SAS Programming in the Pharmaceutical Industry, Second Edition

Jack Shostak

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.

Sujets

• Clinical Data Interchange Standards Consortium
• Health care
• Clinical trial
• Pharmaceutical drug

Informations

• Publié par: SAS Institute
• Date de parution: 01 mars 2014
• Nombre de lectures: 1
• EAN13: 9781629591490
• Langue: English
• Poids de l'ouvrage: 15 Mo

Extrait

® SASProgramming in the Pharmaceutical Industry Second Edition Jack Shostak

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® The correct bibliographic citation for this manual is as follows: Shostak, Jack. 2014.SAS Programming in the Pharmaceutical Industry, Second Edition. Cary, NC: SAS Institute Inc. ® SAS Programming in the Pharmaceutical Industry, Second Edition Copyright © 2014, SAS Institute Inc., Cary, NC, USA ISBN 978-1-62959-150-6 All rights reserved. Produced in the United States of America. For a hard-copy book: No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, or otherwise, without the prior written permission of the publisher, SAS Institute Inc. For a web download or e-book: Your use of this publication shall be governed by the terms established by the vendor at the time you acquire this publication. The scanning, uploading, and distribution of this book via the Internet or any other means without the permission of the publisher is illegal and punishable by law. Please purchase only authorized electronic editions and do not participate in or encourage electronic piracy of copyrighted materials. Your support of others’ rights is appreciated. U.S. Government License Rights; Restricted Rights: The Software and its documentation is commercial computer software developed at private expense and is provided with RESTRICTED RIGHTS to the United States Government. Use, duplication or disclosure of the Software by the United States Government is subject to the license terms of this Agreement pursuant to, as applicable, FAR 12.212, DFAR 227.7202-1(a), DFAR 22 7.7202-3(a) and DFAR 227.7202-4 and, to the extent required under U.S. federal law, the minimum restricted rights as set out in FAR 52.227-19 (DEC 2007). If FAR 52.227-19 is applicable, this provision serves as notice under clause (c) thereof and no other notice is required to be affixed to the Software or documentation. The Government's rights in Software and documentation shall be only those set forth in this Agreement. SAS Institute Inc., SAS Campus Drive, Cary, North Carolina 27513-2414. March 2014 ® SAS provides a complete selection of books and electronic products to help customers use SAS software to its fullest potential. For more information about our offerings, visit support.sas.com/bookstore or call 1-800-727-3228. ® SAS and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute Inc. in the USA and other countries. ® indicates USA registration. Other brand and product names are trademarks of their respective companies.

Contents

List of Programs About This Book About The Author Acknowledgements Chapter 1 Environment and Guiding Principles TheStatistical Programmer’s Working Environment Pharmaceutical Industry Vocabulary Statistical Programmer Work Description The Drug/Device Development Process Industry Regulations and Standards Your Clinical Trial Colleagues Guiding Principles for the Statistical Programmer Understand the Clinical Study Program a Task Once and Reuse Your Code Everywhere Clinical Trial Data Are Dirty Use SAS Macros Judiciously A Good Programmer Is a Good Student Strive to Make Your Programming Readable Chapter 2 Preparing and Classifying ClinicalTrial Data Preparing Clinical Trial Data “Clean” the Data If They Are Needed for Analysis Categorize Data If Necessary Avoid Hardcoding Data Classifying Clinical Trial Data Demographics and Trial-Specific Baseline Data Concomitant or Prior Medication Data Medical History Data Investigational Therapy Drug Log Laboratory Data Adverse Event Data Endpoint/Event Assessment Data Clinical Endpoint Committee (CEC) Data Study Termination Data Treatment Randomization Data Quality-of-Life Data Chapter 3 Importing Data Importing Relational Databases and Clinical Data Management Systems SAS/ACCESS SQL Pass-Through Facility SAS/ACCESS LIBNAME Statement Importing ASCII Text PROC IMPORT and the Import Wizard SAS DATA Step SAS Enterprise Guide Importing Microsoft Office Files LIBNAME Statement

