FAVA

The FAVA R package implements the statistic FAVA, an $F_{ST}$-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, “Quantifying compositional variability in microbial communities with FAVA” by Morrison et al. (2024).

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

Installation

FAVA is available for download on CRAN. Install FAVA with:

install.packages("FAVA")

If you find a bug, check Issues to see if it has been identified already. If it has not yet been identified, please open an issue describing the bug and providing a minimal example. If it has already been identified, it will be fixed in the next CRAN release. In the meantime, you can install the development version of FAVA from GitHub with the following code:

# First, install devtools if you haven't already:
# install.packages("devtools")

devtools::install_github("MaikeMorrison/FAVA@CRAN_development")

Tutorial

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.