Atlas.Rmd

---
title: "HITChip Atlas"
author: "Leo Lahti, Sudarshan Shetty et al."
bibliography: 
- bibliography.bib
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## Intestinal microbiota diversity in 1006 western adults

The data set from [Lahti et al. Nat. Comm. 5:4344, 2014](http://www.nature.com/ncomms/2014/140708/ncomms5344/full/ncomms5344.html) has microbiota profiling of 130 genus-like taxa across 1006 normal western adults from [Data Dryad](http://doi.org/10.5061/dryad.pk75d). Load the data in R:

```{r data2, warning=FALSE, message=FALSE}
# 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: 

```{r div-example, warning=FALSE, message=FALSE}
tab <- microbiome::alpha(atlas1006, index = c("shannon", "invsimpson"))
library(knitr)
kable(head(tab))
```