README.md

In bryandmartin/MicrobiomePack: Tools for Microbiome data analysis

Microbiome

Description of Files (10/6)

• XiaChenFungLiModel.R: Complete implementaion of the MC-EM model from Xia et al. (2013)
• XiaTestRun.R: Imports other scripts and demonstrates how to run the MC-EM function. Also includes code for generating the fitting graphs, as in Figure 4 Xia et al.
• getData.R: Loads in raw data files provided by Amy. Includes functions to purturb, take logratio, and select most prevelent OTUs.
• run0A.R: Shows how to select a subset of the data based on experimental conditions. (Not currently used.)
• HQQModel.R: Implementation of a simple posterior predictive Dirichlet-Multinomial distribution.
• fittingPlots.R: Compares DayAmdmt 11 and 21, contains code for various plots.
• varFitPlotsComp.R: Contains code for plotting variance fit for simple multinomial, composition, and observed count
• OTU300run.R: Contains code for generating fitting plots with random selection of 300 OTUs

Notes

• Currently implemented to work specifically on my desktop with filepaths.
• Includes parallelization, make sure to check if run on different machines.

bryandmartin/MicrobiomePack documentation built on May 25, 2019, 3:25 p.m.