The set of scripts used to process data with in the paper entitled "Ecological assembly processes are coordinated between bacterial and viral communities in fractured shale ecosystems"
Each script contains a distinct analysis:
- Correlating_S3-Viral_Models.R will allow you to relate the null models used throughout this study according to a Spearman-based Mantel test. It will also generate figures.
- Process_Viral_Eco_Models.R generates viral bNTI and RCBC boxplots
- S3_Community_bNTI.R is the bNTI implementation for the microbial community
- S3_Community_RCBC.R is the RCBC implementation for the microbial community
- S3_Phylogeny_Plot.R generates a stacked-bar chart for each of the fractured shale wells studied, as well as a plot illustrating the proportion represented by Halanaerobiaceae through time
- vContact_Processing.R converts vConTACT viral similarity data into a UPGMA dendrogram
- Viral_Community_bNTI.R is the bNTI implementation for the viral community
- Viral_Community_RCBC.R is the RCBC implementation for the viral community
All necessary files should be located in the "Date Files" folder. If you have any questions, please contact me at [email protected]