How to calculate simpson in qiime2 ? qiime diversity alpha --p-metric simpson .

What is the formula for calculating the simpson index？

What is the relationship between the size of the simpson Index and diversity？

Hi @WangLitt

The command is:

```
qiime diversity alpha \
--i-table table.qza \
--p-metric simpson \
--o-alpha-diversity simpson_diversity.qza
```

A Simpson Index/D value of zero = higher diversity (many species!), whereas a value of 1 = lower diversity (fewer species).

-Mike

Hi @WangLitt,

Welcome to the forum!

Just jumping in for @Mike_Stevenson here with some clarification - there's a bit of subtlety here so we want to be extra clear about what each of these methods is doing!

Within our alpha diversity methods, we support both `simpson`

and `simpson_e`

. I'll explain what each method is, and what their respective indices mean.

The first term we need to define (required for both `simpson`

and `simpson_e`

) is Simpson's Dominance Index. Simpson’s dominance index, a.k.a. Simpson’s *D* measures the degree of concentration of taxon composition of a sample. This is used in both Simpson's Diversity index and Simpson's Evenness Index.

`simpson`

refers to Simpson's Diversity Index, which is often denoted as *1 - D* (with *D* being Simpson's dominance). Simpson's diversity can be interpreted as the probability that two randomly selected individuals belong to different taxa. Values range between 0 to 1, with:

- High scores (close to 1) indicating high diversity.
- Low scores (close to 0) indicating low diversity.

`simpson_e`

refers to Simpson's Evenness (a.k.a., equitability) Index *E* is defined as *1/(D * S)* where *D* is Simpson’s dominance and *S* is the number of taxa in the sample.

Essentially, *E* is the ratio of the minimum-possible Simpson’s dominance index when all taxa have the same number of individuals: (*1/S*), versus the actual Simpson’s dominance index of the sample.

Depending on what you'd like to calculate, you'll either run `qiime diversity alpha`

with `--p-metric`

set to `simpson`

or `simpson_e`

.

Hope this helps! Cheers