Description Usage Arguments Value References Examples
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
1 |
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 |
A symmetrix distance matrix
vegdist
1 2 3 4 5 6 7 8 9 10 11 12 | 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")
## Morisita-Horn beta diversity
horn <- set %>% beta_div(table = "Family", method = "horn")
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