![]() ![]() Sometimes richness, evenness, and dominance are considered General, diversity increases together with increasing richness andĮvenness. Shannon diversity, and generalized diversity as special cases. Single equation that provides observed richness, inverse Simpson, and The Hill coefficient combines many standard indices into a A number of ecological diversity measures areĪvailable. Diversity indices measure the overallĬommunity heterogeneity. Term species diversity, summarizes the distribution of speciesĪbundances in a given sample into a single number that depends on 12.2 Reduced dimension (PCA, t-SNE, UMAP, MDS, etc)Īlpha diversity, also sometimes interchangeably used with the.10 Representation of multiple data tables.7.2.2 PCoA for ASV-level data with Bray-Curtis with DMM clusters shown with colors.7.2.1 Dirichlet Multinomial Mixtures (DMM).6.3.2 Checking the homogeneity condition.6.3.1 Testing differences in community composition between sample groups.6.2.4 Visualizing the most dominant genus on PCoA.3.4.2 Abundances of specific taxa in all samples.3.4.1 Abundances of all taxa in specific sample.3.2.1 Generate a taxonomic tree on the fly.3.2 Functions to access taxonomic information.1.8.3 Resources for TreeSummarizedExperiment.1.5 Microbiome and tree data specific aspects.1.3.2 Conversions between data formats in R.1.3.1 Importing data from external files.1.3 Loading experimental microbiome data. ![]()
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