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Building on the SIR Model

Nimalan Arinaminpathy

Nimalan Arinaminpathy

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.

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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.

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What's inside

Syllabus

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.

Read more

Traffic lights

Read about what's good

what should give you pause

and possible dealbreakers

Explores stochasticity, which is a normal element of epidemic science

Taught by Nimalan Arinaminpathy, who is recognized for their work in Epidemiology

Examines 'population structure', which can influence transmission dynamics

Develops vector-borne disease modeling skills, which is highly relevant in certain biomedical fields

Culminates in a module reserved for assignment and modeling study critique

Requires a foundation in mathematical modeling

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Reviews summary

Advanced epidemic modeling with r

According to students, this course provides a strong expansion on the SIR model, delving into crucial advanced topics like stochasticity, population heterogeneity, and vector-borne diseases. Learners found the content to be highly relevant and practical, particularly benefiting from the application of concepts using R programming. The unique Modelling Study Critique assignment is a consistent highlight, praised for developing critical thinking skills and insight into academic review. While generally receiving largely positive feedback, some suggest a solid foundation in R and statistics is beneficial for a smoother learning experience, as practical exercises can be challenging for those new to R. Overall, it's considered an essential course for serious epidemiology and modeling students.

Utilizes R for hands-on modeling, building tangible skills.

"The R programming examples are practical and the critical peer review assignment is an excellent way to consolidate learning."

"The practical applications with R were spot on, providing tangible skills."

"The R coding examples were generally helpful, though I felt some parts could benefit from more detailed commentary."

"The focus on applying models using R is very practical."

Unique assignment fosters essential critical thinking skills.

"The critical peer review assignment to be an excellent way to consolidate learning and think like a researcher."

"The assignment was challenging but incredibly valuable for developing a critical eye."

"The peer review assignment is unique and genuinely helps with critical thinking."

"The assignment fosters important critical thinking skills."

Expands understanding with advanced epidemiological concepts.

"This course significantly deepened my understanding of epidemic modeling beyond the basic SIR."

"A crucial course for anyone in epidemic modeling. It covers aspects often overlooked in basic courses, like stochasticity and heterogeneity."

"Excellent course! The shift from deterministic to stochastic modeling was crucial and handled superbly."

"This course truly expands on the SIR model, covering essential aspects like stochasticity and population structure."

Strong statistics and R background are highly recommended for success.

"I struggled a bit with the R exercises. They felt a bit disconnected from the theoretical explanations at times..."

"I found this course quite difficult without a very strong background in statistics and R."

"More foundational review or clearer warnings about prerequisites would be helpful."

"The practical coding aspect could be improved for those not expert in R."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Building on the SIR Model with these activities:

Review of Probability and Statistics

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A solid foundation in Probability and Statistics is essential for understanding and working with stochastic epidemic models.

Browse courses on Probability

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Review your old class notes or textbook on Probability and Statistics
Take a practice quiz on Probability and Statistics

Review the SIR Model

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The SIR model will be the foundation of the epidemic models you'll study in this course.

Browse courses on SIR model

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Read your old class notes or textbook on the SIR Model
Solve some basic practice problems using the SIR Model

Create a course notes repository

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Organizing course materials improves accessibility, recall, and retention.

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Create a folder or notebook for your course materials
Add your class notes, assignments, and quizzes to the folder or notebook
Review your materials regularly

Four other activities

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Show all seven activities

Modelling simple epidemics using R

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The first module introduces the use of R for modelling epidemics. Practice with R will help you make the most of this module.

Browse courses on R Programming

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Install R and RStudio on your computer
Complete a basic R tutorial
Follow along with the R code used in the course materials

Form a peer study group

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Working with peers improves understanding, provides support, and aids in retaining information.

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Find other students taking the same course
Meet regularly to discuss the course material
Work together on assignments and projects

Vector-borne disease model development

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The final module will focus on vector-borne disease modelling. A tutorial on the Ross-McDonald Model will jumpstart your learning for this module.

