micro_PERMANOVA: A function to run PERMANOVA on tidi_micro data sets
In tidyMicro: A Pipeline for Microbiome Analysis and Visualization

Description Usage Arguments Details References See Also Examples

A wrapper function to call adonis2 from the vegan package. PERMANOVA is a method for partitioning distance matrices among sources of variation and fitting linear models (e.g., factors, polynomial regression) to distance matrices; uses a permutation test with pseudo-F ratios

1	micro_PERMANOVA(micro_set, beta_div, method, ..., nperm = 999)

`micro_set`	A tidy_micro data set
`beta_div`	A dissimilarity matrix calculated by `beta_div`
`method`	A character string indicating the method used to calculated dissimilarity
`...`	Covariates of interest
`nperm`	Number of permutations

The function adonis2 is based on the principles of McArdle & Anderson (2001) and can perform sequential, marginal and overall tests. Function adonis2 also allows using additive constants or squareroot of dissimilarities to avoid negative eigenvalues

vegdist adonis2

adonis

data(bpd_phy); data(bpd_cla); data(bpd_ord); data(bpd_fam); data(bpd_clin)
otu_tabs = list(Phylum = bpd_phy, Class = bpd_cla,
Order = bpd_ord, Family = bpd_fam)

set <- tidy_micro(otu_tabs = otu_tabs, clinical = bpd_clin) %>%
filter(day == 7) ## Only including the first week

## Bray-Curtis beta diversity
bray <- set %>% beta_div(table = "Family")

set %>% micro_PERMANOVA(bray, method = "bray", bpd1)