feasible_parasites

This repo contains the code necessary to reproduce the results found in docs/feasible_manuscript.pdf and docs/supplementary_material.pdf. The data used for this analysis is not yet publicly distributable, so this repository does not contain the entire workflow from data to compiled manuscript. Rather, we have included a data/archival/dummy_data.csv file that allows the various scripts to be executed, but produces dummy results (because the dummy data is not real). Therefore, do not be surprised when executing run_all.sh produces completely different results than what you see in docs/* (because it should!). A more detailed description of each folder in this repo is given below

code

• agg_fxns.py: This script contains the necessary functions for testing whether a given host-parasite distribution follows a top-down or bottom-up model.
• test_agg_fxns.py: The script provides unit tests for the functions in agg_fxns.py
• manuscript_analysis_*.py: Scripts that use agg_fxns.py to perform constraint-based and process-based analyses on parasite data. Each script contains a description of what it does at the beginning of the script.
• manuscript_plots.ipynb: IPython Notebook for making the figures from the analysis output
• run_all.sh: A bash script that shows the order in which the manuscript analysis scripts should be run. Executing this script will run the analysis on the dummy data.

docs

• feasible_manuscript.pdf: A draft of the manuscript for which the scripts in code are used.
• supplementary_material.pdf: A draft of the supplementary material for which the scripts given in code are used.

results

• Contains the various plots and pickled data generated from the *.py scripts described above using the dummy data

data

• archival
  • dummy_data.csv: A dummy data file so the the above scripts can be executed.
  • make_dummy_data.py: Python script for generating the dummy data