Project for CS523 for recreating the results of Evolutionary Transitions and Top-Down Causation.
The File part1.py outputs vendiagrams and timeseries plots with only slight differances from the ones used in the paper. Text files are creaed which are then manualy plluged into JIDT for calculating the transfer entropy.
The file logistic_map.py was used for generating results in both part 2 and part 3. In the last line of the program if pic = True then it generates the return map figure for 1000 populations and 10000 generations, with global coupling strengths following the values used in the Walker paper. The directory 'logistic_map_figures' contains 10 figures generated with the best-fit figure shown in our paper.
The file logistic_map.py with the last line setting pic = False generates data for 10 metapopulations, each with 3 subpopulations sampled from 1000 subpopulations with 1000 generations. The global coupling strengths are from values 0 to 1 incremented by 0.025. After this population data was generated, the MatLab file TEcalc.m was used to calculate the transfer entropy in both directions and stores it as 'TD_data.csv' and 'BU_data.csv'. The MatLab file plotCI.m reads in these files, calculates the average and 95% confidence intervals, and creates the final plot used in our project. The MatLab file MIcalc.m reads in the population data and computes the mutual information between sub-populations and produces the plot used in the project.
The file part4.py generates all of the plots used in the paper. For further information see comments in the file.