The aim of this course is to introduce learners to open-source R packages that can be used to perform clinical data reporting tasks. The main emphasis of the course will be the clinical data flow from raw data (both CRF and non-CRF) to SDTM to ADaM to final outputs. While several open-source tools to complete these tasks will be introduced, the objective of this course is not to become an expert in any of these tools but rather to introduce participants to the broader concepts behind these tasks. That way the tools simply serve as an example of how the underlying concepts could be put into action in code.

Hands On Clinical Reporting Using R

Hands On Clinical Reporting Using R



Instructors: Adrian Chan
Instructors







Access provided by Universitas Indonesia
2,193 already enrolled
16 reviews
Recommended experience
Recommended experience
Intermediate level
Intermediate R proficiency. Some experience in statistical programming and applying CDISC standards in the pharmaceutical industry would be helpful.
16 reviews
Recommended experience
Recommended experience
Intermediate level
Intermediate R proficiency. Some experience in statistical programming and applying CDISC standards in the pharmaceutical industry would be helpful.
Skills you'll gain
Tools you'll learn
Details to know

Add to your LinkedIn profile
20 assignments
See how employees at top companies are mastering in-demand skills

There are 8 modules in this course
In this module, we will introduce this course and provide a brief outline of what you will be learning. We will provide context on clinical reporting in R and the motivation for the recent shift in industry trends for the support of open-source tools. We will describe the challenges in current statistical programming practices and the benefits of applying open-source tools, as well as provide additional resources to learn more.
What's included
1 video1 reading1 discussion prompt
1 video⢠Total 2 minutes
- Welcome to Hands On Clinical Reporting Using R!⢠2 minutes
1 reading⢠Total 30 minutes
- Pre-requisite Reading: Why open-source tools?⢠30 minutes
1 discussion prompt⢠Total 10 minutes
- Introductions and Background⢠10 minutes
In this module, we will cover several important topics related to Phase 3 clinical trials and clinical data. We will start with a brief introduction to Phase 3 trials and discuss the type of data that is collected during these trials. Following that, we will provide an overview of two data models that are commonly used to handle clinical trial data, namely SDTM and ADaM. Next, we will delve into the process of preparing a data submission package for health authorities, with a specific focus on the Food and Drug Administration (FDA) in the United States. We will explore the requirements and guidelines for submitting clinical trial data to the FDA. Lastly, we will wrap up this module by summarizing our understanding of the clinical data flow, highlighting the key points we have covered throughout the course.
What's included
6 videos1 reading1 assignment
6 videos⢠Total 23 minutes
- Introduction Fundamentals⢠1 minute
- Phase 3 Clinical Trials - Protocol & SAP⢠6 minutes
- Data Collection - Using CRFs and Other Means⢠6 minutes
- CDISC SDTM and ADaM Standards⢠3 minutes
- FDA(U.S.) Submission Package ⢠5 minutes
- Clinical Data Flow: From Raw Data to Final Outputs⢠2 minutes
1 reading⢠Total 60 minutes
- Unlocking the Data Puzzle: further reading on data Collection, Standards, and Health Authorities⢠60 minutes
1 assignment⢠Total 30 minutes
- Deciphering Clinical Trials: A Comprehensive Quiz on SAP, Estimands, and Data Standards⢠30 minutes
In this module, we will provide an introduction to Study Data Tabulation Model (or SDTM) by giving context and highlighting the importance of such data models on clinical trials. We will explore different SDTM data mappings for CRF and non-CRF data. Finally, we will provide an outlook on the programming of SDTMs on R.
What's included
4 videos1 assignment
4 videos⢠Total 29 minutes
- Introduction SDTM⢠1 minute
- Context and Workflow⢠10 minutes
- SDTM Data Mapping⢠13 minutes
- Programming SDTM⢠5 minutes
1 assignment⢠Total 20 minutes
- Mastering SDTM: A Quiz on Study Data Standards and Implementation⢠20 minutes
