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Analysis scripts, data files and plots used in the manuscript

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roey-angel/Rock_weathering

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Arid_rock_weathering

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Data, sequence analysis ploting for figures included in the paper: Wieler, N., Ginat, H., Gillor, O. and Angel, R.: The origin and role of biological rock crusts in rocky desert weathering, Biogeosciences, 16(6), 1133–1145, doi:https://doi.org/10.5194/bg-16-1133-2019, 2019. .

Abstract

Overview

├── Data          # Primary data
│   ├── desiccation_data_full.csv
│   ├── Isotopes_data.csv
│   ├── Rock_weathering_metadata_RA.csv
│   ├── Rock_weathering_new2_otuTab.txt
│   └── Rock_weathering_new2_silva.nrv119.taxonomy
├── LICENCE            # Copyright information
├── packrat.tgz          # R packages needed by the RMD file (available upon request)
├── README.md          # Overview of the repo
├── references.bib          # Bibtex formatted refereces cited in the RMD file
├── Results         # Result files generated while running the RMD file
│   ├── Rock_weathering_Diversity.csv
│   ├── Rock_weathering_Diversity.Rds
│   ├── Rock_weathering_filt3_GMPR_Order_CI.csv
│   ├── Rock_weathering_filt3_GMPR_Order_Pvals.csv
│   ├── Rock_weathering_filt3_GMPR_Phylum_CI.csv
│   ├── Rock_weathering_filt3_GMPR_Phylum_Pvals.csv
│   ├── Rock_weathering_Richness.csv
│   └── Rock_weathering_Richness.Rds
├── Rock_wathering_analysis_files.Rproj          # R project file
├── Rock_weathering_analysis4paper.html          # HTML output of the RMD file
├── Rock_weathering_analysis4paper.md          # MD output of the RMD file
├── Rock_weathering_analysis4paper.RMD            # Executable R markdown script
├── Rock_weathering_figures/          # Figure files generated while running the RMD file
└── Rock_weathering_process_sequences.sh          # Shell excecutable for processing the sequence data

Running the analysis

The RMD file is best executed using knitr on RStudio. The packrat folder holds the specific package versions used for the analysis.