SAS Programming In The Pharmaceutical Industry, Second .

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From SAS Programming in the Pharmaceutical Industry,Second Edition. Full book available for purchase here.ContentsList of Programs . xiAbout This Book .xvAbout The Author .xixAcknowledgements .xxiChapter 1 Environment and Guiding Principles . 1The Statistical Programmer’s Working Environment . 2Pharmaceutical Industry Vocabulary . 2Statistical Programmer Work Description . 2The Drug/Device Development Process . 3Industry Regulations and Standards . 4Your Clinical Trial Colleagues . 8Guiding Principles for the Statistical Programmer . 10Understand the Clinical Study . 10Program a Task Once and Reuse Your Code Everywhere. 11Clinical Trial Data Are Dirty . 13Use SAS Macros Judiciously . 15A Good Programmer Is a Good Student . 17Strive to Make Your Programming Readable . 17Chapter 2 Preparing and Classifying Clinical Trial Data . 19Preparing Clinical Trial Data . 20“Clean” the Data If They Are Needed for Analysis . 20Categorize Data If Necessary . 21Avoid Hardcoding Data . 24Classifying Clinical Trial Data . 26Demographics and Trial-Specific Baseline Data. 27

vi ContentsConcomitant or Prior Medication Data . 27Medical History Data . 28Investigational Therapy Drug Log . 29Laboratory Data . 30Adverse Event Data . 31Endpoint/Event Assessment Data . 34Clinical Endpoint Committee (CEC) Data . 35Study Termination Data . 36Treatment Randomization Data . 36Quality-of-Life Data . 38Chapter 3 Importing Data . 39Importing Relational Databases and Clinical Data Management Systems . 40SAS/ACCESS SQL Pass-Through Facility . 40SAS/ACCESS LIBNAME Statement . 41Importing ASCII Text . 41PROC IMPORT and the Import Wizard . 42SAS DATA Step . 48SAS Enterprise Guide . 49Importing Microsoft Office Files . 52LIBNAME Statement . 53Import Wizard and PROC IMPORT . 55SAS/ACCESS SQL Pass-Through Facility . 58SAS Enterprise Guide . 59Importing XML . 62XML LIBNAME Engine . 63SAS XML Mapper . 67Importing CDISC Model Content Files . 68Importing CDISC SAS Transport Format Files . 69Importing define.xml . 69Importing CDISC ODM Files . 70Chapter 4 Transforming Data and Creating Analysis Data Sets . 71Key Concepts for Creating Analysis Data Sets. 72Defining Variables Once . 72Defining Study Populations . 72

Contents viiDefining Baseline Observations . 73Last Observation Carried Forward (LOCF) . 73Defining Study Day . 78Windowing Data . 78Transposing Data . 82Categorical Data and Why Zero and Missing Results Differ Greatly . 90Performing Many-to-Many Comparisons/Joins . 93Using Medical Dictionaries . 95Other Tricks and Traps in Data Manipulation . 99Common Analysis Data Sets . 105Subject Level Analysis Data Set. 105Change-from-Baseline Data Set . 105Time-to-Event Data Set. 108Chapter 5 Creating Tables and Listings . 113Creating Tables . 114General Approach to Creating Tables . 114A Typical Clinical Trial Table . 114Using PROC TABULATE to Create Clinical Trial Tables . 116Using PROC REPORT to Create Clinical Trial Tables . 118Creating Typical Continuous/Categorical Summary Tables . 122Creating Adverse Event Summaries . 130Creating Concomitant or Prior Medication Tables . 140Creating a Laboratory Shift Table . 145Creating Kaplan-Meier Survival Estimates Tables . 152Creating Listings . 159Output Appearance Options and Issues . 164Creating ASCII Text Output . 164Creating Rich Text Format (RTF) Output. 165Creating Portable Document Format (PDF) Files . 167“Page X of N” Pagination Solutions . 168Footnote Indicating SAS Program and Date . 170ODS Report Writing Interface. 170The Power of ODS STYLE . 170SAS Macro-Based Reporting Systems . 172Chapter 6 Creating Clinical Trial Graphs . 173

viii ContentsCommon Clinical Trial Graphs . 174Scatter Plot . 174Line Plot . 174Bar Chart . 175Box Plot. 176Forest Plot . 176Kaplan-Meier Survival Estimates Plot . 177SAS Tools for Creating Clinical Trial Graphs . 178Sample Graphs . 179Creating a Scatter Plot . 179Creating a Line Plot . 182Creating a Bar Chart. 185Creating a Box Plot . 189Creating a Forest Plot . 193Creating a Kaplan-Meier Survival Estimates Plot . 198Using SAS Graphics Assistants . 212Graph-N-Go . 212SAS Enterprise Guide . 213ODS Graphics Designer . 213ODS Graphics Editor . 213When You Should Use SAS Graphics. 214Chapter 7 Performing Common Analyses and Obtaining Statistics . 215Obtaining Descriptive Statistics . 216Using PROC FREQ to Export Descriptive Statistics . 216Using PROC UNIVARIATE to Export Descriptive Statistics . 217Obtaining Inferential Statistics from Categorical Data Analysis . 218Performing a 2x2 Test for Association . 218Performing an NxP Test for Association . 219Performing a Stratified NxP Test for Association . 220Performing Logistic Regression . 221Obtaining Inferential Statistics from Continuous Data Analysis . 221Performing a One-Sample Test of the Mean . 221Performing a Two-Sample Test of the Means . 223Performing an N-Sample Test of the Means . 224Obtaining Time-to-Event Analysis Statistics . 225

Contents ixObtaining Correlation Coefficients . 226General Approach to Obtaining Statistics . 226Chapter 8 Exporting Data . 229Exporting Data to the FDA . 229Using the SAS XPORT Transport Format . 230Creating ODM XML and define.xml . 231Exporting Data Not Destined for the FDA. 232Exporting Data with PROC CPORT . 232Exporting ASCII Text . 233Exporting Data to Microsoft Office Files . 240Exporting Other Proprietary Data Formats . 243Encryption and File Transport Options . 244Chapter 9 The Future of SAS Programming in Clinical Trials . 245Changes in the Business Environment . 245Changes in Technology . 246Changes in Regulations . 246Changes in Standards . 247Use of SAS Software in the Clinical Trial Industry . 247Chapter 10 Further Resources. 249Regulatory Resources . 250SAS Programming Validation . 250FDA Resources . 250Standards and Industry Organizations . 251SAS Help. 252Google Search. 252lexjansen.com . 252SAS-L . 252SAS Technical Support . 252SAS Users Groups . 253SAS Manuals and Online Documentation . 253SAS Press . 253SAS Focus Areas . 253Third-Party SAS Web Pages . 254Useful Technica

Contents. ix Obtaining Correlation Coefficients. 226 General Approach to Obtaining Statistics . 226

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