% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocess.R
\name{phymapnet_prepare_inputs}
\alias{phymapnet_prepare_inputs}
\title{Prepare inputs for PhyMapNet}
\usage{
phymapnet_prepare_inputs(otu, tree, prune = TRUE)
}
\arguments{
\item{otu}{A samples x taxa count/abundance matrix (rownames=samples, colnames=taxa).}

\item{tree}{A \code{phylo} object with tip labels as taxa names, or a named,
symmetric taxa x taxa phylogenetic distance matrix.}

\item{prune}{Logical; if TRUE and \code{tree} is a \code{phylo} object, prunes tree
tips not found in OTU before distances are computed. Input taxa are always
aligned to their shared set.}
}
\value{
A list with otu (aligned), dist (aligned), taxa.
}
\description{
Computes a patristic distance matrix from a phylogenetic tree, or validates
a supplied phylogenetic distance matrix, then aligns taxa to the OTU table.
}
