Parallel and Memory-Efficient Ecological Diversity Metrics
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Documentation for package ‘ecodive’ version 2.2.6
Help Pages
| ace | Abundance-based Coverage Estimator (ACE) |
| aitchison | Aitchison distance |
| alpha_div | Alpha Diversity Wrapper Function |
| berger | Berger-Parker Index |
| beta_div | Beta Diversity Wrapper Function |
| bhattacharyya | Bhattacharyya distance |
| bray | Bray-Curtis dissimilarity |
| brillouin | Brillouin Index |
| canberra | Canberra distance |
| chao1 | Chao1 Richness Estimator |
| chebyshev | Chebyshev distance |
| chord | Chord distance |
| clark | Clark's divergence distance |
| divergence | Divergence |
| euclidean | Euclidean distance |
| ex_counts | Example counts matrix |
| ex_tree | Example phylogenetic tree |
| faith | Faith's Phylogenetic Diversity (PD) |
| fisher | Fisher's Alpha |
| generalized_unifrac | Generalized UniFrac (GUniFrac) |
| gower | Gower distance |
| hamming | Hamming distance |
| hellinger | Hellinger distance |
| horn | Horn-Morisita dissimilarity |
| inv_simpson | Inverse Simpson Index |
| jaccard | Jaccard distance |
| jensen | Jensen-Shannon distance |
| jsd | Jensen-Shannon divergence (JSD) |
| list_metrics | Find and Browse Available Metrics |
| lorentzian | Lorentzian distance |
| manhattan | Manhattan distance |
| margalef | Margalef's Richness Index |
| match_metric | Find and Browse Available Metrics |
| matusita | Matusita distance |
| mcintosh | McIntosh Index |
| menhinick | Menhinick's Richness Index |
| minkowski | Minkowski distance |
| morisita | Morisita dissimilarity |
| motyka | Motyka dissimilarity |
| normalized_unifrac | Normalized Weighted UniFrac |
| n_cpus | Number of CPU Cores |
| observed | Observed Features |
| ochiai | Otsuka-Ochiai dissimilarity |
| psym_chisq | Probabilistic Symmetric Chi-Squared distance |
| rarefy | Rarefy Observation Counts |
| read_tree | Read a newick formatted phylogenetic tree. |
| shannon | Shannon Diversity Index |
| simpson | Gini-Simpson Index |
| soergel | Soergel distance |
| sorensen | Dice-Sorensen dissimilarity |
| squared_chisq | Squared Chi-Squared distance |
| squared_chord | Squared Chord distance |
| squared_euclidean | Squared Euclidean distance |
| squares | Squares Richness Estimator |
| topsoe | Topsoe distance |
| unweighted_unifrac | Unweighted UniFrac |
| variance_adjusted_unifrac | Variance-Adjusted Weighted UniFrac |
| wave_hedges | Wave Hedges distance |
| weighted_unifrac | Weighted UniFrac |