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SAS Programming in the Pharmaceutical Industry, Second Edition, 2nd Edition

Book Description

This comprehensive resource provides on-the-job training for statistical programmers who use SAS in the pharmaceutical industry This one-stop resource offers a complete review of what entry- to intermediate-level statistical programmers need to know in order to help with the analysis and reporting of clinical trial data in the pharmaceutical industry. SAS Programming in the Pharmaceutical Industry, Second Edition begins with an introduction to the pharmaceutical industry and the work environment of a statistical programmer. Then it gives a chronological explanation of what you need to know to do the job. It includes information on importing and massaging data into analysis data sets, producing clinical trial output, and exporting data. This edition has been updated for SAS 9.4, and it features new graphics as well as all new examples using CDISC SDTM or ADaM model data structures. Whether you're a novice seeking an introduction to SAS programming in the pharmaceutical industry or a junior-level programmer exploring new approaches to problem solving, this real-world reference guide offers a wealth of practical suggestions to help you sharpen your skills. This book is part of the SAS Press program.

Table of Contents

  1. List of Programs
  2. About This Book
  3. About The Author
  4. Acknowledgements
  5. Chapter 1 Environment and Guiding Principles
    1. The Statistical Programmer’s Working Environment
      1. Pharmaceutical Industry Vocabulary
      2. Statistical Programmer Work Description
    2. The Drug/Device Development Process
      1. Industry Regulations and Standards
      2. Your Clinical Trial Colleagues
    3. Guiding Principles for the Statistical Programmer
      1. Understand the Clinical Study
      2. Program a Task Once and Reuse Your Code Everywhere
      3. Clinical Trial Data Are Dirty
      4. Use SAS Macros Judiciously
      5. A Good Programmer Is a Good Student
      6. Strive to Make Your Programming Readable
  6. Chapter 2 Preparing and Classifying ClinicalTrial Data
    1. Preparing Clinical Trial Data
      1. “Clean” the Data If They Are Needed for Analysis
      2. Categorize Data If Necessary
      3. Avoid Hardcoding Data
    2. Classifying Clinical Trial Data
      1. Demographics and Trial-Specific Baseline Data
      2. Concomitant or Prior Medication Data
      3. Medical History Data
      4. Investigational Therapy Drug Log
      5. Laboratory Data
      6. Adverse Event Data
      7. Endpoint/Event Assessment Data
      8. Clinical Endpoint Committee (CEC) Data
      9. Study Termination Data
      10. Treatment Randomization Data
      11. Quality-of-Life Data
  7. Chapter 3 Importing Data
    1. Importing Relational Databases and Clinical Data Management Systems
      1. SAS/ACCESS SQL Pass-Through Facility
      2. SAS/ACCESS LIBNAME Statement
    2. Importing ASCII Text
      1. PROC IMPORT and the Import Wizard
      2. SAS DATA Step
      3. SAS Enterprise Guide
    3. Importing Microsoft Office Files
      1. LIBNAME Statement
      2. Import Wizard and PROC IMPORT
      3. SAS/ACCESS SQL Pass-Through Facility
      4. SAS Enterprise Guide
    4. Importing XML
      1. XML LIBNAME Engine
      2. SAS XML Mapper
    5. Importing CDISC Model Content Files
      1. Importing CDISC SAS Transport Format Files
      2. Importing define.xml
      3. Importing CDISC ODM Files
  8. Chapter 4 Transforming Data and Creating Analysis Data Sets
    1. Key Concepts for Creating Analysis Data Sets
      1. Defining Variables Once
      2. Defining Study Populations
      3. Defining Baseline Observations
      4. Last Observation Carried Forward (LOCF)
      5. Defining Study Day
      6. Windowing Data
      7. Transposing Data
      8. Categorical Data and Why Zero and Missing Results Differ Greatly
      9. Performing Many-to-Many Comparisons/Joins
      10. Using Medical Dictionaries
      11. Other Tricks and Traps in Data Manipulation
