Pit-foaming manuscript

Author: Fan Yang

Description:

This repository stores data analysis procedures and methods used in the manuscript titled above. To reproduce the results and associated figures, please follow the instructions below.

Software prerequisites:

• bash shell
• git
• R 3.2.0+ and packages:
  • vegan
  • phyloseq
  • ggplot2
  • RColorBrewer
  • ggthemes
  • BayesFactor
• python 2.7.5+

To begin, in terminal type the following code to obtain data and scripts needed.

cd ~  
git clone https://github.com/germs-lab/pit_foaming_manuscript

Procedures:

1. Preprocessing data and assess the overall community data
2. Community analyses with incorporated manure measurements
3. Correlation analyses