R/maxDist.R

In heibl/megaptera: MEGAPhylogeny Techniques in R

## This code is part of the megaptera package
## © C. Heibl 2017 (last update 2017-11-28)

#' @export

getMaxDist <- function(s, tolerance = 0) {
  d <- dist.dna(s, model = "N", pairwise.deletion = TRUE,
                as.matrix = TRUE)
  max(d, na.rm = TRUE)
}

# maxDist <- function(s, tolerance = 0) {
#   d <- dist.dna(s, model = "N", pairwise.deletion = TRUE,
#                 as.matrix = TRUE)
#   diag(d) <- NA
#   min.dist <- min(d, na.rm = TRUE)
#   if ( min.dist > tolerance ) out <- min.dist
#   else {
#     diag(d) <- 0
#     id <- which.min(apply(d, 2, sum, na.rm = TRUE))
#     id <- d[, id] <= tolerance
#     names(id) <- NULL
#     out <- if (any(id)) s[id, ]
#   }
#   out
# }