    2. Common Analysis Data Sets
      1. Subject Level Analysis Data Set
      2. Change-from-Baseline Data Set
      3. Time-to-Event Data Set
  9. Chapter 5 Creating Tables and Listings
    1. Creating Tables
      1. General Approach to Creating Tables
      2. A Typical Clinical Trial Table
      3. Using PROC TABULATE to Create Clinical Trial Tables
      4. Using PROC REPORT to Create Clinical Trial Tables
      5. Creating Typical Continuous/Categorical Summary Tables
      6. Creating Adverse Event Summaries
      7. Creating Concomitant or Prior Medication Tables
      8. Creating a Laboratory Shift Table
      9. Creating Kaplan-Meier Survival Estimates Tables
    2. Creating Listings
    3. Output Appearance Options and Issues
      1. Creating ASCII Text Output
      2. Creating Rich Text Format (RTF) Output
      3. Creating Portable Document Format (PDF) Files
      4. “Page X of N” Pagination Solutions
      5. Footnote Indicating SAS Program and Date
      6. ODS Report Writing Interface
      7. The Power of ODS STYLE
    4. SAS Macro-Based Reporting Systems
  10. Chapter 6 Creating Clinical Trial Graphs
    1. Common Clinical Trial Graphs
      1. Scatter Plot
      2. Line Plot
      3. Bar Chart
      4. Box Plot
      5. Forest Plot
      6. Kaplan-Meier Survival Estimates Plot
    2. SAS Tools for Creating Clinical Trial Graphs
    3. Sample Graphs
      1. Creating a Scatter Plot
      2. Creating a Line Plot
      3. Creating a Bar Chart
      4. Creating a Box Plot
      5. Creating a Forest Plot
      6. Creating a Kaplan-Meier Survival Estimates Plot
    4. Using SAS Graphics Assistants
      1. Graph-N-Go
      2. SAS Enterprise Guide
      3. ODS Graphics Designer
      4. ODS Graphics Editor
    5. When You Should Use SAS Graphics
  11. Chapter 7 Performing Common Analyses and Obtaining Statistics
    1. Obtaining Descriptive Statistics
      1. Using PROC FREQ to Export Descriptive Statistics
      2. Using PROC UNIVARIATE to Export Descriptive Statistics
    2. Obtaining Inferential Statistics from Categorical Data Analysis
      1. Performing a 2x2 Test for Association
      2. Performing an NxP Test for Association
      3. Performing a Stratified NxP Test for Association
      4. Performing Logistic Regression
    3. Obtaining Inferential Statistics from Continuous Data Analysis
      1. Performing a One-Sample Test of the Mean
      2. Performing a Two-Sample Test of the Means
      3. Performing an N-Sample Test of the Means
    4. Obtaining Time-to-Event Analysis Statistics
    5. Obtaining Correlation Coefficients
    6. General Approach to Obtaining Statistics
  12. Chapter 8 Exporting Data
    1. Exporting Data to the FDA
      1. Using the SAS XPORT Transport Format
      2. Creating ODM XML and define.xml
    2. Exporting Data Not Destined for the FDA
      1. Exporting Data with PROC CPORT
      2. Exporting ASCII Text
      3. Exporting Data to Microsoft Office Files
      4. Exporting Other Proprietary Data Formats
    3. Encryption and File Transport Options
  13. Chapter 9 The Future of SAS Programming in Clinical Trials
    1. Changes in the Business Environment
    2. Changes in Technology
    3. Changes in Regulations
    4. Changes in Standards
    5. Use of SAS Software in the Clinical Trial Industry
  14. Chapter 10 Further Resources
    1. Regulatory Resources
      1. SAS Programming Validation
      2. FDA Resources
    2. Standards and Industry Organizations
    3. SAS Help
      1. Google Search
      3. SAS-L
      4. SAS Technical Support
      5. SAS Users Groups
      6. SAS Manuals and Online Documentation
      7. SAS Press
      8. SAS Focus Areas
      9. Third-Party SAS Web Pages
    4. Useful Technical Skills
      1. Scripting
      2. Version Control Software
      3. VBScript/JavaScript for Applications
      4. Systems Development Methodology
      5. Modeling Tools
      6. Markup Languages
      7. File Transport and Data Encryption Technologies
      8. Other Applications Development Languages
    5. Qualifying for and Obtaining a Job
  15. Glossary
  16. Index