Package: FAVA 1.0.7

Maike Morrison

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 (2024) <doi:10.1101/2024.07.03.601929>.

Authors:Maike Morrison [aut, cre, cph]

FAVA_1.0.7.tar.gz
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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 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:

5.00 score 2 stars 7 scripts 12 exports 36 dependencies

Last updated 15 days agofrom:92bfbf8c29. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 12 2024
R-4.5-win	OK	Dec 12 2024
R-4.5-linux	OK	Dec 12 2024
R-4.4-win	OK	Dec 12 2024
R-4.4-mac	OK	Dec 12 2024
R-4.3-win	OK	Dec 12 2024
R-4.3-mac	OK	Dec 12 2024

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 colorspace cpp11 dplyr fansi farver generics ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R6 RColorBrewer rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Analysis of microbiome data with FAVA

Maike Morrison

Rendered frommicrobiome_tutorial.Rmdusingknitr::rmarkdownon Dec 12 2024.

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