Get Site Counts Matrix (Internal) — get_site

Extract and tabulate amino acid counts for a specific site across all partitions.

Usage

get_site_counts(partitions, site_index, alphabet_size)

Arguments

partitions: List of data frames, one per time window. Each must have integer-encoded amino acid columns.
site_index: Integer. Index of the site (column) to count.
alphabet_size: Integer. Size of the amino acid alphabet (typically 25 for the package's default encoding).

Value

Integer matrix with alphabet_size rows (one per amino acid code, 1 through alphabet_size) and one column per partition. Each cell is the count of that amino acid at site_index in that partition.

Details

Built on tabulate for fast integer counting. Consumed internally by calculate_hellinger_matrix.