For a nicer version of this tutorial go to http://rpubs.com/NCI-biostats/microbiome-fixed-reference.
In that tutorial we describe and show examples of R code implementing methods to use standard microbiome reference groups to simplify beta-diversity analyses and faclitate independent validation as described in Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation by Marlena Maziarz, Ruth M. Pfeiffer, Yunhu Wan and Mitchell H. Gail. The code, test files, HMP reference sets and any other necessary files are on https://github.com/NCI-biostats/microbiome-fixed-reference.
Specifically, the tutorial describes the use of two functions: HMPdistance and GHotelling. HMPdistance calculates distance to the HMP stool and nasal reference sets, GHotelling is a generalized Hotelling test, which accounts for correlation between samples from the same individual.
Visit http://rpubs.com/NCI-biostats/microbiome-fixed-reference for details.