Second year practical students: click here for an SIR model written in R with a Runge-Kutta approximation (kindly written by Mike Bonsall).

Here are the handouts of four computer practicals in the (free) programming language R, together with the starting programs that are emailed to each student. They are aimed at students with no previous experience of computing or modelling. I have demonstrators’ copies, which have the answers in, available on request and would welcome feedback from anyone thinking of using these for their teaching.

BD2_1_Pr5.doc -- An introduction to R, how to execute a SI model that has been emailed to them, how to develop this into an SIR model, and understanding the Basic Reproductive Number of a disease.

BD2_1_Pr6.doc -- Introducing births and deaths into the SIR model, finding the critical immunisation threshold, and understanding the Effective Reproductive Number of a disease.

BD3_3&4.doc -- A simple macroparasite model. (file macro_for_students.r is emailed to the students.)

BD3_6.doc -- Introducing evolution into an SIR model: waning immunity and drug resistance. (file SIR_no_phi.r is emailed to the students.)

Also, here is a link to an on-line practical that uses an Individual Based Model approach to investigate the effect of social networks on disease dynamics.

Many thanks to Colin Harrower for helping design these R practicals, and to Ken Kahn and Howard Noble for writing the on-line practical for me as part of their excellent Modelling4All initiative.

PowerPoint and pdf files of four lectures on basic virology (BD2.1_lect1), viral pathogenesis (BD2.1_lect2), viral genetics (BD3.5_lect1) and the quasispecies concept (BD3.5_lect8) are here.

varese.tar is a link to the materials of a short course on modelling emergent virus disease that I gave recently at the University of Insubria, Varese, Italy (answers etc available on request).