Creating PDF documents including hyper-links, bookmarks and a table of contents with the SAS software. Lex Jansen NV Organon Oss, The Netherlands
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1 Creating PDF documents including hyper-links, bookmarks and a table of contents with the SAS software. Lex Jansen NV Organon Oss, The Netherlands
2 Contents Data flow Why PDF? Types of appendices From SAS to Postscript to PDF SAS output conventions Postscript PDF mark operator %_SAS2PS Demo
3 The Data Flow CRF ClinTrial Investigator Data Entry (ClinTrial) SAS Clinical Data Warehouse Electronic Submission Document Management System (Documentum)
4 CRF The Data Flow ClinTrial SAS SAS Clinical Data Warehouse PDF Electronic Submission Document Management System (Documentum)
5 Why the PDF Format? Independent of environment Easy navigation (hyperlinks, bookmarks) Easy distribution (free acrobat reader) The FDA wants it
6 Types of Appendices Statistical analyses (STAT( STAT) (different sections with: tables, analyses, graphics, listings) Individual data listings (IDL( IDL) Case report form tabulations (CRF( CRF)
7 Statistical Analysis
8 Individual Data Listing
9 Case Report Form Tabulation
10 Environment Windows NT, SP 4 Sas 6.12, TS045, only SAS/base Acrobat distiller 3.02 / 4.05
11 How Do We Get From SAS to PDF? Install complete acrobat package and use the acrobat pdfwriter printerdriver But, no bookmarks and hyperlinks SAS version 8 can generate PDF output for graphics output The future might bring PDF output with the output delivery system (ODS) Bookmarks and hyperlinks??? Solution: create postscript with SAS and use acrobat distiller and the pdfmark operator!!
12 How to Get From SAS to PDF Tables Analyses Graphics Listings %_sas2ps %_ps2pdf + Acrobat Distiller Postscript file SAS output PDF file
13 From Postscript to PDF Convert!! Acrobat Distiller watches IN X PS2PDF Acrobat Distiller converts OUT
14 SAS Output Conventions Portrait linesize=94 pagesize=87 landscape linesize=145 pagesize=56 Options NOCENTER NODATE NONUMBER Conventions for TITLES and FOOTNOTES Graphic output uses postscript DEVICE=PSL
15 SAS Output Conventions - Titles Table B Summary statistics of minimum cycle length. All-Subjects-Treated Group. Restricted to subjects with irregular cycle length < 41 days. Minimum cycle length (days) Puregon Table, Analysis, Listing, Figure #Table B <section>-<number> or <number> #Table B Summary statistics of minimum cycle length. All-Subjects-Treated Group. Restricted to subjects with irregular cycle length < 41 days. Minimum cycle length (days) Puregon
16 Table of Contents
17 SAS Output Conventions - Footnotes SD 3.54 Minimum (CONTINUED) Compound: Puregon (E1650), SAS program: tab_cycle /Date:21MAR :23
18 SAS Output Conventions - Graphics Graphics are generated with a postscript device (PSL) Every graphic has a corresponding text file with the title in it Postscript file Text file with title
19 SAS Output Conventions - Graphics Graphics are generated with a postscript device (PSL) Every Outcome graphic variable: has (Prothrombin) a corresponding Fragment 1+2 [nmol/l] text Outliers excluded file with the title in it Per Protocol group #Figure 6.1.E ANCOVA model check: normal Q-Q plot of studentized residuals Postscript file Text file with title
20
21 What Is Postscript? Page description language A page is a graphic that can contain: Lines, rectangles, curves Text in various typefaces of any size and orientation Device independent Closely related to PDF (both adobe)
22 Postscript - Coordinate System 1 inch = 72 points A4 (595,842) = 8,3 inch x 11,7 inch (0,0)
23 Postscript - Coordinate System 1 inch = 72 points Letter (612,792) = 8,5 inch x 11 inch (0,0)
