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bootstrap_fava()
- Statistically compare FAVA values between pairs of relative abundance matrices.
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fava()
- Compute the Fst of a matrix of compositional vectors
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fava_norm()
- Compute the normalized Fst of a matrix of compositional vectors
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gini_simpson()
- Compute the Gini-Simpson index of a compositional vector
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gini_simpson_mean()
- Compute the mean Gini-Simpson index of the rows in a matrix of compositional vectors
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gini_simpson_pooled()
- Compute the pooled Gini-Simpson index of the rows in a matrix of compositional vectors
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plot_relabund()
- Visualize a relative abundance matrix as a stacked bar plot.
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relab_phyloseq()
- Generate a relative abundance matrix with sample metadata and OTU abundances from a phyloseq object.
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time_weights()
- Compute a normalized weighting vector based on a vector of sampling times.
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window_fava()
- Compute FAVA in sliding windows.
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window_list()
- Generate sliding windows of specified length given the maximum number of samples
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window_plot()
- Generate a plot of FAVA in sliding windows.
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xue_microbiome_sample
- Temporal microbiome composition data
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xue_species_info
- Table of species information
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xue_species_similarity
- Species similarity matrix for the species included in xue_microbiome_sample
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xue_species_tree
- Phylogenetic tree for the species included in xue_microbiome_sample