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Find a tutorial on the Ross-McDonald model
Follow along with the tutorial, taking notes as you go
Try to implement the model yourself in R

Simulate an epidemic outbreak in R

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To fully grasp the concepts covered in this course, you will need to apply them to real-world situations. Simulating an epidemic outbreak will provide valuable hands-on experience.

Browse courses on R Programming

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Simulate the model for different parameter values
Choose a simple epidemic model, such as the SIR model
Implement the model in R
Analyze the simulation results

Career center

Learners who complete Building on the SIR Model will develop knowledge and skills that may be useful to these careers:

Public Health Epidemiologist

Public Health Epidemiologists investigate the factors that determine the frequency of diseases within a population, and use this information to develop programs to prevent and control diseases. This course provides a strong foundation in the principles of epidemiology and mathematical modeling, which are essential skills for epidemiologists. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for public health epidemiologists working in the field.

See salaries and explore the career path for Public Health Epidemiologist

Data Scientist

Data Scientists use data to solve problems and make informed decisions. This course provides a strong foundation in the principles of data science, including data analysis, visualization, and modeling. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for data scientists working in the healthcare field.

See salaries and explore the career path for Data Scientist

Operations Research Analyst

Operations Research Analysts use mathematical models to solve problems and improve decision-making in a variety of industries. This course provides a strong foundation in the principles of operations research, including modeling, optimization, and simulation. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for operations research analysts working in the healthcare field.

See salaries and explore the career path for Operations Research Analyst

Biostatistician

Biostatisticians use statistical methods to design and analyze studies that investigate the effects of medical treatments and interventions. This course provides a strong foundation in the principles of biostatistics, including study design, data analysis, and interpretation. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for biostatisticians working in the field.

See salaries and explore the career path for Biostatistician

Quantitative Analyst

Quantitative Analysts use mathematical and statistical models to analyze financial data and make investment decisions. This course provides a strong foundation in the principles of quantitative analysis, including financial modeling, risk management, and portfolio optimization. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for quantitative analysts working in the healthcare field.

See salaries and explore the career path for Quantitative Analyst

Health Policy Analyst

Health Policy Analysts research and analyze health policy issues and develop recommendations for policy changes. This course provides a strong foundation in the principles of health policy analysis, including health economics, health law, and health ethics. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for health policy analysts working in the healthcare field.

See salaries and explore the career path for Health Policy Analyst

Medical Physicist

Medical Physicists use physics principles to develop and use medical imaging technologies and radiation therapy treatments. This course provides a strong foundation in the principles of medical physics, including radiation physics, imaging techniques, and treatment planning. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for medical physicists working in the healthcare field.

See salaries and explore the career path for Medical Physicist

Clinical Research Scientist

Clinical Research Scientists design and conduct clinical trials to investigate the effects of new medical treatments and interventions. This course provides a strong foundation in the principles of clinical research, including study design, data analysis, and interpretation. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for clinical research scientists working in the healthcare field.

See salaries and explore the career path for Clinical Research Scientist

Public Health Nurse

Public Health Nurses promote health and prevent disease in communities. This course provides a strong foundation in the principles of public health nursing, including health assessment, health promotion, and disease prevention. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for public health nurses working in the healthcare field.

See salaries and explore the career path for Public Health Nurse

Health Educator

Health Educators promote health and prevent disease through education and outreach programs. This course provides a strong foundation in the principles of health education, including behavior change theory, communication strategies, and program evaluation. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for health educators working in the healthcare field.

See salaries and explore the career path for Health Educator

Science Writer

Science Writers communicate scientific information to the public through writing and other media. This course provides a strong foundation in the principles of science writing, including scientific communication, journalism, and public relations. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for science writers working in the healthcare field.

See salaries and explore the career path for Science Writer

Medical Librarian

Medical Librarians manage and provide access to medical information resources for healthcare professionals and patients. This course provides a strong foundation in the principles of medical librarianship, including medical information retrieval, database management, and consumer health information. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for medical librarians working in the healthcare field.

