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Survival Analysis in R for Public Health

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Survival Analysis in R for Public Health

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4.5

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Intermediate level

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1 week at 10 hours a week
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Gain insight into a topic and learn the fundamentals.
4.5

331 reviews

Intermediate level

Recommended experience

Flexible schedule
1 week at 10 hours a week
Learn at your own pace
90%
Most learners liked this course

What you'll learn

  • Run Kaplan-Meier plots and Cox regression in R and interpret the output

  • Describe a data set from scratch, using descriptive statistics and simple graphical methods as a necessary first step for more advanced analysis

  • Describe and compare some common ways to choose a multiple regression model

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Assessments

9 assignments

Taught in English

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This course is part of the Statistical Analysis with R for Public Health Specialization
When you enroll in this course, you'll also be enrolled in this Specialization.
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There are 4 modules in this course

Welcome to Survival Analysis in R for Public Health!

The three earlier courses in this series covered statistical thinking, correlation, linear regression and logistic regression. This one will show you how to run survival – or “time to event” – analysis, explaining what’s meant by familiar-sounding but deceptive terms like hazard and censoring, which have specific meanings in this context. Using the popular and completely free software R, you’ll learn how to take a data set from scratch, import it into R, run essential descriptive analyses to get to know the data’s features and quirks, and progress from Kaplan-Meier plots through to multiple Cox regression. You’ll use data simulated from real, messy patient-level data for patients admitted to hospital with heart failure and learn how to explore which factors predict their subsequent mortality. You’ll learn how to test model assumptions and fit to the data and some simple tricks to get round common problems that real public health data have. There will be mini-quizzes on the videos and the R exercises with feedback along the way to check your understanding. Prerequisites Some formulae are given to aid understanding, but this is not one of those courses where you need a mathematics degree to follow it. You will need basic numeracy (for example, we will not use calculus) and familiarity with graphical and tabular ways of presenting results. The three previous courses in the series explained concepts such as hypothesis testing, p values, confidence intervals, correlation and regression and showed how to install R and run basic commands. In this course, we will recap all these core ideas in brief, but if you are unfamiliar with them, then you may prefer to take the first course in particular, Statistical Thinking in Public Health, and perhaps also the second, on linear regression, before embarking on this one.

What is survival analysis? You’ll see what it is, when to use it and how to run and interpret the most common descriptive survival analysis method, the Kaplan-Meier plot and its associated log-rank test for comparing the survival of two or more patient groups, e.g. those on different treatments. You’ll learn about the key concept of censoring.

What's included

4 videos11 readings3 assignments2 discussion prompts1 plugin

4 videosTotal 16 minutes
  • Welcome to Course3 minutes
  • What is Survival Analysis?4 minutes
  • The KM plot and Log-rank test4 minutes
  • What is Heart Failure and How to run a KM plot in R4 minutes
11 readingsTotal 123 minutes
  • About Imperial College & the team10 minutes
  • How to be successful in this course10 minutes
  • Grading policy10 minutes
  • Data set and glossary10 minutes
  • Additional Readings10 minutes
  • Life tables20 minutes
  • Feedback: Life Tables10 minutes
  • The Course Data Set20 minutes
  • Feedback: Running a KM plot and log-rank test3 minutes
  • Practice in R: Run another KM Plot and log-rank test10 minutes
  • Feedback: Running another KM plot and log-rank test10 minutes
3 assignmentsTotal 80 minutes
  • Life tables30 minutes
  • Survival Analysis Variables30 minutes
  • Practice in R: Running a KM plot and log-rank test20 minutes
2 discussion promptsTotal 20 minutes
  • Nice to meet you!10 minutes
  • Share and Reflect: What experience do you have of Survival Analysis?10 minutes
1 pluginTotal 15 minutes
  • Complete our short pre-course survey15 minutes

This week you’ll get to know the most commonly used survival analysis method for incorporating not just one but multiple predictors of survival: Cox proportional hazards regression modelling. You’ll learn about the key concepts of hazards and the risk set. From now and until the end of this course, there’ll be plenty of chance to run Cox models on data simulated from real patient-level records for people admitted to hospital with heart failure. You’ll see why missing data and categorical variables can cause problems in regression models such as Cox.

