bootpq provides bootstrapping tools for phyloseq objects based on repeated rarefaction to even sequencing depth. Instead of drawing conclusions from a single, possibly atypical, rarefaction, statistical analyses are computed across many rarefaction permutations — each with a different random seed — and summarized (mean and quantiles).
bootpq is part of the pqverse ecosystem and builds on top of MiscMetabar.
Installation
You can install the development version of bootpq from GitHub with:
# install.packages("remotes")
remotes::install_github("adrientaudiere/bootpq")Functions
| Function | Description |
|---|---|
adonis_rarperm_pq() |
PERMANOVA across rarefaction permutations |
hill_test_rarperm_pq() |
Hill-number group tests across rarefaction permutations |
var_par_rarperm_pq() |
Variation partitioning across rarefaction permutations |
Example
library(bootpq)
library(MiscMetabar)
data(data_fungi_mini)
data_fungi_woNA <- subset_samples(
data_fungi_mini,
!is.na(Time) & !is.na(Height)
)
# PERMANOVA summarized over 99 rarefaction permutations
res <- adonis_rarperm_pq(data_fungi_woNA, "Time*Height", na_remove = TRUE)
res$mean