README.md
In lucasnell/myvatn_terrestrial_foodweb: Myvatn Terrestrial Foodweb

Code for the following paper:

by

Matthew A. McCary, Joseph S. Phillips, Tanjona Ramiadantsoa, Lucas A. Nell, Amanda R. McCormick, and Jamieson C. Botsch

We've organized much of the code into an R package, mtf. Inside the R folder, you'll find...

data.R: a description of the default-parameter estimates present in the mtf::par_estimates object
equil_pools.R: The equil_pools function that re-estimates equilibrium pool sizes, for use when you adjust parameter values that affect equilibria
food_web.R: The food_web function (and required inner functions) that simulates the food web through time, given a set of parameter values
zzz.R: The miscellaneous functions .onLoad and color_pal that set the ggplot2 theme and create the color palette for figures, respectively

Obviously man contains the documentation for the package, and data contains the data files (the only data object in mtf is par_estimates).

The folder data-raw contains the pre-processed data for the parameter estimates, plus the code to clean it for the package. The script data-raw/par_estimates.R cleans the data. The folder data-raw/parameters contains the following pre-processed data files:

full_pars.csv: The "final" parameter values that are solved using the specified equilibrium pool sizes and the initially specified parameter values
structure_eqs.csv: The equilibrium pool sizes for different model configurations, based on full_pars.csv
iN_eqs.csv The equilibrium pool sizes for different values of the nutrient input rate i_I (with all other values based on full_pars.csv)

The analysis folder contains the files that use the mtf package to produce the figures and supplemental information file.

fig_2-4.R: Creates figures 2, 3, and 4
fig_5.R: Creates figure 5
AppendixS1.Rmd Creates Appendix S1
AppendixS2.Rmd Creates Appendix S2
template.tex: LaTeX template that helps generate the supplemental information PDF