3/17/2023 0 Comments Datathief matlabThis is an R package containing multiple Infectious Disease Epidemiology models that the user/student can run through a graphical user interface.ĭSAIRM - Dynamical Systems Approach to Immune Response Modeling. SoftwareĭSAIDE - Dynamical Systems Approaches to Infectious Disease Epidemiology. Them independently from any of my courses. I use the materials in this section for several of the classes and workshops I teach. Details about the mathematical model can be found in Handel et al (2006) PLoS Comp Bio. Note that this uses the lightspeed collection of Matlab functions.Ĭompensatory Mutations - (sparsely documented) Matlab and Fortran programs to simulate the evolution and spread of drug resistance through compensatory mutations. A version of this code was used in Handel and Rozen 2009 BMC Evo Bio. The simulation is described and used inīacteria evolution simulation - A Matlab program that simulates the evolution of a bacterial population in repeated exponential growth and serial dilution cycles. The code simulates gap junction mediated antigen transport during the local spread of virus and clearance by CTL. Gapjunction ABM - An agent-based simulation, written for the freely available Netlogo platform. A version of this code was used in Handel et al. Resimmcode.m - A short Matlab program that simulates the dynamics of bacteria and drugs during emergence of resistance. tuberculosis latency.Īvian flu - a collection of R scripts and accompanying data to do the various analyses described in Handel et al. TB Persistence - A collection of R scripts to run the simulations described in our 2014 PLoS One publication Modeling the potential impact of host population survival on the evolution of M. The results are described in Houben et al. TB-MAC UGA Model - A file containing the R code and description of the model that was used by us to produce the results described in a multi-model project on TB intervention analysis. The manuscript describing this work is Handel et al 2019 IJTLD. TB Cough duration analysis - A zip file containing various supplementary R scripts and codebooks for a superspreading/supercoughing study in TB patients. That’s especially true for anything Matlab or Fortran since I haven’t used either in years. But my time is limited, and for a lot of the old programs, I might not even remember anymore what exactly I did. If you need help understanding certain programs, I will try to help. Feel free to use and modify the programs any way you want. Some of the code is relatively well documented, some isn’t. You can get the publications from the publication section of this webpage. To allow as much access and reproducibility to our work as possible, we link here to a collection of programs, scripts and descriptions to produce results in various publications. In the past, this was not always possible. In recent years, we made sure that for our publications, all code is supplied as supplementary material. This page provides brief descriptions and links to various tools we produced or use for our research and teaching.
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