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#' Collect the postive and negative overlap between two paths.
#'
#' Collects the postive and negative overlap between two paths.
#'
#' @param path1 The first path.
#' @param path2 The second path.
#'
#' @return The (admixture) probability of seeing the two paths together with the
#' positive and negative edges in the overlap.
#'
#' @export
path_overlap <- function(path1, path2) {
rev_path2 <- data.frame(from = path2$to, to = path2$from, prob = path2$prob)
list(prob = c(path_probability(path1), path_probability(path2)),
positive = merge(path1, path2)[,1:2],
negative = merge(path1, rev_path2)[,1:2])
}
#' Get the list of overlaps of all paths.
#'
#' Gets the list of overlaps of all paths.
#'
#' @param paths1 Paths between one pair of leaves.
#' @param paths2 Paths between another pair of leaves.
#' @return A list of the overlaps of all combinations of paths from \code{paths1}
#' and \code{paths2}.
#'
#' @export
all_path_overlaps <- function(paths1, paths2) {
n1 <- length(paths1)
n2 <- length(paths2)
if (n1 == 0 || n2 == 0) return(list())
overlaps <- list(rep(NA, n1 * n2))
idx <- 1
for (i in 1:n1) {
for (j in 1:n2) {
overlaps[[idx]] <- path_overlap(paths1[[i]], paths2[[j]])
idx <- idx + 1
}
}
overlaps
}
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