See salaries and explore the career path for Medical Librarian

Laboratory Scientist

Laboratory Scientists perform laboratory tests and analyze results to diagnose and treat diseases. This course provides a strong foundation in the principles of laboratory science, including clinical chemistry, microbiology, and immunology. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for laboratory scientists working in the healthcare field.

See salaries and explore the career path for Laboratory Scientist

Health Information Manager

Health Information Managers manage and analyze health information data to improve healthcare quality and efficiency. This course provides a strong foundation in the principles of health information management, including health information systems, data analysis, and quality improvement. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for health information managers working in the healthcare field.

See salaries and explore the career path for Health Information Manager

Medical Record Technician

Medical Record Technicians maintain and manage medical records for healthcare facilities. This course provides a strong foundation in the principles of medical records management, including medical terminology, coding, and filing. The course also covers topics such as population structure and vector-borne diseases, which are important considerations for medical record technicians working in the healthcare field.

See salaries and explore the career path for Medical Record Technician

Reading list

We've selected six books that we think will supplement your learning. Use these to develop background knowledge, enrich your coursework, and gain a deeper understanding of the topics covered in Building on the SIR Model.

Cover image

Cover image

Estimation of Mortality Rates in Stage-Structured...

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Provides a comprehensive overview of the mathematical modelling of ecological systems. It would be a valuable reference for anyone interested in learning more about the mathematical aspects of ecology, including the modelling of infectious diseases.

Estimation of Mortality Rates in Stage-Structured...

Estimation of Mortality Rates in Stage-Structured...

Cover image

Cover image

Statistical Models in Epidemiology

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Provides a comprehensive overview of modern epidemiology, including the design, conduct, and analysis of epidemiologic studies. It would be a valuable reference for anyone interested in learning more about the methods used in epidemiology.

Statistical Models in Epidemiology

Statistical Models in Epidemiology

Cover image

Cover image

Critical Needs and Gaps in Understanding Prevention...

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A comprehensive report from the Institute of Medicine on vector-borne diseases. It covers the biology of vectors, the transmission of diseases, and the public health response.

Critical Needs and Gaps in Understanding Prevention...

Critical Needs and Gaps in Understanding Prevention...

Cover image

Cover image

A Resource-Based Habitat View for Conservation

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Provides a comprehensive overview of the mathematical modelling of population ecology. It would be a valuable reference for anyone interested in learning more about the mathematical aspects of population ecology, including the modelling of infectious diseases.

A Resource-Based Habitat View for Conservation:...

Cover image

Cover image

The Cambridge Dictionary of Statistics

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Provides an introduction to the statistical methods used in epidemiology. It would be a valuable resource for anyone interested in learning more about the statistical aspects of epidemiology.

The Cambridge Dictionary of Statistics

The Cambridge Dictionary of Statistics

Cover image

Cover image

Neuroimaging Workflow Design and Data-Mining

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A comprehensive textbook on spatial epidemiology. It includes chapters on spatial data analysis, disease mapping, and outbreak investigation.

Neuroimaging Workflow Design and Data-Mining

Neuroimaging Workflow Design and Data-Mining

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Level

Intermediate

Via

Coursera

Institution

Imperial College London

Instructor

Nimalan Arinaminpathy

Language

English

Transcripts

Español Français Português Deutsch Italiano 中文 العربية 한국어 日本語 हिंदी Nederlands Svenska Pусский Türkçe Polski Ελληνικά українська мова Bahasa Indonesia ไทย қазақша

This course belongs to a collection called Infectious Disease Modelling. It's comprised of three courses:

Interventions and Calibration
Building on the SIR Model (viewing)
Developing the SIR Model

Traffic lights

Read about what's good

what should give you pause

and possible dealbreakers

Explores stochasticity, which is a normal element of epidemic science

Taught by Nimalan Arinaminpathy, who is recognized for their work in Epidemiology

Examines 'population structure', which can influence transmission dynamics

Develops vector-borne disease modeling skills, which is highly relevant in certain biomedical fields

Culminates in a module reserved for assignment and modeling study critique

Requires a foundation in mathematical modeling

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