View source: R/beta_div_test.R
adonis_pq | R Documentation |
A wrapper for the vegan::adonis2()
function in the case of physeq
object.
adonis_pq(
physeq,
formula,
dist_method = "bray",
merge_sample_by = NULL,
na_remove = FALSE,
correction_for_sample_size = FALSE,
rarefy_nb_seqs = FALSE,
verbose = TRUE,
...
)
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. |
correction_for_sample_size |
(logical, default FALSE) If set to TRUE,
the sample size (number of sequences by samples) is add to formula in
the form |
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. |
... |
Other arguments passed on to |
This function is mainly a wrapper of the work of others.
Please make a reference to vegan::adonis2()
if you
use this function.
The function returns an anova.cca result object with a
new column for partial R^2. See help of vegan::adonis2()
for
more information.
Adrien Taudière
data(enterotype)
adonis_pq(enterotype, "SeqTech*Enterotype", na_remove = TRUE)
adonis_pq(enterotype, "SeqTech", dist_method = "jaccard")
adonis_pq(enterotype, "SeqTech", dist_method = "robust.aitchison")
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