Project: Mathematics-of-Epidemics-on-Networks (GitHub Link)

Mathematics-of-Epidemics-on-Networks-master
- license.txt
- readthedocs.yml
- EpidemicSonnetWorks.md
- EoN
  - class_based_visualization.py
  - notes.txt
  - function_list.txt
  - legacy.py
  - auxiliary.py
  - analytic.py
  - simulation_investigation.py
  - __init__.py
  - tests
    - test_sim_sweep_parameters.py
    - perf_run2.json
    - test_from_joel.py
    - perf_run.json
    - compare_pngs.bat
    - perf_run.py
    - readme.md
    - ExpectedPng
  - simulation.py
- setup.py
- README.md
- requirements.txt
- errata.md
- docs
  - functions
    - EoN.Epi_Prob_non_Markovian.rst
    - EoN.SIS_super_compact_pairwise_from_graph.rst
    - EoN.SIR_homogeneous_pairwise_from_graph.rst
    - EoN.SIR_super_compact_pairwise_from_graph.rst
    - EoN.discrete_SIR.rst
    - EoN.SIR_compact_effective_degree.rst
    - EoN.SIR_individual_based.rst
    - EoN.Simulation_Investigation.sim_update_kwargs.rst
    - EoN.SIR_heterogeneous_pairwise.rst
    - EoN.directed_percolate_network.rst
    - EoN.estimate_SIR_prob_size_from_dir_perc.rst
    - EoN.Simulation_Investigation.update_ts_color_dict.rst
    - EoN.fast_nonMarkov_SIR.rst
    - EoN.SIS_heterogeneous_meanfield.rst
    - EoN.SIS_homogeneous_pairwise_from_graph.rst
    - EoN.Gillespie_SIR.rst
    - EoN.Attack_rate_non_Markovian.rst
    - EoN.Simulation_Investigation.node_status.rst
    - EoN.estimate_nonMarkov_SIR_prob_size.rst
    - EoN.EBCM_discrete_from_graph.rst
    - EoN.Simulation_Investigation.R.rst
    - EoN.Simulation_Investigation.set_pos.rst
    - EoN.fast_SIR.rst
    - EoN.SIS_compact_pairwise.rst
    - EoN.fast_SIS.rst
    - EoN.SIS_pair_based.rst
    - EoN.percolation_based_discrete_SIR.rst
    - EoN.Simulation_Investigation.sim_update_label.rst
    - EoN.SIS_super_compact_pairwise.rst
    - EoN.Gillespie_Arbitrary.rst
    - EoN.basic_discrete_SIR.rst
    - EoN.EBCM_pref_mix.rst
    - EoN.SIR_individual_based_pure_IC.rst
    - EoN.estimate_directed_SIR_prob_size.rst
    - EoN.basic_discrete_SIS.rst
    - EoN.SIS_effective_degree_from_graph.rst
    - EoN.Simulation_Investigation.summary.rst
    - EoN.SIR_compact_effective_degree_from_graph.rst
    - EoN.get_PGFPrime.rst
    - EoN.SIR_effective_degree.rst
    - EoN.Simulation_Investigation.animate.rst
    - EoN.Simulation_Investigation.transmission_tree.rst
    - EoN.Attack_rate_cts_time_from_graph.rst
    - EoN.SIR_homogeneous_pairwise.rst
    - EoN.SIR_compact_pairwise_from_graph.rst
    - EoN.SIS_homogeneous_meanfield.rst
    - EoN.Simulation_Investigation.node_history.rst
    - EoN.Attack_rate_discrete_from_graph.rst
    - EoN.Simulation_Investigation.I.rst
    - EoN.SIR_homogeneous_meanfield.rst
    - EoN.get_PGFDPrime.rst
    - EoN.Gillespie_simple_contagion.rst
    - EoN.Epi_Prob_discrete.rst
    - EoN.EBCM_discrete.rst
    - EoN.SIS_compact_effective_degree_from_graph.rst
    - EoN.SIR_super_compact_pairwise.rst
    - EoN.Simulation_Investigation.display.rst
    - EoN.SIS_individual_based.rst
    - EoN.estimate_nonMarkov_SIR_prob_size_with_timing.rst
    - EoN.estimate_R0.rst
    - EoN.get_Pk.rst
    - EoN.hierarchy_pos.rst
    - EoN.fast_nonMarkov_SIS.rst
    - EoN.SIR_compact_pairwise.rst
    - EoN.percolate_network.rst
    - EoN.Simulation_Investigation.update_ts_tex.rst
    - EoN.SIR_pair_based_pure_IC.rst
    - EoN.Simulation_Investigation.update_ts_kwargs.rst
    - EoN.Gillespie_complex_contagion.rst
    - EoN.Gillespie_SIS.rst
    - EoN.Simulation_Investigation.transmissions.rst
    - EoN.get_time_shift.rst
    - EoN.SIR_effective_degree_from_graph.rst
    - EoN.Attack_rate_discrete.rst
    - EoN.SIR_heterogeneous_meanfield.rst
    - EoN.nonMarkov_directed_percolate_network_with_timing.rst
    - EoN.EBCM_uniform_introduction.rst
    - EoN.EBCM_from_graph.rst
    - EoN.SIS_heterogeneous_pairwise_from_graph.rst
