View source: R/beta_div_test.R
adonis_rarperm_pq | R Documentation |
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)),
...
)
physeq |
(required): a |
formula |
(required) the right part of a formula for |
dist_method |
(default "bray") the distance used. See
|
merge_sample_by |
a vector to determine
which samples to merge using the |
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
|
verbose |
(logical, default TRUE) If TRUE, prompt some messages. |
nperm |
(int) The number of permutations to perform. |
progress_bar |
(logical, default TRUE) Do we print progress during the calculation. |
quantile_prob |
(float, |
sample.size |
(int) A single integer value equal to the number of
reads being simulated, also known as the depth. See
|
... |
Other params for be passed on to |
A list of three dataframe representing the mean, the minimum quantile
and the maximum quantile value for adonis results. See adonis_pq()
.
Adrien Taudière
adonis_pq()
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)
}
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