24 Listing 4 Postscript - Adding Text Dosing Compliance. Descriptives per Subject and per Cycle. Intent-to-Treat Group. Choose font X-coordinate Y-coordinate moveto (text to show) show /Helvetica-Bold findfont 8 scalefont setfont moveto (Listing 4) ushow moveto (Dosing Compliance.) show /Helvetica findfont 8 scalefont setfont moveto (Descriptives per Subject and per Cycle.) show moveto (Intent-to-Treat Group.) show
25 Postscript - Document Structuring Conventions %!PS-Adobe-3.0 %%Title: Protocol Appendix F %%CreationDate: 29MAR :31 %%Generated by: _SAS2PS 1.0 May 1999 ((c) NV Organon, SAS 6.12, WIN_NT)... %%EndComments %%BeginProlog Define procedures and fonts %%EndProlog %%BeginSetup... Define Hyperlinks and Bookmarks %%EndSetup %%Page: 1 Describe page 1 %%Page: 2 Describe page 2 %%Trailer %%DocumentFonts: Courier Helvetica-Bold Helvetica %%Pages: 474 %%EOF
26 How to Use the Pdfmark Operator? Used in postscript files to represent PDF features. General syntax: [. Various key-value pairs kind pdfmark
27 How to Define PDF Bookmarks? [ /Title string /Count int action-specific key-value pairs /OUT pdfmark
28 How to Define PDF Bookmarks? [/Title (F.3 Extent of Exposure) /Count 3 /Page 121 /View [/XYZ null] /OUT pdfmark [/Title (TAB 3.A Summary statistics of extent of exposure*per Protocol group) /Page 122 /View [/XYZ null] /OUT pdfmark [/Title (TAB 3.B Summary statistics of extent of exposure*all-subjects-treated group) /Page 125 /View [/XYZ null] /OUT pdfmark [/Title (LIS 3.A Extent of exposure \(treatment duration in days\)*all-subjects-treated group) /Page 128 /View [/XYZ null] /OUT pdfmark
29 How to Define PDF Hyperlinks? [ /Rect [llx[ lly urx ury] /Border [bx[ by c [d]] /SrcPg pagenum /Color array /Subtype /Link action-specific key-value pairs /ANN pdfmark
30 How to Define PDF Hyperlinks? moveto (Listing 1.3-A) ushow moveto (Subjects for whom the blind was broken during the study) show moveto (All-Subjects-Randomized group) show (F-26) Calc Dots [ /Rect [ ] /Color [0 0 1] /Page 25 /View [/XYZ null] /Subtype /Link /ANN pdfmark
31 From SAS to Postscript SAS macro %_SAS2PS Parameters: Author Apptype creator of the appendix type of appendix (STAT, IDL or CRF) Apptype=stat stat,, sections will be generated. Apptype=idl idl,, no sections will be generated. Apptype=crf crf,, no sections will be generated. No table of contents will be generated. Special formatting can be applied with tags: <1> and <2> for bookmarks, <u>=underline, <b>=bold, <h>=helvetica helvetica
32 Pagetext Filemask Maketoc T1,..., t24 From SAS to Postscript SAS macro %_SAS2PS Parameters: text in pagenumber selection of files to include generate table of contents (Y/N)? Maketoc generate table of contents (Y/N)? T1,..., t24 character strings with section titles. Watermrk generate watermark (Y/N)? Wmtext watermark text in case watermrk=y Bookmark generate bookmarks (Y/N)?
33 From SAS to Postscript SAS macro %_SAS2PS Parameters: Firstpag Inlib Outlib Outfile starting pagenumber in output file. libname of library with input SAS files libname of library where postscript file will be written. name of postscript file.
34 %_SAS2PS Macro Read in all text files Sort by section, type and number Generate table of contents Generate postscript, including: Bookmark / hyperlink information Graphics
35 Conclusion With SAS/Base and Acrobat Distiller it is possible to create PDF documents from SAS output. This process is completely automated
36 Where to Get the Info? First guide to postscript: Edu/docproject/ programming/postscript/postscript.html Pdfmark reference manual: asn/developer/ technotes.html Pdfmark primer by thomas merz: Pdflib.Com/pdfmark/index.Html Get ghostscript/ghostview ghostview: Wisc.Edu/~ghost/index.Html
37
38 Questions? PDFMark?? PDF?? Postscript?? SAS??
39 Thank You!! Contact:
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