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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

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