alpha_diversity_metrics – List of available metrics

Non-phylogeny based metrics:

• berger_parker_d
• brillouin_d
• chao1
• chao1_confidence
• dominance
• doubles (# otus with exactly two individuals in sample)
• equitability
• fisher_alpha
• gini index
• goods coverage
• heip_e (note, using heip_e at low (<5) individuals may cause errors
• kempton_taylor_q
• margalef
• mcintosh_d
• mcintosh_e
• menhinick
• michaelis_menten_fit
• observed_species
• osd (observed # otus, singleton OTUs, doubleton OTUs)
• robbins
• shannon (base 2 is used in the logarithms)
• simpson (1 - Dominance)
• simpson_reciprocal (1 / Dominance)
• simpson_e
• singles (# OTUs with exactly one individual present in sample)
• strong

Phylogeny based metrics:

• PD_whole_tree