In this module, we explore what are analysis data model (ADaM) datasets, the 3 structures of ADaM, and how to create ADaM in R using Pharmaverse packages.
What's included
16 videos4 readings4 assignments
16 videos⢠Total 62 minutes
- Introduction⢠1 minute
- What is ADaM?⢠2 minutes
- Subject-Level Analysis Dataset Structure (ADSL)⢠2 minutes
- Occurrence Data Structure (OCCDS)⢠3 minutes
- Basic Data Structure (BDS)⢠4 minutes
- The Vision⢠2 minutes
- admiral and pharmaverse for ADaM Development⢠3 minutes
- Storing and Using ADaM Metadata⢠2 minutes
- Part 1 - Metacore Object⢠8 minutes
- Part 2 - Metacore Object⢠5 minutes
- Part 3 - Metacore Object⢠4 minutes
- QCing and Exporting ADaM⢠3 minutes
- Part 1 - ADSL demo⢠11 minutes
- Part 2 - ADSL demo⢠8 minutes
- Part 3 - ADSL demo⢠3 minutes
- Module Review⢠1 minute
4 readings⢠Total 90 minutes
- Supplemental Resources on Understanding ADaM Standards in the Industry⢠60 minutes
- Links to Pharmaverse Github Repos and Sites⢠10 minutes
- Links on ADaM Documentation and Github Repos for Code Used in the Demos⢠10 minutes
- Quiz Resources⢠10 minutes
4 assignments⢠Total 120 minutes
- Lesson One - Test your knowledge⢠20 minutes
- Lesson Two - Test your knowledge⢠20 minutes
- Lesson Three - Test your knowledge⢠20 minutes
- Module Quiz - ADaM Transformations (Introductory) using Pharmaverse R Packages⢠60 minutes
In this module, we explore ADaM and R using Pharmaverse packages, one step further. We will focus on the ADaM Occurence Data Structure known as OCCDS using the example Analysis Dataset Adverse Events (ADAE). We'll go over what an OCCDS is, Adverse Events, and how to create ADAE using {admiral} and other R Pharmaverse packages. As you may be going through this training with a hands-on approach, when working in R, please first follow the installation instructions here to ensure you are using the same R version and R packages needed for both the Training and the Quiz at the end. You may do steps 1-6 now : https://www.coursera.org/learn/hands-on-clinical-reporting-using-r/supplement/enxGp/adae-quiz-resources (copy and paste if you need to), then proceed with the training. Once you get to the quiz, then you may start from step 7 on.
What's included
36 videos2 readings8 assignments
36 videos⢠Total 180 minutes
- Introduction to OCCDS and ADAE⢠1 minute
- ADAE Training Overview⢠5 minutes
- What to expect going into Session 1⢠2 minutes
- Adverse Events background⢠2 minutes
- R Packages, Tools and Resources for this training.⢠1 minute
- Getting started programming ADAE in R⢠1 minute
- Let's read in the source data⢠4 minutes
- Converting blanks to values to NA⢠4 minutes
- Merging in ADSL variables⢠5 minutes
- Deriving Adverse Event Start datetime⢠5 minutes
- Deriving Adverse Event End datetime⢠5 minutes
- Relative days of an AE from first exposure to study drug⢠3 minutes
- AE Durations⢠4 minutes
- What to expect in Session 4⢠1 minute
- Last Dose datetime⢠6 minutes
- How to check Last Dose datetime derivation⢠7 minutes
- Severity and Causality⢠3 minutes
- What will be covered in this Session?⢠3 minutes
- Flagging Treatment-Emergent AEs⢠8 minutes
- Treatment-Emergent Flag window⢠6 minutes
- Flagging AE Occurence⢠12 minutes
- What are Standard MedDRA Queries (SMQs) and Custom Queries (CQs)?⢠6 minutes
- Deriving Standard MedDRA Queries (SMQs) and Custom Queries (CQs)⢠17 minutes
- What to expect in Session 6⢠3 minutes
- Adding in ADSL variables⢠8 minutes
- Deriving Analysis sequence⢠8 minutes
- Reading in your ADaM specifications⢠7 minutes
- Checking variables between your dataset and specifications⢠14 minutes
- Dropping unneeded variables from your dataset⢠4 minutes
- Ordering variables in your dataset⢠3 minutes
- Sorting your dataset by the sort key per your specfications⢠4 minutes
- Variable Length attributes⢠5 minutes
- Variable Label attributes⢠3 minutes
- Controlled-Terminology checks⢠6 minutes
- Final XPT check and conversion⢠6 minutes
- Module Review⢠2 minutes
2 readings⢠Total 20 minutes
- Instructions to Install R environment for the training demos ahead.⢠10 minutes
- ADAE Quiz Resources⢠10 minutes
8 assignments⢠Total 220 minutes
- Lesson 1 : Test your knowledge⢠15 minutes
- Lesson 2 : Test your knowledge⢠15 minutes
- Lesson 3 : Test your knowledge⢠15 minutes
- Lesson 4 : Test your knowledge⢠15 minutes
