This readme file is to help recreate some of the stochastic results obtained in the
paper "Extinction Pathways and Outbreak Vulnerability in a Stochastic Ebola Model" 
written by Garrett T. Nieddu, Lora Billings, James H. Kaufman, Eric Forgoston, 
and Simone Bianco.

Goal : Compile a fortran file that will run a Gillespie type algorithm. When executed
the program will recreate exactly one stochastic simulation, although if you were to 
tweak the code you might easily have thousands of simulations.

Instructions:

1. Create directory with unique name 'Name.Dir'

2. Save EVD_stochastic.f into 'Name.Dir'

3. Compile EVD_stochastic.f. If you are running a linux based OS then see the following fortran
for an example procedure. Otherwise use other method to compile and go to step 4.

     a)Open Terminal, change directory until you are in 'Name.Dir'. 
     b)>>gfortran EVD_stochastic.f -o EVD
     c)>>./EVD
     d)Follow the prompts and enter a three or four digit number.
     c)The program should save 'Simulation_data' and 'Extinction_Times'.

4. Save load_data.m to 'Name.Dir'.
5. Open Matlab, go to directory 'Name.Dir'. Run load_data.m by typing in 'load_data'. 
This will allow you to see a visual representation of the stochastic progression of the
infectious class over time for 1000 days.