### This repo contains the supplemental files for the article "Structure and contingency determine mutational hotspots for flower color evolution". These files can be used to recreate the analyses done for the paper.
### Details
-- alternative_model_simulations/ contains the scripts, data, and Jupyter notebooks for analysis of "control" simulations with different
models
-- cya-to-pel_subset_cc_trajectory_files/ and del-to-cya_subset_cc_trajectory_files/ contain the reconstructed control coefficient trajectories
-- main_simulation_ouputs/ contains the output from the main simulations and the scripts used to generate them. The datasets are stored
as zipped serialized (pickle) files that can be unzipped and imported into python in the "complete-analysis*.ipynb" Jupyter notebooks use
for analyzing the simulations.
-- DFR_concentration_effects.ipynb contains the analysis used to generate supplement figures S4 and S5, which show the effects of changes in
enzyme concentration in differing pathway backgrounds
-- del-cya-Simpson's_paradox_selection_curves.ipynb and cya-pel-Simpson's_paradox_selection_curves.ipynb contain the analysis of fitness
effect ordering across individual simulated trajectories
-- PathwayDiffEq.TeX and PathwayDiffEq.pdf contain the differential equations describing pathway dynamics in our model.
### Link to the associated pre-print
