Quantify Compositional Variability Across Relative Abundance Vectors

Documentation for package ‘FAVA’ version 1.0.9

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