The data set from Lahti et al.ย Nat. Comm. 5:4344, 2014 has microbiota profiling of 130 genus-like taxa across 1006 normal western adults from Data Dryad. Load the data in R:
# Download the required R packages and then the HITChip Atlas data set
library(microbiome)
data(atlas1006)Estimate ecosystem alpha diversity and related indicators for this data set:
tab <- microbiome::alpha(atlas1006, index = c("shannon", "invsimpson"))
library(knitr)
kable(head(tab))| diversity_shannon | |
|---|---|
| Sample-1 | 3.187815 |
| Sample-2 | 3.394462 |
| Sample-3 | 2.864855 |
| Sample-4 | 3.056922 |
| Sample-5 | 3.073742 |
| Sample-6 | 2.941993 |