hill_taxa: Sparse implementation of Hill numbers

In OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data

Sparse implementation of Hill numbers

Description

Computes the hill numbers for q is 0, 1 or 2. Code is adapted from hill_taxa and uses sparseMatrix in triplet format over the dense matrix. The code is much faster and memory efficient, while still being mathematical correct.

Usage

hill_taxa(x, q = 0, normalize = TRUE, base = exp(1))

Arguments

x	A matrix or sparseMatrix.
q	A wholenumber for 0, 1 or 2, default is 0.
normalize	A boolean variable for sample normalization by column sums.
base	Input for log to use natural logarithmic scale, log2, log10 or other.

Value

A numeric vector with type double.

See Also

hill_taxa

Examples

library("Matrix")

n_row <- 1000
n_col <- 100
density <- 0.2
num_entries <- n_row * n_col
num_nonzero <- round(num_entries * density)

set.seed(123)
positions <- sample(num_entries, num_nonzero, replace=FALSE)
row_idx <- ((positions - 1) %% n_row) + 1
col_idx <- ((positions - 1) %/% n_row) + 1

values <- runif(num_nonzero, min = 0, max = 1)
sparse_mat <- sparseMatrix(
  i = row_idx,
  j = col_idx,
  x = values,
  dims = c(n_row, n_col)
)

result <- OmicFlow::hill_taxa(
 x = sparse_mat,
 q = 2
)

OmicFlow documentation built on Sept. 9, 2025, 5:24 p.m.