Model code from the epicookbook, an online textbook made with Markdown/Jekyll and Jupyter Notebooks. The original notebooks can be found here and here or here. Code is provided in multiple languages and libraries, including R, Python, Julia, and others. As the authors state:
This project aims to collate mathematical models of infectious disease transmission, with implementations in R, Python, and Julia.
Categories of models include:
- Simple deterministic models using ordinary differential equations
- Standard compartmental models
- Non-exponential distributions of infectious periods
- Delay differential equations
- Method of stages
- Infection-age models
- Simple stochastic models
- Gillespie’s stochastic simulation algorithm
- Discrete time
- Stochastic differential equations
- Models with time-varying parameters
- Spatial models
- Network models
- Pair approximations
- Edge based models
- Applications to specific disease systems
The directory structure of the model folder is provided below (using the Bash tree command):
models/
├── applications
│ ├── acute_hiv.r
│ ├── deterministic_seir_ebola_pygom.py
│ ├── deterministic_seir_ebola_scipy.py
│ ├── hiv_2_risk_groups.r
│ └── stochastic_seasonal_discrete_t_rotavirus.r
├── bjornstad_2018
│ ├── chapter1.r
│ ├── chapter2_sir.r
│ ├── chapter3_r0.r
│ ├── chapter4_foi_age_incidence.r
│ └── chapter5_seasonality.r
├── epidemic_final_size
│ ├── ere_si4r.jl
│ ├── ere_si4r.m
│ ├── ere_si4r.sce
│ ├── ere_sir.jl
│ ├── ere_sir.m
│ ├── ere_sir.r
│ └── ere_sir.sce
├── host_vector_models
│ ├── 1host_1vector.jl
│ ├── nhost_1vector.jl
│ └── nhost_mvector.jl
├── keeling_rohani_2008
│ ├── program_2_1.c
│ ├── program_2_1.f90
│ ├── program_2_1.m
│ ├── program_2_1.py
│ ├── program_2_6_seir.jl
│ ├── program_2_6_seir.r
│ ├── program_3_1_sis.jl
│ ├── program_3_1_sis.r
│ ├── program_3_2_sis.r
│ ├── program_3_4_age_structured_seir.r
│ └── program_4_4_multi_seir.r
├── metapopulation_models
│ ├── deterministic_seir.r
│ └── large_population_sirs.jl
├── microparasite_models
│ ├── may_anderson_1978.jl
│ └── may_anderson_1978.r
├── network_models
│ ├── edge_based_sir.js
│ ├── edge_based_sir.r
│ ├── london_sir.r
│ └── pneumococcal_ibm.r
├── nonexponential_passage_times
│ ├── discrete_erlang_sir.jl
│ └── discrete_erlang_sir.r
├── phylodynamics
│ └── simple_coalescent.r
├── simple_deterministic_models
│ ├── scaling
│ │ ├── scaling.jl
│ │ ├── scaling.py
│ │ └── scaling_desolve.r
│ ├── seir
│ │ ├── seir.jl
│ │ └── seir_desolve.r
│ ├── sir
│ │ ├── sir.cpp
│ │ ├── sir.jl
│ │ ├── sir.js
│ │ ├── sir.m
│ │ ├── sir.py
│ │ ├── sir.sce
│ │ ├── sir.vf
│ │ ├── sir.xpp
│ │ ├── sir_desolve.r
│ │ └── sir_odin.r
│ └── sis
│ └── sis.js
├── simple_stochastic_models
│ ├── continuous_t_sir
│ │ ├── ssir.jl
│ │ ├── ssir.r
│ │ ├── ssir_gillespie.r
│ │ └── ssir_rcpp.r
│ ├── discrete_t_seird
│ │ └── seird_odin.r
│ └── discrete_t_sir
│ ├── ssir.jl
│ ├── ssir.py
│ ├── ssir_libbi.r
│ ├── ssir_odin.r
│ └── ssir_pomp.r
└── time_varying_parameters
├── seasonally_forced_deterministic.js
├── seasonally_forced_deterministic.r
├── semiparametric_sir.jl
└── semiparametric_sir.r