## ---- 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)

## ----install, eval=FALSE---------------------------------------------------
#  library(BiocManager)
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install(version = "devel")
#  BiocManager::install("microbiome")

## ----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()