Import Wizard and PROC IMPORT SAS/ACCESS SQL Pass-Through Facility SAS Enterprise Guide Importing XML XML LIBNAME Engine SAS XML Mapper Importing CDISC Model Content Files Importing CDISC SAS Transport Format Files Importing define.xml Importing CDISC ODM Files Chapter 4 Transforming Data and Creating Analysis Data Sets Key Concepts for Creating Analysis Data Sets Defining Variables Once Defining Study Populations Defining Baseline Observations Last Observation Carried Forward (LOCF) Defining Study Day Windowing Data Transposing Data Categorical Data and Why Zero and Missing Results Differ Greatly Performing Many-to-Many Comparisons/Joins Using Medical Dictionaries Other Tricks and Traps in Data Manipulation Common Analysis Data Sets Subject Level Analysis Data Set Change-from-Baseline Data Set Time-to-Event Data Set Chapter 5 Creating Tables and Listings Creating Tables General Approach to Creating Tables A Typical Clinical Trial Table Using PROC TABULATE to Create Clinical Trial Tables Using PROC REPORT to Create Clinical Trial Tables Creating Typical Continuous/Categorical Summary Tables Creating Adverse Event Summaries Creating Concomitant or Prior Medication Tables Creating a Laboratory Shift Table Creating Kaplan-Meier Survival Estimates Tables Creating Listings Output Appearance Options and Issues Creating ASCII Text Output Creating Rich Text Format (RTF) Output Creating Portable Document Format (PDF) Files “Page X of N” Pagination Solutions Footnote Indicating SAS Program and Date ODS Report Writing Interface The Power of ODS STYLE SAS Macro-Based Reporting Systems Chapter 6 Creating Clinical Trial Graphs

Common Clinical Trial Graphs Scatter Plot Line Plot Bar Chart Box Plot Forest Plot Kaplan-Meier Survival Estimates Plot SAS Tools for Creating Clinical Trial Graphs Sample Graphs Creating a Scatter Plot Creating a Line Plot Creating a Bar Chart Creating a Box Plot Creating a Forest Plot Creating a Kaplan-Meier Survival Estimates Plot Using SAS Graphics Assistants Graph-N-Go SAS Enterprise Guide ODS Graphics Designer ODS Graphics Editor When You Should Use SAS Graphics Chapter 7 Performing Common Analyses and Obtaining Statistics Obtaining Descriptive Statistics Using PROC FREQ to Export Descriptive Statistics Using PROC UNIVARIATE to Export Descriptive Statistics Obtaining Inferential Statistics from Categorical Data Analysis Performing a 2x2 Test for Association Performing an NxP Test for Association Performing a Stratified NxP Test for Association Performing Logistic Regression Obtaining Inferential Statistics from Continuous Data Analysis Performing a One-Sample Test of the Mean Performing a Two-Sample Test of the Means Performing an N-Sample Test of the Means Obtaining Time-to-Event Analysis Statistics Obtaining Correlation Coefficients General Approach to Obtaining Statistics Chapter 8 Exporting Data Exporting Data to the FDA Using the SAS XPORT Transport Format Creating ODM XML and define.xml Exporting Data Not Destined for the FDA Exporting Data with PROC CPORT Exporting ASCII Text Exporting Data to Microsoft Office Files Exporting Other Proprietary Data Formats Encryption and File Transport Options Chapter 9 The Future of SAS Programming in Clinical Trials Changes in the Business Environment

Changes in Technology Changes in Regulations Changes in Standards Use of SAS Software in the Clinical Trial Industry Chapter 10 Further Resources Regulatory Resources SAS Programming Validation FDA Resources Standards and Industry Organizations SAS Help Google Search lexjansen.com SAS-L SAS Technical Support SAS Users Groups SAS Manuals and Online Documentation SAS Press SAS Focus Areas Third-Party SAS Web Pages Useful Technical Skills Scripting Version Control Software VBScript/JavaScript for Applications Systems Development Methodology Modeling Tools Markup Languages File Transport and Data Encryption Technologies Other Applications Development Languages Qualifying for and Obtaining a Job Glossary Index

List of Programs

**** There are no programs for Chapter 7, 9, and 10***********

Chapter 1 Program 1.1 Librefs That Commonly Appear at the Start of a SAS Program Program 1.2 Using a SAS Macro to Define Common Librefs Program 1.3 Subsetting a Data Set for Patients with an Adverse Event Program 1.4 Subsetting a Data Set for Patients with an Adverse Event Using Defensive Programming Techniques Program 1.5 Example of Simple Conditional Logic IF-THEN/ELSE Program 1.6 Example of Simple Conditional Logic IF-THEN/ELSE Using Defensive Programming Techniques Program 1.7 Example of Simple Conditional Logic SELECT Program 1.8 Example of SAS Macro Code That You Should Not Write Program 1.9 Reinventing SAS BY Processing with a SAS Macro Program 1.10 Using SAS BY Processing Instead of a SAS Macro

