Repository navigation
The Directories
Here is an overview of the main directories in the repositories and brief description of what they contain.
Should contain scripts running on the local computer (and not on the HPC), as well as non-data files needed for running them (like Infomap). The scripts are mostly part of the pipeline and detailed descriptions of them are on the "Pipeline scripts" page.
Contains scripts that are implemented to run on the HPC, as well as Infomap execution file able to run on linux, and CSVs relevant to the observed results from the HPC. Detailed descriptions of the scripts are on the "Pipeline scripts" page.
Contains the network building results for each experiment. What experiment each number in the folder name represents is found in the experiments.csv file in the upper directory (~/HPC)
Contains the shuffling results from the HPC server, and the analyses results done on them. Each sub-directory is a shuffling method.
Contains the output files that are produced by scripts running on the local computer (and not on the HPC). This directory assembles files containing data (CSVs and .rds) with no specific connection to one another. Figures and sets of data files are located in the following sub-directories.
All figures produced locally are placed in this folder.
contain the shuffling results that are done locally - so each contain X files with ASV occurrence data (this is not a network), X is the number of shuffling. The name of each directory mentions:
- Level of shuffling (e.g. Farm level).
- Type of shuffling as expected in the vegan r package (e.g. curveball or r00).
- Percentage of core ASVs used (e.g. 30, for filtering out of 30%).
- Number of shuffling iterations done, if they are NOT 100 (e.g. 500)
The original raw data as taken from this paper, untouched by us.