The difference between the simpson and simpson_e indices

General Discussion
1

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？

2

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

1 Like
4

Hi @WangLitt,

Welcome to the :qiime2: 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 :lizard:

7 Likes
5

Thank you.！！That's really helpful！