Journal Club - 'The construction of next-generation matrices for compartmental epidemic models'
The journal club is a forum for MfPH Next Generation members to discus journal articles or pre-prints that interest them.
The construction of next-generation matrices for compartmental epidemic models, O. Diekmann, J. A. P. Heesterbeek and M. G. Roberts, Published:05 November 2009
Article can be accessed here: https://doi.org/10.1098/rsif.2009.0386
This session will be chaired by Dr. Martin Grunnill
"The journal club this week is on deriving R0. The journal article is a very good piece on the mathematical methods, but the focus of the journal club will be on the 2nd file. The file is a jupyter notebook demonstrating how the methods can be employed in two different python packages. The 2 examples both follow an example outlined in the journal article. Below are iinstallation instructions outlining how to get everything setup."
SETUP FOR JUPYTER NOTEBOOK RUNNING SYMPY & PYGOM
Installing Anaconda (Python)
Instructions on installing anaconda for python can be found at:
https://docs.conda.io/projects/conda/en/latest/user-guide/install/
Installing Jupyter Notebooks
With Anaconda installed open Anaconda Prompt (or Terminal if you are using Mac or Linux) and type the command: conda install -c conda-forge notebook
Installing Sympy
With Anaconda installed open Anaconda Prompt (or Terminal if you are using Mac or Linux) and type the command: conda install -c conda-forge sympy
Installing PyGOM
1. Navigate to https://github.com/MGrunnill/pygom/tree/MG-Loss_funcs and download PyGOM. A zipped version can be downloaded from https://github.com/MGrunnill/pygom/archive/refs/heads/MG-Loss_funcs.zip.
2. Once unzipped to a directory or downloaded open the setup.py file and change line 82 of the from “use_scm_version=True,” to “version=0.17,”. Then save and close file.
3. Open Anaconda Prompt (or Terminal if you are using Mac or Linux) and type the command “cd “ followed by the directory you unzipped/downloaded PyGOM to. Then enter the command “python setup.py install”, or if using Mac/Linux “sudo python setup.py install”.
To access Jupyter notebook
1. Open anaconda prompt (or Terminal if you are using Mac or Linux) and enter command “jupyter notebook”.
2. If it is your first time using jupyter notebooks you will be prompted to select a web browser.
3. Navigate to where you have downloaded the notebook in the selected browser and open the notebook.