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.

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Intermediate R proficiency. Some experience in statistical programming and applying CDISC standards in the pharmaceutical industry would be helpful.
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推荐体验
推荐体验
中级
Intermediate R proficiency. Some experience in statistical programming and applying CDISC standards in the pharmaceutical industry would be helpful.
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20 项作业
了解顶级公司的员工如何掌握热门技能

该课程共有8个模块
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.
涵盖的内容
1个视频1篇阅读材料1个讨论话题
1个视频•总计2分钟
- Welcome to Hands On Clinical Reporting Using R!•2分钟
1篇阅读材料•总计30分钟
- Pre-requisite Reading: Why open-source tools?•30分钟
1个讨论话题•总计10分钟
- Introductions and Background•10分钟
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.
涵盖的内容
6个视频1篇阅读材料1个作业
6个视频•总计23分钟
- Introduction Fundamentals•1分钟
- Phase 3 Clinical Trials - Protocol & SAP•6分钟
- Data Collection - Using CRFs and Other Means•6分钟
- CDISC SDTM and ADaM Standards•3分钟
- FDA(U.S.) Submission Package •5分钟
- Clinical Data Flow: From Raw Data to Final Outputs•2分钟
1篇阅读材料•总计60分钟
- Unlocking the Data Puzzle: further reading on data Collection, Standards, and Health Authorities•60分钟
1个作业•总计30分钟
- Deciphering Clinical Trials: A Comprehensive Quiz on SAP, Estimands, and Data Standards•30分钟
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.
涵盖的内容
4个视频1个作业
4个视频•总计29分钟
- Introduction SDTM•1分钟
- Context and Workflow•10分钟
- SDTM Data Mapping•13分钟
- Programming SDTM•5分钟
1个作业•总计20分钟
- Mastering SDTM: A Quiz on Study Data Standards and Implementation•20分钟
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.
涵盖的内容
16个视频4篇阅读材料4个作业
16个视频•总计62分钟
- Introduction•1分钟
- What is ADaM?•2分钟
- Subject-Level Analysis Dataset Structure (ADSL)•2分钟
- Occurrence Data Structure (OCCDS)•3分钟
- Basic Data Structure (BDS)•4分钟
- The Vision•2分钟
- admiral and pharmaverse for ADaM Development•3分钟
- Storing and Using ADaM Metadata•2分钟
- Part 1 - Metacore Object•8分钟
- Part 2 - Metacore Object•5分钟
- Part 3 - Metacore Object•4分钟
- QCing and Exporting ADaM•3分钟
- Part 1 - ADSL demo•11分钟
- Part 2 - ADSL demo•8分钟
- Part 3 - ADSL demo•3分钟
- Module Review•1分钟
4篇阅读材料•总计90分钟
- Supplemental Resources on Understanding ADaM Standards in the Industry•60分钟
- Links to Pharmaverse Github Repos and Sites•10分钟
- Links on ADaM Documentation and Github Repos for Code Used in the Demos•10分钟
- Quiz Resources•10分钟
4个作业•总计120分钟
- Module Quiz - ADaM Transformations (Introductory) using Pharmaverse R Packages•60分钟
- Lesson One - Test your knowledge•20分钟
- Lesson Two - Test your knowledge•20分钟
- Lesson Three - Test your knowledge•20分钟
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://hua.dididi.sbs/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.
