Package: FAVA 1.0.9

FAVA: Quantify Compositional Variability Across Relative Abundance Vectors

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, “Quantifying compositional variability in microbial communities with FAVA” by Morrison, Xue, and Rosenberg (2025) <doi:10.1073/pnas.2413211122>.

Authors:Maike Morrison [aut, cre, cph]

FAVA_1.0.9.tar.gz
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FAVA_1.0.9.tgz(r-4.6-any)FAVA_1.0.9.tgz(r-4.5-any)
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FAVA_1.0.9.tgz(r-4.5-emscripten)
FAVA.pdf |FAVA.html✨
FAVA/json (API)
NEWS

# Install 'FAVA' in R:

install.packages('FAVA', repos = c('https://maikemorrison.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/maikemorrison/fava/issues

Pkgdown/docs site:https://maikemorrison.github.io

Datasets:

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

On CRAN:

4.75 score 7 stars 16 scripts 263 downloads 12 exports 29 dependencies

Last updated from:383a576d5e. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	895
source / vignettes	OK	414
linux-release-x86_64	OK	883
macos-release-arm64	OK	424
macos-oldrel-arm64	OK	381
windows-devel	OK	663
windows-release	OK	671
windows-oldrel	OK	642
wasm-release	OK	130

Exports:bootstrap_fava fava fava_norm gini_simpson gini_simpson_mean gini_simpson_pooled plot_relabund relab_phyloseq time_weights window_fava window_list window_plot

Dependencies:cli cpp11 dplyr farver generics ggplot2 glue gtable isoband labeling lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Analysis of microbiome data with FAVA

Maike Morrison

Rendered frommicrobiome_tutorial.Rmdusingknitr::rmarkdownon Apr 18 2026.

Last update: 2024-12-11
Started: 2023-06-12

Citation

Development and contributors

Readme and manuals

Help Manual

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