Chapter 2 Program 2.1 Categorizing Numeric Data Program 2.2 Summarizing Free-Text Adverse Event Data Program 2.3 Summarizing Coded Adverse Event Data Program 2.4 A Hardcoding Example Program 2.5 An Improved Hardcoding Example

Chapter 3 Program 3.1 Using the SQL Pass-Through Facility to Get Data from Oracle Program 3.2 Using the SQL Pass-Through Facility to Get Selected Data from Oracle Program 3.3 Using the SAS/ACCESS LIBNAME Statement to Get Data from Oracle Program 3.4 PROC IMPORT Code Written by the Import Wizard to Read an ASCIIFile Program 3.5 Writing Custom SAS Code to Import Lab Normal Data Program 3.6 Using the LIBNAME Statement to Read Microsoft Excel Data Program 3.7 Using the LIBNAME Statement to Read Microsoft Access Data Program 3.8 PROC IMPORT Code Generated by the Import Wizard to Read a Microsoft Excel File Program 3.9 Using the SQL Pass-Through Facility to Read Microsoft Excel Data Program 3.10 Using the SQL Pass-Through Facility to Read Microsoft Access Data Program 3.11 Using the XML LIBNAME Engine to Read XML Data Program 3.12 Using PROC COPY to Read a SAS Transport File

Chapter 4 Program 4.1 Deriving Last Observation Carried Forward (LOCF) Variables

Program 4.2 Calculating Study Day Program 4.3 Deriving an Analysis Visit Based on Visit Windowing Program 4.4 Transposing Data with PROC TRANSPOSE Program 4.5 Using PROC TRANSPOSE without and with an ID Statement Program 4.6 Transposing Data with the DATA Step Program 4.7 Summary of Analysis Data Where Unknown Equals Zero Program 4.8 Summary of Analysis Data Where Unknown is Missing Program 4.9 Performing a Many-to-Many Join with PROC SQL Program 4.10 Bringing the MedDRA Dictionary Tables Together Program 4.11 Pulling Preferred Terms out of WHO Drug Program 4.12 Using Implicit or Explicit Centuries with Dates Program 4.13 Errantly Redefining a Variable within a DATA Step Program 4.14 Properly Redefining a Variable within a DATA Step Program 4.15 Using the ROUND Function with Floating-Point Comparisons Program 4.16 Creating a Blood Pressure Change-from-Baseline Data Set Program 4.17 Creating a Time-to-Event Data Set for Seizures

Chapter 5 Program 5.1 Using PROC TABULATE to Create a Summary of Demographics Program 5.2 Using PROC REPORT to Create a Summary of Demographics Program 5.3 Creating a Typical Summary of Demographics Program 5.4 Summary of Adverse Events by Maximum Severity Program 5.5 Summary of Concomitant Medications Program 5.6 Laboratory Shift Table Program 5.7 Kaplan-Meier Survival Estimates Table Program 5.8 Listing of Demographic Data Using PROC REPORT

Chapter 6 Program 6.1 Laboratory Data Scatter Plot Using PROC SGPLOT Program 6.2 Clinical Response Line Plot Using PROC SGPLOT Program 6.3 Clinical Response Bar Chart Using PROC SGPANEL Program 6.4 Creating a Box Plot Using PROC SGPLOT Program 6.5 Creating a Forest Plot Using PROC SGPLOT Program 6.6 Creating a Forest Plot Directly via PROC LOGISTIC Program 6.7 Creating a Kaplan-Meier Survival Estimates Plot Using PROC SGPLOT Program 6.8 Creating a Kaplan-Meier Failure Estimates Plot Using PROC SGPLOT Program 6.9 Creating a Kaplan-Meier Survival Estimates Plot with Patients Remaining at Risk Using PROC SGPLOT Program 6.10 Creating a Kaplan-Meier Survival Estimates Plot Using LIFETEST

Chapter 8 Program 8.1 Creating SAS XPORT Transport Format Data Sets for the FDA Program 8.2 Creating Several SAS XPORT Transport Format Data Sets Program 8.3 Using PROC CPORT to Create a SAS Transport File