涵盖的内容
36个视频2篇阅读材料8个作业
36个视频•总计180分钟
- Introduction to OCCDS and ADAE•1分钟
- ADAE Training Overview•5分钟
- What to expect going into Session 1•2分钟
- Adverse Events background•2分钟
- R Packages, Tools and Resources for this training.•1分钟
- Getting started programming ADAE in R•1分钟
- Let's read in the source data•4分钟
- Converting blanks to values to NA•4分钟
- Merging in ADSL variables•5分钟
- Deriving Adverse Event Start datetime•5分钟
- Deriving Adverse Event End datetime•5分钟
- Relative days of an AE from first exposure to study drug•3分钟
- AE Durations•4分钟
- What to expect in Session 4•1分钟
- Last Dose datetime•6分钟
- How to check Last Dose datetime derivation•7分钟
- Severity and Causality•3分钟
- What will be covered in this Session?•3分钟
- Flagging Treatment-Emergent AEs•8分钟
- Treatment-Emergent Flag window•6分钟
- Flagging AE Occurence•12分钟
- What are Standard MedDRA Queries (SMQs) and Custom Queries (CQs)?•6分钟
- Deriving Standard MedDRA Queries (SMQs) and Custom Queries (CQs)•17分钟
- What to expect in Session 6•3分钟
- Adding in ADSL variables•8分钟
- Deriving Analysis sequence•8分钟
- Reading in your ADaM specifications•7分钟
- Checking variables between your dataset and specifications•14分钟
- Dropping unneeded variables from your dataset•4分钟
- Ordering variables in your dataset•3分钟
- Sorting your dataset by the sort key per your specfications•4分钟
- Variable Length attributes•5分钟
- Variable Label attributes•3分钟
- Controlled-Terminology checks•6分钟
- Final XPT check and conversion•6分钟
- Module Review•2分钟
2篇阅读材料•总计20分钟
- Instructions to Install R environment for the training demos ahead.•10分钟
- ADAE Quiz Resources•10分钟
8个作业•总计220分钟
- Quiz - ADaM Transformations (Advanced) using Pharmaverse R Packages•120分钟
- Lesson 1 : Test your knowledge•15分钟
- Lesson 2 : Test your knowledge•15分钟
- Lesson 3 : Test your knowledge•15分钟
- Lesson 4 : Test your knowledge•15分钟
- Lesson 5 : Test your knowledge•15分钟
- Lesson 6a : Test your knowledge•10分钟
- Lesson 6b: Test your knowledge•15分钟
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.
涵盖的内容
36个视频2个作业
36个视频
- Creating static TLGs for clinical reporting with R•0分钟
- Lesson 1: Introduction & Concepts •0分钟
- Basic concepts of TLGs•0分钟
- How to decide on which TLGs are needed?•0分钟
- Stages of TLG development•0分钟
- Introduction to NEST•0分钟
- Key packages for TLG development•0分钟
- Lesson 1 Overview•0分钟
- Introduction to Lesson 2•0分钟
- Introduction to the Tern package•0分钟
- Tern analyze functions•0分钟
- What is rtables?•0分钟
- Concept of rtables •0分钟
- Introduction to demonstrations•0分钟
- Demography table•0分钟
- Demography table walk-through•0分钟
- Demography table conclusion•0分钟
- Adverse Event table introduction•0分钟
- Adverse Event walk-through•0分钟
- Adverse Event Table conclusion•0分钟
- Response Table Introduction•0分钟
- Response table - preprocessing the data•0分钟
- Response table walk-through part 1•0分钟
- Response Table walk-through part 2•0分钟
- Response Table part 3•0分钟
- Response table walk-through part 4•0分钟
- Response Table walk-through conclusion•0分钟
- Lesson 2 conclusion•0分钟
- Introduction to TLG Catalog•0分钟
- Anatomy of TLG Catalog•0分钟
- Feedback to TLG Catalog•0分钟
- TLG Catalog Demo Part 1•0分钟
- TLG Catalog Demo Part 2•0分钟
- Lesson 3 Summary•0分钟
- More on NEST packages•0分钟
- Industry collaboration efforts•0分钟
2个作业•总计210分钟
- Quiz - Creating Static TLGs using NEST packages•30分钟
- Lesson 2 Quiz - Creating Static TLGs with NEST•180分钟
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.
涵盖的内容
26个视频1篇阅读材料4个作业
26个视频•总计80分钟
- Motivation for Interactive Data Displays•4分钟
- Introduction•1分钟
- What is teal?•3分钟
- Teal demo•8分钟
- Teal key features•2分钟
- How does teal work?•1分钟
- Demo modules using teal.gallery •1分钟
- Using teal as a data scientist•1分钟
- Introduction•0分钟
- Teal installation guide•1分钟
- App development worflow•1分钟
- App project setup•4分钟
- First teal app•4分钟
- Filters in teal•2分钟
- Advanced filters•4分钟
- Introduction•1分钟
- Teal app development workflow•1分钟
- Data review modules•7分钟
- Loading data•1分钟
- Code reproducibility•5分钟
- Processing input data•4分钟
- Adding a demographics table module•4分钟
- Adding an adverse events table module•6分钟
- Adding a KM plot module•7分钟
- Build the full app•4分钟
- Module review•4分钟
1篇阅读材料•总计5分钟
- Teal universe product map•5分钟
4个作业•总计60分钟
- Module assessment quiz•30分钟
- Teal framework quiz•10分钟
- Teal basic concepts quiz•10分钟
- Teal advanced concepts quiz•10分钟
In this final module we will briefly review the course and suggest next steps in your learning journey.
涵盖的内容
1个视频
1个视频•总计3分钟
- Conclusion•3分钟
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