The FAVA R package implements the statistic FAVA, an FST-based Assessment of Variability across vectors of relative Abundances, as well as a suite of helper functions which enable the visualization and statistical analysis of relative abundance data. The FAVA R package accompanies the paper, âQuantifying compositional variability in microbial communities with FAVAâ by Morrison et al. (2025).
The FAVA R package includes the following core functions:
fava: Quantify variability across many compositional vectors in a single, normalized index, called FAVA
bootstrap_fava: Compare values of FAVA between pairs of abundance matrices
window_fava: Compute FAVA in sliding windows along the rows of a relative abundance matrix
plot_relabund: Visualize a relative abundance matrix as a stacked bar plot
Install FAVA with:
You can install the development version of FAVA from GitHub with:
# First, install devtools if you haven't already:
# install.packages("devtools")
devtools::install_github("MaikeMorrison/FAVA")
# If you wish to access the tutorial (also accessible below) from within
# the package:
devtools::install_github("MaikeMorrison/FAVA", build_vignettes = TRUE)The package website, maikemorrison.github.io/FAVA/, contains documentation and examples for all package functions. It also contains a tutorial on the usage of FAVA for the analysis of microbiome data. The tutorial vignette is available at this link.
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