheap <- function(seq_data, timestamp)
{
  num_sequences <- length(seq_data$sequences[[1]])
  num_seq_pairs <- (num_sequences * (num_sequences-1))/2
  size <- num_seq_pairs

  pair_data <- data.frame(time = rep(NA_integer_, size),
                          seq1 = rep(NA_integer_, size),
                          seq2 = rep(NA_integer_, size),
                          seq_dist = rep(NA, size))

  assign_row <- function(time_index, seq_data, num_seq_pairs)
  {
    new_rows <- dist_to_data_frame(stringdist_ape(seq_data$sequences[[1]]))

    assign_row_inner <- function(seq_index, new_rows, time_index)
    {
      row_index <- seq_index
      new_row <- list(time_index,
                      new_rows$seq1[seq_index], new_rows$seq2[seq_index],
                      new_rows$dist_1_2[seq_index])
      pair_data[row_index, ] <<- new_row
    }
    map(1:num_seq_pairs, assign_row_inner, new_rows, time_index)
  }
  assign_row(timestamp, seq_data, num_seq_pairs)

  return(pair_data)
}