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.
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
Show info about module content
1 video•Total 2 minutes
Welcome to Hands On Clinical Reporting Using R!•2 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.
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
SDTM : Study Data Tabulation Model
Module 3•1 hour to complete
Module details
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
Show info about module content
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
ADaM Transformations (Introductory)
Module 4•5 hours to complete
Module details
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.
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
Module Quiz - ADaM Transformations (Introductory) using Pharmaverse R Packages•60 minutes
Lesson One - Test your knowledge•20 minutes
Lesson Two - Test your knowledge•20 minutes
Lesson Three - Test your knowledge•20 minutes
ADaM Transformations (Advanced)
Module 5•7 hours to complete
Module details
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
Show info about module content
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
Quiz - ADaM Transformations (Advanced) using Pharmaverse R Packages•120 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
Static TLGs (NEST)
Module 6•4 hours to complete
Module details
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
Show info about module content
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
Quiz - Creating Static TLGs using NEST packages•30 minutes
Lesson 2 Quiz - Creating Static TLGs with NEST•180 minutes
Interactive Data Displays
Module 7•2 hours to complete
Module details
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
Show info about module content
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
Module assessment quiz•30 minutes
Teal framework quiz•10 minutes
Teal basic concepts quiz•10 minutes
Teal advanced concepts quiz•10 minutes
Conclusion
Module 8•3 minutes to complete
Module details
In this final module we will briefly review the course and suggest next steps in your learning journey.
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