Python Programs for Modelling Infectious Diseases book
chengjun wang
Python Programs for Modelling Infectious Diseases book
Here you can find the Python Programs for the Book of M. Keeling & P. Rohani "Modeling Infectious Diseases in Humans and Animals". There is a website with on-line material for the book, where you can find the programs and the background of each program in C++, FORTRAN and Matlab. These Python programs were contributed to the on-line material and the code will be soon available on it.
In this section of the wiki you will find the programs and the graphical results by chapter of the book with the name and the equations of the model and the page number of the book where you can look for more information. The programs were written as scripts that can be run as is, including all the parameters provided from the on-line material. They were not written as loadable functions or libraries that can be used from other programs, since they have a demonstrating role. In this way, even readers, that have no or small experience with Python, can use the programs. The readers, who want to experiment with different starting conditions, can change the parameters in the script and re-run it. In some cases, where using different starting parameters has a special effect, alternative set(s) of parameters were provided in the scripts, along with their results, and the reader should advise the comments of the programs.Python 2.5.x, NumPy 1.0.4 or 1.1.0, SciPy 0.6.0 and Matplotlib 0.92.x or 0.98.x are required. The programs are under GNU GPL license. For Licenses and Copyright issues please advise the special DeductiveThinking_Wiki:Copyrights section. The Programs by chapter are:
- Chapter 2 Introduction to Simple Epidemic Model
- Program 2.1 Simple SIR (without births and deaths)
- Program 2.2 SIR model with births and deaths
- Program 2.3 SIR model with disease induced mortality and density dependent transmission
- Program 2.4 SIR model, disease induced mortality and frequency dependent transmission
- Program 2.5 SIS model without births or deaths
- Program 2.6 SEIR model with births and deaths
- Program 2.7 SIR with a carrier state
- Chapter 3 Host Heterogeneities
- Program 3.1 SIS model with high/low risk groups
- Program 3.2 SIS model with n risk groups
- Program 3.3 SIR model with children/adult age groups
- Program 3.4 SEIR model with n age groups and yearly aging
- Program 3.5 SEIR model with multiple E and I classes
- Chapter 4 Multi-Pathogen/Multi-Host Models
- Program 4.1 SIR model with partial immunity
- Program 4.2 Partial immunity model that cycles
- Program 4.4 SIR model for mosquito vectors
- Chapter 5 Temporally Forced Models
- Program 5.1 SIR model with sinusoidal forcing
- Program 5.2 SIR model with corrected term-time forcing
- Program 5.3 SIR model with sinusoidal births
- Program 5.4 Rabbit Hemorrhagic Disease model
- Chapter 6 Stochastic Dynamics
- Program 6.1 SIR model with Constant additive noise
- Program 6.2 SIR model with Scaled additive noise
- Program 6.3 SIS model with demographic stochasticity
- Program 6.4 SIR model with demographic stochasticity
- Program 6.5 SIR model with tau leap method
- Program 6.6 SIR model with two types of imports
- Chapter 7 Spatial Models
- Program 7.1 SIR metapopulation model for animals
- Program 7.2 SIR metapopulation model for humans
- Program 7.3 Coupled lattice model with commuter-like coupling
- Program 7.4 Forest fire model
- Program 7.8 Pairwise SIS approximation model
--Ilias.soumpasis 18:08, 11 October 2008 (UTC)
Cheng-Jun Wang
Web Mining Lab
Department of Media and Communication
City University of Hong Kong.
Room 5013, 18 Tat Hong Avenue, Run Run Shaw Creative Media Centre
Kowloon. Hong Kong
Email: wang...@gmail.com; cheng...@student.cityu.edu.hk
Mobile: +852-96442905
chengjun wang
Cheng-Jun Wang
Web Mining Lab
Department of Media and Communication
City University of Hong Kong.
Room 5013, 18 Tat Hong Avenue, Run Run Shaw Creative Media Centre
Kowloon. Hong Kong
Email: wang...@gmail.com; cheng...@student.cityu.edu.hk
Mobile: +852-96442905
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