Examining diversity in metacommunities with dormant seed banks.

This repository contains the code to reproduce the manuscript:

Wisnoski NI, and LG Shoemaker. "Seed banks alter metacommunity diversity: the interactive effects of competition, dispersal, and dormancy"

To reproduce the analysis and figures from the manuscript, run the following:

1. 1_mc_sim.R = this file includes the main simulation across parameter space in the paper. It generates output files that are used in figures 2 and 3.
2. sim_output/extract_sim_output.sh = commands included here parse the simulation output and split it into files for above and belowground data for equal and stable interactions. Paths and filenames will be user-specific and need to be specified for your system.
3. 2_mc_sim_sensitivity.R = this file includes the simulation model for the sensitivity analysis. It generates output files that are used to make figure 4.
4. 3_make_diversity_plots.R = this file makes figures 2 and 3 from the output of the simulations reformated by the extract_sim_output.sh script.
5. 4_plot_sensitivity_analysis.R = this script creates figure 4 from the output of the sensitivity analysis simulation script.
6. s1_mc_sim_tradeoff.R = simulation model for the scenario where species exhibit interspecific trait variation in dispersal, germination, and survival.
7. s2_analyze_tradeoff.R = this script makes the tradeoff related figures included in the supplement.
8. s3_visualize_example_tradeoffs.R = this script demonstrates the differences in none, weak, and strong tradeoff scenarios explored in the supplement.