adonis_rarperm_pq: Permanova (adonis) on permutations of rarefaction even depth

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Permanova (adonis) on permutations of rarefaction even depth

Description

Permanova are computed on a given number of rarefaction with different seed.number. This reduce the risk of a random drawing of a exceptional situation of an unique rarefaction.

Usage

adonis_rarperm_pq(
  physeq,
  formula,
  dist_method = "bray",
  merge_sample_by = NULL,
  na_remove = FALSE,
  rarefy_nb_seqs = FALSE,
  verbose = TRUE,
  nperm = 99,
  progress_bar = TRUE,
  quantile_prob = 0.975,
  sample.size = min(sample_sums(physeq)),
  ...
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
formula	(required) the right part of a formula for vegan::adonis2(). Variables must be present in the physeq@sam_data slot.
dist_method	(default "bray") the distance used. See phyloseq::distance() for all available distances or run phyloseq::distanceMethodList(). For aitchison and robust.aitchison distance, vegan::vegdist() function is directly used.
merge_sample_by	a vector to determine which samples to merge using the merge_samples2() function. Need to be in physeq@sam_data
na_remove	(logical, default FALSE) If set to TRUE, remove samples with NA in the variables set in formula.
rarefy_nb_seqs	(logical, default FALSE) Rarefy each sample (before merging if merge_sample_by is set) using phyloseq::rarefy_even_depth(). if correction_for_sample_size is TRUE, rarefy_nb_seqs will have no effect.
verbose	(logical, default TRUE) If TRUE, prompt some messages.
nperm	(int, default = 99) The number of permutations to perform.
progress_bar	(logical, default TRUE) Do we print progress during the calculation.
quantile_prob	(float, ⁠[0:1]⁠) the value to compute the quantile. Minimum quantile is computed using 1-quantile_prob.
sample.size	(int) A single integer value equal to the number of reads being simulated, also known as the depth. See phyloseq::rarefy_even_depth().
...	Other params to be passed on to adonis_pq() function

Value

A list of three dataframe representing the mean, the minimum quantile and the maximum quantile value for adonis results. See adonis_pq().

Author(s)

Adrien Taudière

See Also

adonis_pq()

Examples

if (requireNamespace("vegan")) {
  data_fungi_woNA <-
    subset_samples(data_fungi, !is.na(Time) & !is.na(Height))
  adonis_rarperm_pq(data_fungi_woNA, "Time*Height", na_remove = TRUE, nperm = 3)
}

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.