    - EoN.SIS_heterogeneous_pairwise.rst
    - EoN.Simulation_Investigation.S.rst
    - EoN.get_PGF.rst
    - EoN.estimate_SIR_prob_size.rst
    - EoN.Simulation_Investigation.t.rst
    - EoN.Simulation_Investigation.get_statuses.rst
    - EoN.nonMarkov_directed_percolate_network.rst
    - EoN.Simulation_Investigation.add_timeseries.rst
    - EoN.EBCM.rst
    - EoN.Epi_Prob_cts_time.rst
    - EoN.Simulation_Investigation.sim_update_tex.rst
    - EoN.EBCM_pref_mix_from_graph.rst
    - EoN.SIR_heterogeneous_meanfield_from_graph.rst
    - EoN.SIS_individual_based_pure_IC.rst
    - EoN.SIS_homogeneous_pairwise.rst
    - EoN.EBCM_pref_mix_discrete_from_graph.rst
    - EoN.SIR_pair_based.rst
    - EoN.Attack_rate_cts_time.rst
    - EoN.SIS_compact_effective_degree.rst
    - EoN.SIS_heterogeneous_meanfield_from_graph.rst
    - EoN.get_infected_nodes.rst
    - EoN.SIS_pair_based_pure_IC.rst
    - EoN.SIR_heterogeneous_pairwise_from_graph.rst
    - EoN.subsample.rst
    - EoN.Simulation_Investigation.update_ts_label.rst
    - EoN.SIS_compact_pairwise_from_graph.rst
    - EoN.SIS_effective_degree.rst
    - EoN.Simulation_Investigation.sim_update_color_dict.rst
    - EoN.EBCM_pref_mix_discrete.rst
  - examples
    - fig5p5.py
    - fig6p24.py
    - fig3p2.py
    - fig7p4.py
    - fig6p1.rst
    - fig9p4.py
    - SEIRT.rst
    - fig9p2.rst
    - Compete.rst
    - changing_parameters
      - responsive_tau_change.py
      - SIR_change_tau.py
      - SIS_change_tau.py
    - fig9p2.py
    - Cooperate.rst
    - fig5p3.py
    - SIS_display.rst
    - arbitrary_dynamics
      - SIRS.py
      - SEIRT.py
      - Cooperate.py
      - SEIR.py
      - SIRS_heterogeneous.py
      - Compete.py
    - fig5p4.rst
    - SIRV_display.rst
    - fig6p24.rst
    - fig5p4.py
    - SIR_display.rst
    - fig4p7.rst
    - fig4p11.py
    - fig6p1.py
    - fig5p3.rst
    - fig1p5.rst
    - fig4p8.py
    - fig2p11.rst
    - weighted_graph
      - SIS_weighted.py
    - fig7p3.py
    - fig7p2.py
    - fig4p9.rst
    - fig7p4.rst
    - bipartite
      - bipartite.py
    - fig4p7.py
    - fig9p5.rst
    - fig1p2.py
    - fig4p1.py
    - fig6p4.py
    - SIS_weighted.rst
    - fig7p3.rst
    - SIRS.rst
    - fig4p5.py
    - SEIR.rst
    - fig4p5.rst
    - SIRS_heterogeneous.rst
    - fig11p7.py
    - SIS_change_tau.rst
    - fig4p1.rst
    - fig4p8.rst
    - fig4p13.rst
    - fig1p2.rst
    - fig9p5.py
    - SIRV_display.py
    - fig1p5.py
    - SIR_display.py
    - fig5p5.rst
    - fig6p2.py
    - fig4p10.py
    - fig6p4.rst
    - fig4p11.rst
    - SIS_display.py
    - fig5p2.rst
    - bipartite.rst
    - fig2p11.py
    - fig7p2.rst
    - fig9p4.rst
    - fig4p12.py
    - fig4p10.rst
    - fig4p9.py
    - fig6p2.rst
    - fig4p12.rst
    - fig3p2.rst
    - fig4p13.py
    - fig5p2.py
  - GettingStarted.rst
  - EoN.rst
  - paper
    - paper.md
    - paper.bib
  - Changes.rst
  - _build
    - html
      - _static
  - index.rst
  - conf.py
  - Examples.rst
  - _static

Springer Source Code

This repository accompanies Mathematics of Epidemics on Networks by Kiss, Miller, and Simon (Springer, 2017).

Cover image

It contains the EoN (Epidemics on Networks) python software accompanying the book.

Corrections

For corrections or to report an error to the content in the published book, see the file errata.md and follow instructions there.

To report a bug in the code please use the new issue option on the issues page.

Software Documentation

Documentation (including installation instructions) is available at http://epidemicsonnetworks.readthedocs.io/en/latest/

Software Releases

We released v1.0 on 9 Aug 2018

To see changes since v1.0, please look at our list of changes

We released v1.1 on 13 Dec 2019. This is the version described in our paper.

Contributions

We welcome new contributors. Please help test the code or suggest improvements.