These scripts (IM#: LLNL-CODE-823962) document the code used to analyze the Death Valley Regional Flow System (DVRFS) microbial community for a manuscript titled "Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow". The R packages used for this manuscript can be found in the file "Packages_and_Paths_microbe.r". The associated scripts for figures/tables in the manuscript are:
- 01.Dada2.r : Table S4
- 02.FilteringOTUs.r : Table S11; Figure S1
- 03.PhylogeneticTree.sh : None
- 04.Barplots.r : Figure S5
- 05.AlphaDiversity.r : Figure 3, Figure S6
- 06.BetaDiversity.r : Figure 4, Figure S7, Table 1
- 07.NetworkAnalysis.r : Figure 5, Figure S3, Figure S8, Table S6, Table S7
- 08.EcologicalProcess.r : Figure 6, Figure S2, Table S8
- Geochem.r : Figure 2, Table S2, Table S3, Table S9, Table S10
Merino, N., Jackson, T.R., Campbell, J.H., Kersting, A.B., Sackett, J., Fisher, J.C., et al. (2022) Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow. Science of The Total Environment 842: 156768. 10.1016/j.scitotenv.2022.156768
Open Source Distribution, under the terms of the LGPL, v3.0 license.
These code will not be updated once the manuscript has been accepted.