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 HAECO Americas
2,240 already enrolled
17 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.
17 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
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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 videoā¢Ā Total 2 minutes
- Welcome to Hands On Clinical Reporting Using R!ā¢Ā 2 minutes
1 readingā¢Ā Total 30 minutes
- Pre-requisite Reading: Why open-source tools?ā¢Ā 30 minutes
1 discussion promptā¢Ā Total 10 minutes
- Introductions and Backgroundā¢Ā 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 videosā¢Ā Total 23 minutes
- Introduction Fundamentalsā¢Ā 1 minute
- Phase 3 Clinical Trials - Protocol & SAPā¢Ā 6 minutes
- Data Collection - Using CRFs and Other Meansā¢Ā 6 minutes
- CDISC SDTM and ADaM Standardsā¢Ā 3 minutes
- FDA(U.S.) Submission Package ā¢Ā 5 minutes
- Clinical Data Flow: From Raw Data to Final Outputsā¢Ā 2 minutes
1 readingā¢Ā Total 60 minutes
- Unlocking the Data Puzzle: further reading on data Collection, Standards, and Health Authoritiesā¢Ā 60 minutes
1 assignmentā¢Ā Total 30 minutes
- Deciphering Clinical Trials: A Comprehensive Quiz on SAP, Estimands, and Data Standardsā¢Ā 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 videosā¢Ā Total 29 minutes
- Introduction SDTMā¢Ā 1 minute
- Context and Workflowā¢Ā 10 minutes
- SDTM Data Mappingā¢Ā 13 minutes
- Programming SDTMā¢Ā 5 minutes
1 assignmentā¢Ā Total 20 minutes
- Mastering SDTM: A Quiz on Study Data Standards and Implementationā¢Ā 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 videosā¢Ā Total 62 minutes
- Introductionā¢Ā 1 minute
- What is ADaM?ā¢Ā 2 minutes
- Subject-Level Analysis Dataset Structure (ADSL)ā¢Ā 2 minutes
- Occurrence Data Structure (OCCDS)ā¢Ā 3 minutes
- Basic Data Structure (BDS)ā¢Ā 4 minutes
- The Visionā¢Ā 2 minutes
- admiral and pharmaverse for ADaM Developmentā¢Ā 3 minutes
- Storing and Using ADaM Metadataā¢Ā 2 minutes
- Part 1 - Metacore Objectā¢Ā 8 minutes
- Part 2 - Metacore Objectā¢Ā 5 minutes
- Part 3 - Metacore Objectā¢Ā 4 minutes
- QCing and Exporting ADaMā¢Ā 3 minutes
- Part 1 - ADSL demoā¢Ā 11 minutes
- Part 2 - ADSL demoā¢Ā 8 minutes
- Part 3 - ADSL demoā¢Ā 3 minutes
- Module Reviewā¢Ā 1 minute
4 readingsā¢Ā Total 90 minutes
- Supplemental Resources on Understanding ADaM Standards in the Industryā¢Ā 60 minutes
- Links to Pharmaverse Github Repos and Sitesā¢Ā 10 minutes
- Links on ADaM Documentation and Github Repos for Code Used in the Demosā¢Ā 10 minutes
- Quiz Resourcesā¢Ā 10 minutes
4 assignmentsā¢Ā Total 120 minutes
- Module Quiz - ADaM Transformations (Introductory) using Pharmaverse R Packagesā¢Ā 60 minutes
- Lesson One - Test your knowledgeā¢Ā 20 minutes
- Lesson Two - Test your knowledgeā¢Ā 20 minutes
- Lesson Three - Test your knowledgeā¢Ā 20 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 videosā¢Ā Total 180 minutes
- Introduction to OCCDS and ADAEā¢Ā 1 minute
- ADAE Training Overviewā¢Ā 5 minutes
- What to expect going into Session 1ā¢Ā 2 minutes
- Adverse Events backgroundā¢Ā 2 minutes
- R Packages, Tools and Resources for this training.ā¢Ā 1 minute
- Getting started programming ADAE in Rā¢Ā 1 minute
- Let's read in the source dataā¢Ā 4 minutes
- Converting blanks to values to NAā¢Ā 4 minutes
- Merging in ADSL variablesā¢Ā 5 minutes
- Deriving Adverse Event Start datetimeā¢Ā 5 minutes
- Deriving Adverse Event End datetimeā¢Ā 5 minutes
- Relative days of an AE from first exposure to study drugā¢Ā 3 minutes
- AE Durationsā¢Ā 4 minutes
- What to expect in Session 4ā¢Ā 1 minute
- Last Dose datetimeā¢Ā 6 minutes
- How to check Last Dose datetime derivationā¢Ā 7 minutes
- Severity and Causalityā¢Ā 3 minutes
- What will be covered in this Session?ā¢Ā 3 minutes
- Flagging Treatment-Emergent AEsā¢Ā 8 minutes
- Treatment-Emergent Flag windowā¢Ā 6 minutes
- Flagging AE Occurenceā¢Ā 12 minutes
- What are Standard MedDRA Queries (SMQs) and Custom Queries (CQs)?ā¢Ā 6 minutes
- Deriving Standard MedDRA Queries (SMQs) and Custom Queries (CQs)ā¢Ā 17 minutes
- What to expect in Session 6ā¢Ā 3 minutes
- Adding in ADSL variablesā¢Ā 8 minutes
- Deriving Analysis sequenceā¢Ā 8 minutes
- Reading in your ADaM specificationsā¢Ā 7 minutes
