About this course: This course focuses on the concepts and tools behind reporting modern data analyses in a reproducible manner. Reproducible research is the idea that data analyses, and more generally, scientific claims, are published with their data and software code so that others may verify the findings and build upon them. The need for reproducibility is increasing dramatically as data analyses become more complex, involving larger datasets and more sophisticated computations. Reproducibility allows for people to focus on the actual content of a data analysis, rather than on superficial details reported in a written summary. In addition, reproducibility makes an analysis more useful to others because the data and code that actually conducted the analysis are available. This course will focus on literate statistical analysis tools which allow one to publish data analyses in a single document that allows others to easily execute the same analysis to obtain the same results.
Created by: Johns Hopkins University
Taught by: Roger D. Peng, PhD, Associate Professor, Biostatistics
Bloomberg School of Public Health
Taught by: Jeff Leek, PhD, Associate Professor, Biostatistics
Bloomberg School of Public Health
Taught by: Brian Caffo, PhD, Professor, Biostatistics
Bloomberg School of Public Health
| Basic Info | Course 5 of 10 in the Data Science Specialization |
| Commitment | 4-9 hours/week |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
Week 1: Concepts, Ideas, & Structure
This week will cover the basic ideas of reproducible research since they may be unfamiliar to some of you. We also cover structuring and organizing a data analysis to help make it more reproducible. I recommend that you watch the videos in the order that they are listed on the web page, but watching the videos out of order isn't going to ruin the story.
9 videos, 3 readings
- Video: Introduction
- Reading: Syllabus
- Reading: Pre-course survey
- Reading: Course Book: Report Writing for Data Science in R
- Video: What is Reproducible Research About?
- Video: Reproducible Research: Concepts and Ideas (part 1)
- Video: Reproducible Research: Concepts and Ideas (part 2)
- Video: Reproducible Research: Concepts and Ideas (part 3)
- Video: Scripting Your Analysis
- Video: Structure of a Data Analysis (part 1)
- Video: Structure of a Data Analysis (part 2)
- Video: Organizing Your Analysis
Graded: Week 1 Quiz
WEEK 2
Week 2: Markdown & knitr
This week we cover some of the core tools for developing reproducible documents. We cover the literate programming tool knitr and show how to integrate it with Markdown to publish reproducible web documents. We also introduce the first peer assessment which will require you to write up a reproducible data analysis using knitr.
9 videos
- Video: Coding Standards in R
- Video: Markdown
- Video: R Markdown
- Video: R Markdown Demonstration
- Video: knitr (part 1)
- Video: knitr (part 2)
- Video: knitr (part 3)
- Video: knitr (part 4)
- Video: Introduction to Course Project 1
Graded: Week 2 Quiz
Graded: Course Project 1
WEEK 3
Week 3: Reproducible Research Checklist & Evidence-based Data Analysis
This week covers what one could call a basic check list for ensuring that a data analysis is reproducible. While it's not absolutely sufficient to follow the check list, it provides a necessary minimum standard that would be applicable to almost any area of analysis.
10 videos
- Video: Communicating Results
- Video: RPubs
- Video: Reproducible Research Checklist (part 1)
- Video: Reproducible Research Checklist (part 2)
- Video: Reproducible Research Checklist (part 3)
- Video: Evidence-based Data Analysis (part 1)
- Video: Evidence-based Data Analysis (part 2)
- Video: Evidence-based Data Analysis (part 3)
- Video: Evidence-based Data Analysis (part 4)
- Video: Evidence-based Data Analysis (part 5)
WEEK 4
Week 4: Case Studies & Commentaries
This week there are two
case studies involving the importance of reproducibility in science for you to watch.
5 videos, 1 reading
- Video: Caching Computations
- Video: Case Study: Air Pollution
- Video: Case Study: High Throughput Biology
- Video: Commentaries on Data Analysis
- Video: Introduction to Peer Assessment 2
- Reading: Post-Course Survey
Graded: Course Project 2
FAQs
How It Works
Coursework
Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.
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Creators
Johns Hopkins University
The mission of The Johns Hopkins University is to educate its students and cultivate their capacity for life-long learning, to foster independent and original research, and to bring the benefits of discovery to the world.
Pricing
| Purchase Course | Audit | |
|---|---|---|
| Access to course materials | Available | Available |
| Access to graded materials | Available | Not available |
| Receive a final grade | Available | Not available |
| Earn a shareable Course Certificate | Available | Not available |
Ratings and Reviews
Very good course
Perfect
I was able to learn very good base to assure my work can be reproduced within my peers.
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Nice course. But I'm always worried about the estimated lengths of the assignments.