This course is part of the Infectious Disease Modelling Specialization

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Nimalan Arinaminpathy

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Infectious Disease Modelling SpecializationImperial College London

About this Course

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The other two courses in this specialisation require you to perform deterministic modelling - in other words, the epidemic outcome is predictable as all parameters are fully known. However, this course delves into the many cases – especially in the early stages of an epidemic – where chance events can be influential in the future of an epidemic. So, you'll be introduced to some examples of such ‘stochasticity’, as well as simple approaches to modelling these epidemics using R. You will examine how to model infections for which such ‘population structure’ plays an important role in the transmission dynamics, and will learn some of the basic approaches to modelling vector-borne diseases, including the Ross-McDonald Model. 
Even if you are not designing and simulating mathematical models in future, it is important to be able to critically assess a model so as to appreciate its strengths and weaknesses, and identify how it could be improved. One way of gaining this skill is to conduct a critical peer review of a modelling study as a reviewer, which is an opportunity you'll get by taking this course.

Flexible deadlines

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Shareable Certificate

Earn a Certificate upon completion

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Coursera Labs

Includes hands on learning projects.

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Course 3 of 3 in the

Infectious Disease Modelling Specialization

Intermediate Level

Approx. 20 hours to complete

English

What you will learn

Distinguish between stochastic and deterministic models, explain when either are appropriate, and perform simple simulations of a stochastic model
Identify where it is important to incorporate population structure in a model and design and simulate a transmission model capturing such structure
Evaluate the assumptions behind the Ross MacDonald model, and code such a model using R to simulate the dynamics of a vector-borne disease
Critically evaluate a modelling study and communicate its strengths and weaknesses to a scientifically literate audience

Skills you will gain

Mathematical Model
R Programming
Infectious Diseases

Flexible deadlines

Reset deadlines in accordance to your schedule.

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Coursera Labs

Includes hands on learning projects.

Learn more about Coursera Labs

Course 3 of 3 in the

Infectious Disease Modelling Specialization

Intermediate Level

Approx. 20 hours to complete

English

Instructor

Nimalan Arinaminpathy

Faculty of Medicine, School of Public Health

10,006 Learners

4 Courses

Offered by

Imperial College London

Imperial College London is a world top ten university with an international reputation for excellence in science, engineering, medicine and business. located in the heart of London. Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.

Start working towards your Master's degree

This course is related to the 100% online Global Master of Public Health from Imperial College London. It will provide you with a preview of the topics, materials and instructors so you can decide if the full online degree program is right for you.

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Syllabus - What you will learn from this course

Week1

Week 1

7 hours to complete

Building on the SIR Model: Stochasticity

The other two courses in this specialisation have focused on performing deterministic modelling - that is, the epidemic outcome is predictable as all parameters are fully known. However, there are many cases, especially in the early stages of an epidemic, where chance events can be influential in the future of an epidemic. In this module, you will be introduced to some examples of such ‘stochasticity’, as well as, simple approaches to modelling these epidemics using R.

7 hours to complete

5 videos (Total 14 min), 8 readings

5 videos

Welcome to the Course1mAn Insider's View of IDM4mStochastic and Deterministic Models2mSimulating Stochasticity2mPopulations with Pre-Existing Immunity2m

8 readings

Welcome to Infectious Disease Modelling10mAbout the Infectious Disease Modelling Team10mGlossary10mModelling Infectious Disease Dynamics35mBuilding on the SIR Model3m The Story of MERS Coronavirus10mCalculating Incidence in a Deterministic Model45mThe Resurgence of Measles15m

Week2

Week 2

6 hours to complete

Building on the SIR model: Heterogeneity

In the basic deterministic SIR model, all susceptible individuals in a population are subject to the same risks of infection. However, there are many important infectious diseases where certain groups of the population account for a disproportionate amount of transmission: these are not always the same groups that bear the greatest amount of morbidity and mortality. In this module, you will examine how to model infections for which such ‘population structure’ plays an important role in the transmission dynamics.

6 hours to complete

2 videos (Total 7 min), 2 readings

Week3

Week 3

5 hours to complete

Building on the SIR model: Vector-borne Diseases

Many important diseases are not directly transmitted between hosts, but depend on ‘vectors’ to pass infection between hosts, for example biting insects. It is important to be able to extend the modelling approaches you have studied so far to capture these more complex forms of natural history. In this module, you will learn some of the basic approaches to modelling vector-borne diseases, including the Ross-McDonald model, which is a framework that provides an important foundation for such diseases.

5 hours to complete

6 videos (Total 25 min), 1 reading

Week4

Week 4

2 hours to complete

Assignment: Modelling Study Critique

Even if you are not designing and simulating mathematical models in future, it is important to be able to critically assess a model, to appreciate its strengths and weaknesses, and to identify how it could be improved. One way of gaining this skill is to conduct a critical peer review of a modelling study in the position of a reviewer evaluating it for publication in a journal. This module is reserved for the completion of your assignment - for you to apply the knowledge and skills you've developing throughout this specialisation.

2 hours to complete

Reviews

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TOP REVIEWS FROM BUILDING ON THE SIR MODEL

by DGJun 19, 2021

a great follow up to the R coding course and a good entree into the world of public health

by IHSep 20, 2020

A great learning opportunity. Advanced content presented in a convincing and understandable manner. Simply amazing.

by DTAug 13, 2020

I have found it useful for increasing my insights into infectious disease modelling.

by GCJun 23, 2020

I thought it was clear, the syntax problems were about the same topic and needed the solution talked about in the videos. The subject was completely covered. I already recommended it to like 5 people.

View all reviews

About the Infectious Disease Modelling Specialization

Mathematical modelling is increasingly being used to support public health decision-making in the control of infectious diseases. This specialisation aims to introduce some fundamental concepts of mathematical modelling with all modelling conducted in the programming language R - a widely used application today.

The specialisation will suit you if you have a basic working knowledge of R, but would also like to learn the necessary basic coding skills to write simple mathematical models in this language. While no advanced mathematical skills are required, you should be familiar with ordinary differential equations, and how to interpret them. You'll receive clear instruction in the basic theory of infectious disease modelling alongside practical, hands-on experience of coding models in the programming language R.

Frequently Asked Questions

When will I have access to the lectures and assignments?
Access to lectures and assignments depends on your type of enrollment. If you take a course in audit mode, you will be able to see most course materials for free. To access graded assignments and to earn a Certificate, you will need to purchase the Certificate experience, during or after your audit. If you don't see the audit option:
The course may not offer an audit option. You can try a Free Trial instead, or apply for Financial Aid.
The course may offer 'Full Course, No Certificate' instead. This option lets you see all course materials, submit required assessments, and get a final grade. This also means that you will not be able to purchase a Certificate experience.
What will I get if I subscribe to this Specialization?
When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.
Is financial aid available?
Yes. In select learning programs, you can apply for financial aid or a scholarship if you can’t afford the enrollment fee. If fin aid or scholarship is available for your learning program selection, you’ll find a link to apply on the description page.

More questions? Visit the Learner Help Center.

Building on the SIR Model

About this Course

What you will learn

Skills you will gain