These scripts were created as a part of my master thesis (with Tomás Alarcón as my supervisor and Josep Sardanyés as my co-supervisor. The scripts are used to analysis the determinsitic models for the behaviour of multipartite viruses. More info about multipartie viruses : A. Sicard, et al and A. Lucía Sanz, et al.

There are two main parts of this project, which are deterministic model and stochastic model for each virus replication model and full cycle bipartite viruses.

• 2eq_rk4_bipartite_test.c: simulate the replication model using forth order Runge-Kutta
• 2eq_rk4_bipartite_var_gamma.c: bifurcation analysis as the paramater gamma changes
• 2eq_rk4_bipartite_var_kappa.c: bifurcation analysis as the paramater kappa changes
• 2eq_rk4_rep_var_gamma_tozero.c: estimate the separatrix surface of the model
• 2eq_plot.R: plot the simulation results from 2eq_rk4_bipartite_test.c
• 2eq_phase_portrait.R: plot of simple phase portrait
• 2eq_plot_gamma_var.R: plot the bifurcation diagram for parameter gamma
• 2eq_plot_kappa_var.R: plot the bifurcation diagram for parameter kappa

• 2eq_ssa.c: simulate the Markov chain model of replication model using Gillespie's algorithm (python version 2eq_ssa.py)
• 2eq_ssa_prob_exit.c: calculate the probability of extinction due to intrinsic noise
• 2eq_plot_gillespie.R: plot the simulation results of CTCM model
• 2eq_separatrix_point.R: plot deteministic and stochastic trajectories

• 6eq_rk4_bipartite_test.c: simulate the bipartite viruses' model using forth order Runge-Kutta
• 6eq_rk4_bipartite_var_gamma.c: simulate the bifurcation analysis for parameter gamma
• 6eq_plot.R:plot the simulation results from 6eq_rk4_bipartite_test.c
• 6eq_ratio_plot_gamma.R: plot the ratio of the simulation going to origin over all of the total simulation
• 6eq_plot_gamma_var.R: plot the bifurcation diagram for parameter gamma

• 6eq_ssa.c: simulate the Markov chain model of bipartite virus model using Gillespie's algorithm
• 6eq_rk4_bipartite_var_gamma_3d_tozero.c: find the initial condition that goes to thge origin projected three dimensional phase plane
• 6eq_rk4_bipartite_var_gamma_R1R2_tozero.c: find the initial condition that goes to thge origin projected two dimensional phase plane
• 6eq_plot_gillespie.R: plot the simulation results from 6eq_ssa.c
• 6eq_ssa_prob_extinction_plot.R: plot the probability extinction results
• 6eq_plot_errorbars.R: error bar plot for the probability extinction simulation results

For more information, do not hesitate to contact me [email protected].