vignette.R
In microbiome: Microbiome Analytics

## ---- echo=FALSE, message=FALSE-----------------------------------------------
library(knitr)
require(knitcitations)
# cleanbib()
# options("citation_format" = "pandoc")
bib <- read.bibtex("bibliography.bib")

# Can also write math expressions, e.g. 
# $Y = X\beta + \epsilon$, footnotes^[A footnote here.]
# > "He who gives up [code] safety for [code] speed deserves neither."
# ([via](https://twitter.com/hadleywickham/status/504368538874703872))
knitr::opts_chunk$set(fig.width=10, fig.height=10, message=FALSE, warning=FALSE)

## ----loading------------------------------------------------------------------
library(microbiome)  

## ----atlasdata----------------------------------------------------------------
# Data from 
# http://www.nature.com/ncomms/2014/140708/ncomms5344/full/ncomms5344.html
data(atlas1006) 
atlas1006

## ---- echo=FALSE,results="asis"-----------------------------------------------
bibliography()