beta_div: Beta Diversity Calculations for tidy_micro

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

Description

Calculate beta diversities of your tidy_micro set. This function reformats the data into the original OTU table and then feeds that into the vegdist function

Usage

beta_div(micro_set, table, method = "bray")

Arguments

micro_set	A tidy_micro data set
table	Table you'd like to use when calculating alpha diversity. Your lowest level is recommended
method	A dissimilarity method compatible with vegdist

Value

A symmetrix distance matrix

References

help(vegdist)

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 %>% beta_div(table = "Family")

## Morisita-Horn beta diversity
horn <- set %>% beta_div(table = "Family", method = "horn")

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