What this is for: Alpha diversity from a species-count list (Shannon, Simpson, evenness, richness, Chao1) and beta diversity between two sites (Bray–Curtis, Sørensen, Jaccard).
The formula: Shannon H′ = −Σ p_i × ln p_i; Bray–Curtis similarity = 2W ÷ (A + B)
How to use:
- In Diversity Indices, enter the counts as one row per species: name, count — use 0 for a species not found.
- Read N, S, Shannon H′, Simpson D, 1 − D, 1 ÷ D, evenness, the richness indices and the Chao1 estimates.
- In the two-site section, enter counts for the same species list at both sites as one row per species: name, site A count, site B count.
- Read W, the Bray–Curtis similarity and dissimilarity, and the Sørensen and Jaccard similarities.
Diversity Indices — Shannon, Simpson, Evenness, Richness & Chao1
Enter counts of individuals per species for one sample/site (zero rows are excluded from species richness).
Total individuals N
Species richness S
Shannon index H' (nats)
Simpson dominance D
Simpson diversity 1 − D
Inverse Simpson 1 / D
Pielou evenness J' = H' / ln S
Margalef richness (S−1) / ln N
Menhinick richness S / sqrt(N)
Singletons f1 (species with count 1)
Doubletons f2 (species with count 2)
Chao1 estimate (classic) S + f1²/(2 f2)
Chao1 (bias-corrected)
Bray–Curtis & Sørensen Similarity Between Two Sites
Enter counts for the SAME species list at two sites (0 = absent). W = sum of the smaller count of each species.
Total site A
Total site B
W = sum of minimums
Bray–Curtis SIMILARITY 2W/(A+B)
Bray–Curtis DISSIMILARITY
Shared species a (present at both)
Sørensen similarity 2a/(2a+b+c)
Jaccard similarity a/(a+b+c)
Prefer to work offline or keep a copy? The download link is right below.
Download the Biodiversity Indices workbook (.xlsx)
Download the Biodiversity Indices workbook (.xlsx)
Notes & limits (from the workbook): H' uses natural log (nats); divide by ln 2 for bits. Indices describe THIS sample — comparing sites fairly needs equal sampling effort or rarefaction, which is deliberately left to R (vegan) / PAST. Bray–Curtis uses abundances and ignores joint absences; Sørensen/Jaccard use presence only. Keep the species list identical across sites — a species missing from the list entirely is not the same as a counted zero.