micro_PERMANOVA: A function to run PERMANOVA on tidi_micro data sets

In CharlieCarpenter/tidy.micro: A Pipeline For Microbiome Analysis And Visualization

Description

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

Usage

micro_PERMANOVA(beta_div, micro_set, method, ..., nperm = 999, seed = NULL)

Arguments

beta_div	A dissimilarity matrix calculated by beta_div
micro_set	A tidy_micro data set
method	A character string indicating the method used to calculated dissimilarity
...	Covariates of interest
nperm	Number of permutations
seed	Random seed to use for test. This is highly recommended for reproducibility

Details

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

References

help(vegdist) help(adonis2)

See Also

adonis

Examples

data(phy); data(cla); data(ord); data(fam); data(met)
otu_tabs = list(Phylum = phy, Class = cla, Order = ord, Family = fam)
set <- tidy_micro(otu_tabs = otu_tabs, meta = met) \
filter(day == 7) ## Only including the first week

## Bray-Curtis beta diversity
bray <- set \

bray \

CharlieCarpenter/tidy.micro documentation built on Jan. 19, 2020, 6:28 p.m.