- Lesson 5 : Test your knowledge⢠15 minutes
- Lesson 6a : Test your knowledge⢠10 minutes
- Lesson 6b: Test your knowledge⢠15 minutes
- Quiz - ADaM Transformations (Advanced) using Pharmaverse R Packages⢠120 minutes
In this module, we introduce the concepts of generating outputs used for regulatory purposes, and the NEST packages in particular. We show how you can use NEST effectively to create and customize your tables, listings, and graphs (TLGs) during clinical reporting and introduce the TLG-Catalog to aid output generation using our packages. We will explain the benefits of open-source and the industry collaboration efforts on clinical reporting.
What's included
36 videos2 assignments
36 videos
- Creating static TLGs for clinical reporting with R⢠0 minutes
- Lesson 1: Introduction & Concepts ⢠0 minutes
- Basic concepts of TLGs⢠0 minutes
- How to decide on which TLGs are needed?⢠0 minutes
- Stages of TLG development⢠0 minutes
- Introduction to NEST⢠0 minutes
- Key packages for TLG development⢠0 minutes
- Lesson 1 Overview⢠0 minutes
- Introduction to Lesson 2⢠0 minutes
- Introduction to the Tern package⢠0 minutes
- Tern analyze functions⢠0 minutes
- What is rtables?⢠0 minutes
- Concept of rtables ⢠0 minutes
- Introduction to demonstrations⢠0 minutes
- Demography table⢠0 minutes
- Demography table walk-through⢠0 minutes
- Demography table conclusion⢠0 minutes
- Adverse Event table introduction⢠0 minutes
- Adverse Event walk-through⢠0 minutes
- Adverse Event Table conclusion⢠0 minutes
- Response Table Introduction⢠0 minutes
- Response table - preprocessing the data⢠0 minutes
- Response table walk-through part 1⢠0 minutes
- Response Table walk-through part 2⢠0 minutes
- Response Table part 3⢠0 minutes
- Response table walk-through part 4⢠0 minutes
- Response Table walk-through conclusion⢠0 minutes
- Lesson 2 conclusion⢠0 minutes
- Introduction to TLG Catalog⢠0 minutes
- Anatomy of TLG Catalog⢠0 minutes
- Feedback to TLG Catalog⢠0 minutes
- TLG Catalog Demo Part 1⢠0 minutes
- TLG Catalog Demo Part 2⢠0 minutes
- Lesson 3 Summary⢠0 minutes
- More on NEST packages⢠0 minutes
- Industry collaboration efforts⢠0 minutes
2 assignments⢠Total 210 minutes
- Lesson 2 Quiz - Creating Static TLGs with NEST⢠180 minutes
- Quiz - Creating Static TLGs using NEST packages⢠30 minutes
In this module we will discuss benefits of of using interactive data displays for clinical reporting. We will introduce the teal family of R packages and become familiar with the key features this framework offers. Finally, we will learn how to develop a production level interactive application using teal modules for data review, safety and efficacy analyses.
What's included
26 videos1 reading4 assignments
26 videos⢠Total 80 minutes
- Motivation for Interactive Data Displays⢠4 minutes
- Introduction⢠1 minute
- What is teal?⢠3 minutes
- Teal demo⢠8 minutes
- Teal key features⢠2 minutes
- How does teal work?⢠1 minute
- Demo modules using teal.gallery ⢠1 minute
- Using teal as a data scientist⢠1 minute
- Introduction⢠0 minutes
- Teal installation guide⢠1 minute
- App development worflow⢠1 minute
- App project setup⢠4 minutes
- First teal app⢠4 minutes
- Filters in teal⢠2 minutes
- Advanced filters⢠4 minutes
- Introduction⢠1 minute
- Teal app development workflow⢠1 minute
- Data review modules⢠7 minutes
- Loading data⢠1 minute
- Code reproducibility⢠5 minutes
- Processing input data⢠4 minutes
- Adding a demographics table module⢠4 minutes
- Adding an adverse events table module⢠6 minutes
- Adding a KM plot module⢠7 minutes
- Build the full app⢠4 minutes
- Module review⢠4 minutes
1 reading⢠Total 5 minutes
- Teal universe product map⢠5 minutes
4 assignments⢠Total 60 minutes
- Teal framework quiz⢠10 minutes
- Teal basic concepts quiz⢠10 minutes
- Teal advanced concepts quiz⢠10 minutes
- Module assessment quiz⢠30 minutes
In this final module we will briefly review the course and suggest next steps in your learning journey.
What's included
1 video
1 video⢠Total 3 minutes
- Conclusion⢠3 minutes
Instructors



Instructors







Why people choose Coursera for their career

Felipe M.

Jennifer J.

Larry W.

Chaitanya A.
Explore more from Data Science

Course
UUniversity of Colorado System
Course
SStanford University
Course


