% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/get_site_counts.R
\name{get_site_counts}
\alias{get_site_counts}
\title{Get Site Counts Matrix (Internal)}
\usage{
get_site_counts(partitions, site_index, alphabet_size)
}
\arguments{
\item{partitions}{List of data frames, one per time window. Each must
have integer-encoded amino acid columns.}

\item{site_index}{Integer. Index of the site (column) to count.}

\item{alphabet_size}{Integer. Size of the amino acid alphabet
(typically \code{25} for the package's default encoding).}
}
\value{
Integer matrix with \code{alphabet_size} rows (one per amino
acid code, 1 through \code{alphabet_size}) and one column per
partition. Each cell is the count of that amino acid at
\code{site_index} in that partition.
}
\description{
Extract and tabulate amino acid counts for a specific site
across all partitions.
}
\details{
Built on \code{\link[base]{tabulate}} for fast integer counting.
Consumed internally by \code{\link{calculate_hellinger_matrix}}.
}
\keyword{internal}
