main_dE2.m

main_init;
addpath('C:\Users\bai_f\Documents\research\Axon_growth\DelayedFeedback\mine_dde23');
%% Initial values of bifurcation parameters
% tau = N/nu/(1-rho_bulk)
% N==1, nu==1, rho_bulk==1/2, then we have the following initial values. 
contpar=ind_dE2;
namepar='dE2';


rhobulkK = 0.5;
rhobulkD = 0.5;
pE = 6;
wE = 5;
pI = 6;
wI = 5;
vK = 1;
vD = 1;
dE1 = 1;
dE2 = 2.3;
dI1 = 1;
dI2 = 1;

% N=1-->file_id=1 
% N=2-->file_id=0.11 
% N=3-->file_id=10 (this can be different for different parameters)
N = 10;
file_id=4;
% no_y specifies which signal will be set as y-axis in the bifurcation diagram. 
%E1, E2, I1, I2 -> 1,2,3,4
no_y = 3;
% label_y specify the ylabel in the bifurcation diagram.
label_y = 'I1';

% min max and step for extending 1par branch
min_bound = 0.01;
max_bound = 2.5;
max_step = 0.005;
% number of attempts when extending 1par branch
bf_attempts = 4000;

% time instants for extracting frequencies
t_start = 500;
t_end = 1000;
tspan = [0, t_end];
dt = 0.1;

%% Setup the first fixed point
main_setup_first_fixed_pt;
%% Initialize the branch
main_initialize_branch;
%% Continuation of the branch
main_cont_branch;
%% Plot bifurcation diagram
main_plot_bf;
%% Extract frequency and amplitude of oscillation
main_extract_freq_amp;
%% output
main_save_data_1par;
% save_data_1par(namepar, file_id, N, par_stst, y_stst, label_y, nunst_stst, par_list, freq_list, T_list, amp_list, max_list, min_list, par_bf_hopf, y_bf_hopf);

% save_data_1par(namepar, file_id, N, par_stst, E1_stst, nunst_stst, par_list, freq_list, amp_list, max_list, min_list);