chab-microbial-ecology

Code repository for Berry et al. 2016, "Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities"

Link to manuscript in Environmental Microbiology: http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13640/abstract?campaign=wolacceptedarticle

Analysis

Raw: Rmd and .R files with analysis code used in the manuscript.

• chabs-global.R contains libraries and functions that are sourced in all other .Rmd files.

Rendered: rendered html versions of Rmd files.

Data

Raw: Raw data sets.

Formatted: Cleaned data sets.

• erie-data.RData is an R workspace containing the phyloseq object used throughout the analysis. Import details can be found in Analysis/Raw/chabs-data-import.R.

Plots

Plots and supplementary plots used in mansucript.

Tables

Tables and supplementary tables used in manuscript.