What's included

3 videos4 readings2 assignments1 discussion prompt

3 videosTotal 18 minutes
  • Intro to Cox Model5 minutes
  • How to run Simple Cox model in R7 minutes
  • Introduction to Missing Data6 minutes
4 readingsTotal 80 minutes
  • Hazard Function and Risk Set20 minutes
  • Practice in R: Simple Cox Model30 minutes
  • Feedback: Simple Cox Model10 minutes
  • Further Reading20 minutes
2 assignmentsTotal 20 minutes
  • Hazard function and Ratio5 minutes
  • Simple Cox Model15 minutes
1 discussion promptTotal 15 minutes
  • Share and Reflect: Simple Cox Model15 minutes

You’ll extend the simple Cox model to the multiple Cox model. As preparation, you’ll run the essential descriptive statistics on your main variables. Then you’ll see what can happen with real-life public health data and learn some simple tricks to fix the problem.

What's included

1 video7 readings1 assignment2 discussion prompts

1 videoTotal 6 minutes
  • Interpreting the output from multiple Cox model6 minutes
7 readingsTotal 105 minutes
  • Introduction to Running Descriptives10 minutes
  • Practice in R: Getting to know your data30 minutes
  • Feedback: Getting to know your data10 minutes
  • How to run multiple Cox model in R20 minutes
  • Introduction to Non-convergence10 minutes
  • Practice: Fixing the problem of non-convergence10 minutes
  • Feedback on fixing a non-converging model15 minutes
1 assignmentTotal 10 minutes
  • Multiple Cox Model10 minutes
2 discussion promptsTotal 25 minutes
  • Share and Reflect: Getting to know your data15 minutes
  • Practice in R: Running a multiple Cox model that doesn't converge10 minutes

In this final part of the course, you’ll learn how to assess the fit of the model and test the validity of the main assumptions involved in Cox regression such as proportional hazards. This will cover three types of residuals. Lastly, you’ll get to practise fitting a multiple Cox regression model and will have to decide which predictors to include and which to drop, a ubiquitous challenge for people fitting any type of regression model.

What's included

3 videos7 readings3 assignments1 discussion prompt1 plugin

3 videosTotal 11 minutes
  • How to assess Cox model fit4 minutes
  • Cox proportional hazards assumption5 minutes
  • Summary of Course3 minutes
7 readingsTotal 80 minutes
  • Checking the proportionality assumption10 minutes
  • Feedback on Practice Quiz10 minutes
  • What to do if the proportionality assumption is not met20 minutes
  • How to choose predictors for a regression model20 minutes
  • Practice in R: Running a Multiple Cox Model0 minutes
  • Results of the exercise on model selection and backwards elimination10 minutes
  • Final Code10 minutes
3 assignmentsTotal 40 minutes
  • Testing the proportionality assumption with another variable15 minutes
  • End-of-Module Assessment20 minutes
  • Assessing the proportionality assumption in practice5 minutes
1 discussion promptTotal 10 minutes
  • Issues you encountered during the model selection exercise10 minutes
1 pluginTotal 15 minutes
  • Post-course Survey15 minutes

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Instructor

Instructor ratings
4.7 (63 ratings)
Imperial College London
6 Courses80,609 learners

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Showing 3 of 331

YX
·

Reviewed on Nov 21, 2019

The final quiz is a little bit confusing ,pls provide detailed feedback on it so we can learn further even we did not pass it.

FA
·

Reviewed on Jul 21, 2019

Very nice introductory course on survival analysis in R. Exercises were well designed.

JZ
·

Reviewed on Mar 14, 2020

Very good introduction course for survival analysis in R

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