- Checking variables between your dataset and specificationsā¢Ā 14 minutes
- Dropping unneeded variables from your datasetā¢Ā 4 minutes
- Ordering variables in your datasetā¢Ā 3 minutes
- Sorting your dataset by the sort key per your specficationsā¢Ā 4 minutes
- Variable Length attributesā¢Ā 5 minutes
- Variable Label attributesā¢Ā 3 minutes
- Controlled-Terminology checksā¢Ā 6 minutes
- Final XPT check and conversionā¢Ā 6 minutes
- Module Reviewā¢Ā 2 minutes
2 readingsā¢Ā Total 20 minutes
- Instructions to Install R environment for the training demos ahead.ā¢Ā 10 minutes
- ADAE Quiz Resourcesā¢Ā 10 minutes
8 assignmentsā¢Ā Total 220 minutes
- Quiz - ADaM Transformations (Advanced) using Pharmaverse R Packagesā¢Ā 120 minutes
- Lesson 1 : Test your knowledgeā¢Ā 15 minutes
- Lesson 2 : Test your knowledgeā¢Ā 15 minutes
- Lesson 3 : Test your knowledgeā¢Ā 15 minutes
- Lesson 4 : Test your knowledgeā¢Ā 15 minutes
- Lesson 5 : Test your knowledgeā¢Ā 15 minutes
- Lesson 6a : Test your knowledgeā¢Ā 10 minutes
- Lesson 6b: Test your knowledgeā¢Ā 15 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 Rā¢Ā 0 minutes
- Lesson 1: Introduction & Concepts ā¢Ā 0 minutes
- Basic concepts of TLGsā¢Ā 0 minutes
- How to decide on which TLGs are needed?ā¢Ā 0 minutes
- Stages of TLG developmentā¢Ā 0 minutes
- Introduction to NESTā¢Ā 0 minutes
- Key packages for TLG developmentā¢Ā 0 minutes
- Lesson 1 Overviewā¢Ā 0 minutes
- Introduction to Lesson 2ā¢Ā 0 minutes
- Introduction to the Tern packageā¢Ā 0 minutes
- Tern analyze functionsā¢Ā 0 minutes
- What is rtables?ā¢Ā 0 minutes
- Concept of rtables ā¢Ā 0 minutes
- Introduction to demonstrationsā¢Ā 0 minutes
- Demography tableā¢Ā 0 minutes
- Demography table walk-throughā¢Ā 0 minutes
- Demography table conclusionā¢Ā 0 minutes
- Adverse Event table introductionā¢Ā 0 minutes
- Adverse Event walk-throughā¢Ā 0 minutes
- Adverse Event Table conclusionā¢Ā 0 minutes
- Response Table Introductionā¢Ā 0 minutes
- Response table - preprocessing the dataā¢Ā 0 minutes
- Response table walk-through part 1ā¢Ā 0 minutes
- Response Table walk-through part 2ā¢Ā 0 minutes
- Response Table part 3ā¢Ā 0 minutes
- Response table walk-through part 4ā¢Ā 0 minutes
- Response Table walk-through conclusionā¢Ā 0 minutes
- Lesson 2 conclusionā¢Ā 0 minutes
- Introduction to TLG Catalogā¢Ā 0 minutes
- Anatomy of TLG Catalogā¢Ā 0 minutes
- Feedback to TLG Catalogā¢Ā 0 minutes
- TLG Catalog Demo Part 1ā¢Ā 0 minutes
- TLG Catalog Demo Part 2ā¢Ā 0 minutes
- Lesson 3 Summaryā¢Ā 0 minutes
- More on NEST packagesā¢Ā 0 minutes
- Industry collaboration effortsā¢Ā 0 minutes
2 assignmentsā¢Ā Total 210 minutes
- Quiz - Creating Static TLGs using NEST packagesā¢Ā 30 minutes
- Lesson 2 Quiz - Creating Static TLGs with NESTā¢Ā 180 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 videosā¢Ā Total 80 minutes
- Motivation for Interactive Data Displaysā¢Ā 4 minutes
- Introductionā¢Ā 1 minute
- What is teal?ā¢Ā 3 minutes
- Teal demoā¢Ā 8 minutes
- Teal key featuresā¢Ā 2 minutes
- How does teal work?ā¢Ā 1 minute
- Demo modules using teal.gallery ā¢Ā 1 minute
- Using teal as a data scientistā¢Ā 1 minute
- Introductionā¢Ā 0 minutes
- Teal installation guideā¢Ā 1 minute
- App development worflowā¢Ā 1 minute
- App project setupā¢Ā 4 minutes
- First teal appā¢Ā 4 minutes
- Filters in tealā¢Ā 2 minutes
- Advanced filtersā¢Ā 4 minutes
- Introductionā¢Ā 1 minute
- Teal app development workflowā¢Ā 1 minute
- Data review modulesā¢Ā 7 minutes
- Loading dataā¢Ā 1 minute
- Code reproducibilityā¢Ā 5 minutes
- Processing input dataā¢Ā 4 minutes
- Adding a demographics table moduleā¢Ā 4 minutes
- Adding an adverse events table moduleā¢Ā 6 minutes
- Adding a KM plot moduleā¢Ā 7 minutes
- Build the full appā¢Ā 4 minutes
- Module reviewā¢Ā 4 minutes
1 readingā¢Ā Total 5 minutes
- Teal universe product mapā¢Ā 5 minutes
4 assignmentsā¢Ā Total 60 minutes
- Module assessment quizā¢Ā 30 minutes
- Teal framework quizā¢Ā 10 minutes
- Teal basic concepts quizā¢Ā 10 minutes
- Teal advanced concepts quizā¢Ā 10 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 videoā¢Ā Total 3 minutes
- Conclusionā¢Ā 3 minutes
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