Package: abdiv 0.2.0.9000
abdiv: Alpha and Beta Diversity Measures
A collection of measures for measuring ecological diversity. Ecological diversity comes in two flavors: alpha diversity measures the diversity within a single site or sample, and beta diversity measures the diversity across two sites or samples. This package overlaps considerably with other R packages such as 'vegan', 'gUniFrac', 'betapart', and 'fossil'. We also include a wide range of functions that are implemented in software outside the R ecosystem, such as 'scipy', 'Mothur', and 'scikit-bio'. The implementations here are designed to be basic and clear to the reader.
Authors:
abdiv_0.2.0.9000.tar.gz
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abdiv.pdf |abdiv.html✨
abdiv/json (API)
NEWS
| # Install 'abdiv' in R: |
| install.packages('abdiv', repos = c('https://kylebittinger.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kylebittinger/abdiv/issues
- faith_tree - Example data for Faith's phylogenetic diversity
- leprieur_tree - Example data for phylogenetic nestedness and turnover components
- lozupone_panel_a - Example data for UniFrac distance
- lozupone_panel_b - Example data for UniFrac distance
- lozupone_tree - Example data for UniFrac distance
Last updated 10 months agofrom:f1e5d38eac. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win | OK | Sep 12 2024 |
| R-4.5-linux | OK | Sep 12 2024 |
| R-4.4-win | OK | Sep 12 2024 |
| R-4.4-mac | OK | Sep 12 2024 |
| R-4.3-win | OK | Sep 12 2024 |
| R-4.3-mac | OK | Sep 12 2024 |
Exports:abundance_jaccardabundance_sorensonalpha_diversitiesberger_parker_dbeta_diversitiesbinomial_deviancebray_curtisbray_curtis_balancedbray_curtis_gradientbrillouin_dcanberrachebyshevchordclark_coefficient_of_divergencecorrelation_distancecosine_distancecy_dissimilaritydominanceeuclideanfaith_pdgeneralized_unifracgeodesic_metrichammingheip_ehellingerhorn_morisitainformation_unifracinvsimpsonjaccardjaccard_nestednessjaccard_turnoverkempton_taylor_qkulczynski_firstkulczynski_secondkullback_leibler_divergencemanhattanmargalefmatch_to_treemcintosh_dmcintosh_emean_character_differencemenhinickminkowskimodified_mean_character_differencemorisitaphylogenetic_alpha_diversitiesphylogenetic_beta_diversitiesphylosorphylosor_nestednessphylosor_turnoverpielou_erichnessrms_distancerogers_tanimotorussel_raoruzickaruzicka_balancedruzicka_gradientshannonsimpsonsimpson_esokal_michenersokal_sneathsorensonsorenson_nestednesssorenson_turnoverstrongunweighted_unifracunweighted_unifrac_nestednessunweighted_unifrac_turnovervariance_adjusted_unifracweighted_kulczynski_secondweighted_normalized_unifracweighted_unifracyule_dissimilarity
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chao's abundance-weighted indices | abundance_jaccard abundance_sorenson |
| Berger-Parker dominance | berger_parker_d |
| Binomial deviance and CY index of dissimilarity | binomial_deviance cy_dissimilarity |
| Bray-Curtis distance | bray_curtis |
| Balanced variation and abundance gradient components for abundance data | bray_curtis_balanced bray_curtis_components bray_curtis_gradient ruzicka_balanced ruzicka_gradient |
| Canberra and related distances | canberra clark_coefficient_of_divergence |
| Chebyshev distance | chebyshev |
| Correlation and cosine distance | correlation_distance cosine_distance |
| Diversity measures implemented | alpha_diversities beta_diversities diversity_measures phylogenetic_alpha_diversities phylogenetic_beta_diversities |
| Euclidean and related distances | chord euclidean geodesic_metric hellinger rms_distance |
| Faith's phylogenetic diversity | faith_pd |
| Example data for Faith's phylogenetic diversity | faith_tree |
| Hamming distance | hamming |
| Beta diversity for presence/absence data | jaccard kulczynski_first kulczynski_second rogers_tanimoto russel_rao sokal_michener sokal_sneath sorenson yule_dissimilarity |
| Nestedness and turnover components for presence/absence data | jaccard_components jaccard_nestedness jaccard_turnover sorenson_nestedness sorenson_turnover |
| Kempton-Taylor Q index | kempton_taylor_q |
| Kullback-Leibler divergence | kullback_leibler_divergence |
| Example data for phylogenetic nestedness and turnover components | leprieur_tree |
| Example data for UniFrac distance | lozupone_panel_a lozupone_panel_b lozupone_tree |
| Manhattan and related distances | manhattan mean_character_difference modified_mean_character_difference |
| Margalef's richness index | margalef |
| Match vector of counts to phylogenetic tree | match_to_tree |
| McIntosh dominance index D | mcintosh_d |
| McIntosh's evenness measure E | mcintosh_e |
| Menhinick's richness index | menhinick |
| Minkowski distance | minkowski |
| The Morisita index and Horn-Morisita index | horn_morisita morisita |
| Richness or number of observed species | richness |
| Ruzicka or weighted Jaccard distance | ruzicka |
| Shannon diversity and related measures | brillouin_d heip_e pielou_e shannon |
| Simpson's index and related measures | dominance invsimpson simpson simpson_e |
| Strong's dominance index | strong |
| UniFrac distance | generalized_unifrac information_unifrac phylosor unifrac unweighted_unifrac variance_adjusted_unifrac weighted_normalized_unifrac weighted_unifrac |
| Nestedness and turnover components of unweighted UniFrac distance | phylosor_nestedness phylosor_turnover unifrac_components unweighted_unifrac_nestedness unweighted_unifrac_turnover |
| Weighted Kulczynski distance | weighted_kulczynski_second |
