% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/RcppExports.R
\name{cpp_mutual_clustering_all_pairs}
\alias{cpp_mutual_clustering_all_pairs}
\title{Pairwise mutual clustering information — batch computation}
\usage{
cpp_mutual_clustering_all_pairs(splits_list, n_tip, n_threads = 1L)
}
\arguments{
\item{splits_list}{A list of split matrices (class \code{Splits} or \code{RawMatrix}),
one per tree, all covering the same tip set.  Typically the object
returned by \code{as.Splits(trees, tipLabels = labs, asSplits = FALSE)}.}

\item{n_tip}{Integer; number of tips shared by all trees.}
}
\value{
Numeric vector of length \code{n*(n-1)/2} containing pairwise MCI
scores in \code{combn(n, 2)} column-major order (i.e. the data payload of
an R \code{dist} object).
}
\description{
Internal function. Computes all pairwise MCI scores for a set of trees,
using OpenMP threads when available (falling back to single-threaded
execution otherwise). No interrupt checking is performed inside the
parallel region; the outer R call remains interruptible between batches.
}
\keyword{internal}
