skbio.diversity.alpha.dominance#

skbio.diversity.alpha.dominance(counts)[source]#

Calculate 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. It is defined as

\[D = \sum{p_i^2}\]

where \(p_i\) is the proportion of the entire sample that taxon \(i\) represents.

Simpson’s \(D\) can be interpreted as the probability that two randomly selected individuals belong to the same taxon. It ranges between 0 and 1.

Simpson’s \(D\) is sometimes referred to as “Simpson’s index”. It should be noted that \(D\) is not a measure of community diversity. It is also important to distinguish \(D\) from Simpson’s diversity index (\(1 - D\)) and Simpson’s reciprocal index (\(1 / D\)), both of which are measures of community diversity.

Discrepancy exists among literature in using the term “Simpson index” and the denotion \(D\). It is therefore important to distinguish these metrics according to their mathematic definition.

Parameters:

counts1-D array_like, int: Vector of counts.

Returns:

double: Simpson’s dominance index.