Diversity
| Name | Short Description | Language |
| ACE | Abundance-based Convergence Estimator (ACE, Chao and Lee 1992). | R |
| Alpha | Alpha-diversity | R |
| ADONIS | ADONIS beta-diversity | C++ |
| AlphaDiversity | Alpha-diversity using Qiime (Caporaso et al, 2010) | C++ |
| AlphaPairwise | Pairwise alpha diversity comparison | R |
| AlphaStats | Alpha-diversity statistics | Python |
| AlphaTTest | Non-parametric T-test for Alpha diversity | C++ |
| BergerParker | Berger-Parker diversity (Berger and Parker, 1976) | C++ |
| BetaDiversity | Beta-diversity using Qiime (Caporaso et al, 2010) | C++ |
| BetaInAndOut | Compute Beta-diversity between all pairs of samples within each subcategory, and all pairs of samples in different subcategories. | Python |
| BrayCurtis | Bray-Curtis beta diversity (Bray and Curtis, 1957) | R |
| Breakaway | Breakaway (Willis et al, 2017) | R |
| Brillouin | Brillouin index (Pielou, 1975) | C++ |
| Bulla | Bulla evenness (Bulla, 1994) | R |
| Camargo | Camargo evenness (Camargo, 1992) | R |
| Chao1 | Chao1 alpha-diversity (Chao, 1984) | R |
| Diversity | Various diversity measurements | R |
| Doubletons | Number of doubletons | C++ |
| ENSPIE | Effective Number of Species (ENS)/Probability of intra-or interspecific encounter (PIE) (Chase and Knight, 2013) | C++ |
| EVar | EVar index (Smith and Wilson, 1996) | R |
| Etsy | Etsy's Confidence Interval (Etsy, 1983) | C++ |
| Faith | Faith phylogenetic diversity index (Faith et al, 2017) | R |
| Fisher | Fisher Diversity Index (Fisher et al, 1943) | R |
| Good | Good's coverage of counts (Good, 1950) | C++ |
| Heip | Heip's evenness measure (Heip, 1974) | C++ |
| InterGroup | Intergroup Beta Diversity | Python |
| IntraGroup | Intragroup Beta Diversity | Python |
| InvSimpson | Inverse simpson alpha-diversity (Hill, 1973) | R |
| InverseSimpson | Inverse Simpson Diversity Index | Python |
| KemptonTaylor | Kempton-Taylor Q Index (Kempton and Taylor, 1976) | C++ |
| Lladser | Llader's confidence interval (Lladser et al, 2011) | C++ |
| Margalef | Margalef's richness index (Magurran, 2004) | C++ |
| McIntosh | McIntosh dominance (McIntosh, 1967) | C++ |
| Menhinick | Menhinick’s richness index (Magurran, 2004) | C++ |
| Observed | Observed taxa count | R |
| Pielou | Pielou evenness (Pielou, 1966) | R |
| PlotAlphaDiversity | Plot alpha-diversity for a set of samples (Caporaso et al, 2010) | C++ |
| PlotBetaDiversity | Bar and differential Beta-diversity plots | R |
| PlotBetaDiversity3D | Plot beta-diversity for a set of samples in 3D (Caporaso et al, 2010) | C++ |
| Richness | Sample set richness | R |
| Robbins | Probability of unobserved outcomes (Robbins, 1968) | C++ |
| Shannon | Shannon Diversity Index (Shannon, 1948) | R |
| Simpson | Simpson Diversity Index (Simpson, 1949) | R |
| Singletons | Singleton Taxa | C++ |
| Strong | Strong alpha-diversity (Strong, 2002) | C++ |
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