calc_shannon_index: Calculate the Shannon Diversity Index

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Calculate the Shannon Diversity Index

Description

The Shannon diversity index is calculated to quantify the diversity of molecular formulas based on their relative abundances. This index considers both the richness (number of unique formulas) and the evenness (distribution of abundances). Higher values indicate greater diversity.

The Shannon index is defined as:

H = -\sum (p_i \cdot \ln(p_i))

where:

• p_i is the relative abundance of the i-th molecular formula.

Zero-abundance formulas are excluded from the calculation.

Usage

calc_shannon_index(mf, magnitude)

Arguments

mf	Character vector. A list of unique molecular formulas.
magnitude	Numeric vector. A list of respective abundances (intensities) for each molecular formula. Must be non-negative and have the same length as mf.

Value

A single numeric value representing the Shannon diversity index. Returns 0 if magnitude is all zeros.

Examples

calc_shannon_index(
  mf = c("C10H20O5", "C12H18O3", "C18H30O6"),
  magnitude = c(1982375, 2424, 312410)
)

ume documentation built on Dec. 13, 2025, 1:06 a.m.