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Model fitting and inference for infectious disease dynamics

Overview
Overview - Model fitting and inference for infectious disease dynamics
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Course dates: 25 - 28 July 2017

A short course taught by members of the Centre for the Mathematical Modelling of Infectious Diseases.

There is a growing demand for mathematical modellers in public health to explain observed disease trends and predict the outcome of interventions, often by synthesising information from different data sources. At the same time, increasing computational power and methodological advances are providing exciting opportunities to fit ever more complex mechanistic models to data. In light of the speed of methodological advances and the broad nature of the field, the task of choosing from the available methods and packages, as well as putting them into practice, can be daunting.

With this short course 'linking theory to data: modern methods for fitting models of infectious disease dynamics', we aim to bridge the gap between state-of-the-art statistical inference methods and training in infectious disease modelling. We will introduce key terminology from frequentist and Bayesian approaches as well as methods ranging from Markov-Chain Monte Carlo (MCMC) to particle filters and Approximate Bayesian Computation (ABC).

Our aim is to equip students and researchers using infectious disease models with the theoretical background needed to better understand the literature, as well as with practical knowledge of the tools available to put these methods into practice.

Course objectives
Course objectives - Model fitting and inference for infectious disease dynamics
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Teaching methods and course materials

The course consists of computer practical sessions interspersed with introductory lectures. The practical sessions will use R, which is freely available at http://cran.r-project.org/. Participants are encouraged to bring their own laptop, but where this is not possible a laptop will be made available.

The course lasts four days. On the first day we will introduce the conceptual underpinning of inference using dynamic models and apply this to model fitting using deterministic models in R. On the second day, we will extend the concepts and methods discussed on day one to stochastic models and implement methods for matching these to data in R. On the third day, we will discuss the landscape of available packages (not limited to R) for using the methods introduced on day one and two and provide an overview of further methods available as well as a summary and outlook.

Target audience

This course is aimed at students and researchers who are working with dynamic models of infectious disease (i.e., broadly based on the SIR model) and would like to learn about state-of-the art methods of matching these to data. The course is limited to 24 participants.

Prerequisites

In order to benefit from the course, basic knowledge of infectious disease modelling is required. Participants are expected to have a good understanding of key concepts outlined in Introduction to Infectious Disease Modelling and Its Applications. Moreover, some experience in using R is essential. Those who have never used R but have experience with other mathematical packages (e.g., Matlab, Mathematica) and/or programming languages should also be able to benefit from the course, but would improve their experience by familiarising themselves with the basics of R syntax ahead of the course.

How to apply
How to apply - Model fitting and inference for infectious disease dynamics
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Applying for this course

We are no longer accepting applications for this course.

Visas

The student is responsible for obtaining any visa or other permissions to attend the course, and is encouraged to start the application process as early as possible as obtaining a visa for the UK can sometimes take a long time. The Short Courses team, in the Registry, can provide supporting documentation if requested.

Accommodation and meals

The School cannot provide accommodation for participants. A list of hotels and other accommodation located in the vicinity of the School can be provided on request to Registry. Lunch can be purchased from the School refectory. Evening meals are not catered for at the School, but there is a large choice of restaurants and coffee shops nearby.

The London School of Hygiene & Tropical Medicine is committed to improving global health through its programme of short and full-time postgraduate study.

Please note:

  • If you have been offered a place on the course you will not be able to register without bringing formal ID (Passport) and without having obtained the correct visa.
  • It is essential that you read the current visa requirements for short course students.
  • The School may cancel courses two weeks before the first day of the course if numbers prove insufficient.  In those circumstances, course fees will be refunded.
  • The School cannot accept responsibility for accommodation, travel and other losses incurred as a result of the course being cancelled.