How to calculate biodiversity indices

Drashti Shah

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Bioinformatics with Rust

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2 min read

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Dec 30, 2023

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Rust functions that return Simpson’s Diversity Index and Shannon-Weiner Index based on count of species and count of individuals within a species.

Notes on Interpretation

• These indexes are based on species richness and species evenness measures.
• Species richness refers to unique number of species in a given area.
• Species evenness is based on counts of individuals within a species. If these counts per species are similar, there’s more evenness. And if these counts have a large variation, there’s less evenness.
• The Simpson’s Index value should be between 0 and 1. A higher value implies more implies more species and more evenness.
• The Shannon-Weiner Index value should be more than or equal to 0. A higher value implies more species and more evenness.
• Comparing the Simpson’s Index with the Shannon-Weiner Index is meaningless. Instead, you should choose one and use it to track biodiversity (at species level) across space and time.

Code & Examples

use std::collections::HashMap;

fn main() {
    // Initialize a HashMap with species as keys and their respective counts as values
    // Example of low biodiversity
    let count_of_individuals_per_species: HashMap<String, f64> = HashMap::from([
        ("A".to_string(), 1.0),
        ("B".to_string(), 1.0),
        ("C".to_string(), 1.0),
        ("D".to_string(), 1.0),
        ("E".to_string(), 21.0),
    ]);
    println!("{:?}", simpson_index(count_of_individuals_per_species.clone()));
    println!("{:?}", shannon_weiner_index(count_of_individuals_per_species.clone()));
}

fn simpson_index(mut species_data: HashMap<String, f64>) -> f64 {
    let total: f64 = species_data.values().sum();
    for (_key, value) in species_data.iter_mut() {
        // Simpson's index formula
        *value = (*value / total).powf(2.0);
    }
    1.0 - species_data.values().sum::<f64>()
}

fn shannon_weiner_index(mut species_data: HashMap<String, f64>) -> f64 {
    let total: f64 = species_data.values().sum();
    for (_key, value) in species_data.iter_mut() {
        // Update value for each species using Shannon-Weiner formula
        *value = (*value / total) * (*value / total).ln();
    }
    species_data.values().sum::<f64>() * -1.0
}

Next Steps

• Play with this code in Rust Playground
• Watch this video from Khan Academy on Simpson’s Diversity Index
• Watch this video from Bryan Tripper on Shannon Index