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Simple deterministic models
SIR model
Python using SciPy
R using deSolve
R using odin
Julia
Octave
Scilab
C++
xppaut
VFGEN
Javascript
Javascript using Observable
SEIR model
Julia
R using deSolve
SIS model
Javascript using Observable
Scaling model
Julia
Python
R using deSolve
Simple stochastic models
Continuous time SIR
R
R using GillespieSSA
R using Rcpp
Julia
Discrete time SIR
R using odin
R using POMP
R using LibBi
Python
Julia
Discrete time SEIRD
R using odin
Final size of an epidemic
Exact recursive expressions
Original Matlab code
Julia
Octave
Scilab
R
Non-exponential passage times
Discrete Erlang SEIR model
Julia
R
Host-vector models
One host, one vector
Julia
N hosts, one vector
Julia
N hosts, M vectors
Julia
Macroparasite models
May and Anderson 1978 model
Julia
R using deSolve
Time-varying parameters
Seasonally forced deterministic model
R
Javascript using Observable
Semiparametric SIR model
Julia
R using pomp
Metapopulation models
Deterministic SEIR
R using odin
SIRS dynamics in a large population of households
Julia
Network models
An edge based SIR model on a configuration network
R
Javascript using Observable
An individual based model of pneumococcal transmission
R
An SIR model in London boroughs
R
Phylodynamic models
Simple coalescent model
R
Applications
Acute HIV infection
R
A model of HIV with two risk groups
R
A deterministic SEIR model of Ebola
Python using PyGOM
Python using SciPy
A stochastic, seasonal, discrete-time model of rotavirus
R using POMP
Keeling and Rohani 2008
Program 2.1
Original C
Original Fortran
Original Python
Original Matlab/Octave
Program 2.6: SEIR
R using deSolve
Julia
Program 3.1: SIS with risk groups
R using deSolve
Julia
Program 3.2: SIS with m risk groups
R using deSolve
Program 3.4: Age structured SEIR
R using deSolve
Program 4.4: Multi-host SEIR
R using deSolve
Bjornstad 2018
Chapter 1: Introduction
Original R code
Chapter 2: SIR
Original R code
Chapter 3: R0
Original R code
Chapter 4: FoI and age-dependent incidence
Original R code
Chapter 5: Seasonality
Original R code
Appendices
Style guide for notebooks
Models with time varying parameters
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