The basics of the R statistical progamming language

[After you have read through this module, and have downloaded and worked through the provided R examples, you should be proficient enough in R to be able to download and run other R scripts that will be provided in other posts on this site. You should understand the basics of good programming practices (in any language, not just R). You will also have learned how to read data in a file into a table in R, and produce a plot.]

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Why use R for modelling?

I have programmed in many different computing and scripting languages, but the ones I most commonly use on a day to day basis are C++, Fortran, Perl, and R (with some Python, Java, and Ruby on the side).  In particular, I use R every day because it is not only a programming language, but also has graphics and a very large suite of statistical tools. Connecting models to data is a process that requires statistical tools, and R provides those tools, plus a lot more.

Unlike SAS, Stata, SPSS, and Matlab, R is free and open source (it is hard to beat a package that is more comprehensive than pretty much any other product out there and is free!).

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Epidemic modelling with compartmental models using R

[After reading through this module you should have an intuitive understanding of how infectious disease spreads in the population, and how that process can be described using a compartmental model with flow between the compartments.  You should be able to write down the differential equations of a simple disease model, and you will learn in this module how to numerically solve those differential equations in R to obtain the model estimate of the epidemic curve]

An excellent reference book with background material related to these lectures is Mathematical Epidemiology by Brauer et al. 

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Introduction

Models of disease spread can yield insights into the mechanisms and dynamics most important to the spread of disease (especially when the models are compared to epidemic data).  With this improved understanding, more effective disease intervention strategies can potentially be developed. Sometimes disease models are also used to forecast the course of an epidemic, and doing exactly that for the 2009 pandemic was my introduction to the field of computational epidemiology.

There are lots of different ways to model epidemics, and there are several modules on this site on the topic, but let’s begin with one of the simplest epidemic models for an infectious disease like influenza: the Susceptible, Infected, Recovered (SIR) model.

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SIR infectious disease model with age classes

[After reading through this module, students should have an understanding of contact dynamics in a population with age structure (eg; kids and adults). You should understand how population age structure can affect the spread of infectious disease. You should be able to write down the differential equations of a simple SIR disease model with age structure, and you will learn in this module how to solve those differential equations in R to obtain the model estimate of the epidemic curve]

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Introduction

In a previous module I discussed epidemic modelling with a simple Susceptible, Infected, Recovered (SIR) compartmental model.  The model presented had only a single age class (ie; it was homogenous with respect to age).  But in reality, when we consider disease transmission, age likely does matter because kids usually make more contacts during the day than adults. The differences in contact patterns between age groups can have quite a profound impact on the model estimate of the epidemic curve, and also have implications for development of optimal disease intervention strategies (like age-targeted vaccination, social distancing, or closing schools).
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SIR modelling of influenza with a periodic transmission rate

[After going through this module, students will be familiar with time-dependent transmission rates in a compartmental SIR model, will have explored some of  the complex dynamics that can be created when the transmission is not constant, and will understand applications to the modelling of influenza pandemics.]

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Introduction

Influenza is a seasonal disease in temperate climates, usually peaking in the winter.  This implies that the transmission of influenza is greater in the winter (whether this is due to increased crowding and higher contact rates in winter, and/or due to higher transmissibility of the virus due to favorable environmental conditions in the winter is still being discussed in the literature).  What is very interesting about influenza is that sometimes summer epidemic waves can be seen with pandemic strains (followed by a larger autumn wave).  An SIR model with a constant transmission rate simply cannot replicate the annual dual wave nature of an influenza pandemic.

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Stochastic epidemic modelling with Agent Based Models

[After reading this module, you will be aware of the limitations of deterministic epidemic models, like the SIR model, and understand when stochastic models are important.  You will be introduced to three different methods of stochastic modelling, and understand the appropriate applications of each. By the end of this module, you will be able to implement a simple Agent Based stochastic model in R.]

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Fitting the parameters of an SIR model to influenza data using Least Squares and the Monte Carlo parameter sweep method

[After reading this module, students should understand the Least Squares goodness-of-fit statistic.   Students will be able to read an influenza data set from a comma delimited file into R, and understand the basic steps involved in a Monte Carlo parameter sweep method to fit an SIR model to the data to estimate the R0 of the influenza strain by minimizing the Least Squares statistic.  Students will be aware that parameter estimates have uncertainties associated with them due to stochasticity (randomness) in the data.]

A really good reference for statistical data analysis (including fitting) is Statistical Data Analysis, by G.Cowan.

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Introduction

When a new virus starts circulating in the population, one of the first questions that epidemiologists and public health officials want answered is the value of the reproduction number of the spread of the disease in the population (see, for instance, here and here).

The length of the infectious period can roughly be estimated from observational studies of infected people, but the reproduction number can only be estimated by examination of the spread of the disease in the population.  When early data in an epidemic is being used to estimate the reproduction number, I usually refer to this as “real-time” parameter estimation (ie; the epidemic is still ongoing at the time of estimation).

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