Calculate Shannon's entropy, ENS, Pielou's evenness, and ENS-based evenness

Shannon's H is an entropy (in nats), not a diversity. SHANNON_ENS converts it to an effective number of species via exp(H) — the q=1 Hill number, interpretable as the number of equally abundant species that would produce the same entropy. Two evenness measures are returned: Pielou's J (widely used, entropy-based) and an ENS-based evenness consistent with the Hill number framework.

Usage

get_alpha_shannon(df, feature_id = "feature_id", id_col = "SAMPLE")

Arguments

df

A dataframe with features as rows and samples as columns

feature_id

The name of the column with feature IDs (default is "feature_id")

id_col

The name of the column with sample IDs (default is "SAMPLE")

Value

A tibble with one row per sample and columns:

SHANNON_H

Shannon entropy H (nats); an index, not a diversity

SHANNON_ENS

Effective number of species (exp(H)); the q=1 Hill number

SHANNON_PIELOU

Pielou's J evenness (H / log(S.obs)); ratio of observed to maximum possible entropy

SHANNON_EVENNESS

ENS-based evenness (SHANNON_ENS / S.obs); ranges from 1/S.obs (single dominant) to 1 (all species equal)