Creating PDF documents including
hyper-links, bookmarks and a table of contents

with the SAS software.
Lex Jansen
NV Organon
Oss, The Netherlands
Contents
• Data flow
• Why PDF ?
• Types of appendices
• From SAS to Postscript to PDF
• SAS output conventions
• Postscript
• PDF mark operator
• %_SAS2PS
• Demo
The Data Flow
Investigator
Data Entry
(ClinTrial)
Electronic
Submission
SAS Clinical
Data Warehouse
Document Management
System (Documentum)
The Data Flow
SAS
SAS Clinical
Data Warehouse
PDF
Electronic
Submission
Document Management
System (Documentum)
Why the PDF Format ?
• Independent of environment
• Easy navigation (hyperlinks, bookmarks)
• Easy distribution (free acrobat reader)
• The FDA wants it
Why the PDF Format ? (FDA)
“In general, for documents with a table of contents,
provide bookmarks and hypertext links for each item listed
in the table of contents including all tables, figures,
publications, other references, and appendices. These
bookmarks and hypertext links are essential for the
efficient navigation through documents. In general,
including a bookmark to the main table of contents for a
submission or item is helpful. Make the bookmark
hierarchy identical to the table of contents. Avoid using
bookmark levels in addition to those present in the table
of contents.”
Types of Appendices
• Statistical analyses (STAT)
(different sections with:
tables, analyses, graphics, listings)
• Individual data listings (IDL)
• Case report form tabulations (CRF)
Statistical Analysis
Individual Data Listing
Case Report Form Tabulation
Environment
• Windows NT, SP 4
• Sas 6.12, TS070, only SAS/Base
• Adobe Acrobat distiller 4.05
How Do We Get From SAS to PDF?
•
Install complete Adobe Acrobat package and use the Acrobat
PDFwriter printerdriver
But, no bookmarks and hyperlinks
•
SAS version 8 can generate PDF output for graphics output
•
SAS V8.2 brings PDF output with the output delivery system
(ODS)
Bookmarks and hyperlinks ??? Yes, but….
•
Solution: create postscript with SAS and use Acrobat Distiller
with the pdfmark operator!!
How to Get From SAS to PDF
Tables
Analyses
Postscript
file
%_sas2ps
Graphics
Listings
%_ps2pdf +
Acrobat Distiller
SAS output
PDF file
From Postscript to PDF
Convert!!
IN
x
PS2PDF
Acrobat
Distiller
watches
OUT
Acrobat
Distiller
converts
SAS Output Conventions
•
Portrait
Landscape
•
Options NOCENTER NODATE NONUMBER
•
Conventions for TITLES and FOOTNOTES
•
Graphic output uses postscript DEVICE=PSL
:
:
linesize=94
linesize=145
pagesize=87
pagesize=56
SAS Output Conventions - Titles
Table 2.8-1.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
<section>-<number>
or <number>
#Table 2.8-1.B
#Table 2.8-1.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 of
Contents
SAS Output Conventions - Footnotes
|
SD
|
|
|
3.54|
|
Minimum
|
20|
25|
20|
|____________________________|_________|_________|_________|
(CONTINUED)
Compound: Puregon (E1650), SAS program: tab_cycle
/Date:21MAR2000 16:23
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
SAS Output Conventions
- Graphics
• Graphics are generated with a postscript
device (PSL)
ANCOVA
model check:
normal
Q-Q plot of studentized text
residuals
• Every
graphic
has
a
corresponding
Outcome variable: (Prothrombin) Fragment 1+2 [nmol/L]
excluded
fileOutliers
with
the
title in it
Per Protocol group
#Figure 6.1.E
Postscript file
Text file with title
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)
Postscript - Coordinate System
1 inch
(595,842)
=
=
72 points
A4
(0,0)
8,3 inch x
11,7 inch
Postscript - Coordinate System
1 inch
(612,792)
=
=
72 points
Letter
(0,0)
8,5 inch x
11 inch
Postscript - Adding Text
Listing 4
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
108 730 moveto (Listing 4) ushow
205 730 moveto (Dosing Compliance.) show
/Helvetica findfont 8 scalefont setfont
205 723 moveto (Descriptives per Subject and per Cycle.) show
205 716 moveto (Intent-to-Treat Group.) show
Postscript - Document Structuring
Conventions
%!PS-Adobe-3.0
%%Title: Protocol 068004 Appendix F
%%CreationDate: 29MAR2000 18:31
%%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
How to Use the Pdfmark Operator ?
• Used in postscript files to represent PDF
features.
• General syntax:
[
…. Various key-value pairs…
kind pdfmark
How to Define PDF Bookmarks?
[
/Title string
/Count int
…action-specific key-value pairs
/OUT pdfmark
How to Define PDF Bookmarks?
[/Title (F.3 Extent of Exposure)
/Count 3
/Page 121
/View [/XYZ 103 775 null]
/OUT pdfmark
[/Title (TAB 3.A Summary statistics of extent of exposure*Per Protocol group)
/Page 122
/View [/XYZ 144.6 116.68 null]
/OUT pdfmark
[/Title (TAB 3.B Summary statistics of extent of exposure*All-Subjects-Treated group)
/Page 125
/View [/XYZ 144.6 116.68 null]
/OUT pdfmark
[/Title (LIS 3.A Extent of exposure \(treatment duration in days\)*All-Subjects-Treated group)
/Page 128
/View [/XYZ 144.6 116.68 null]
/OUT pdfmark
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
How to Define PDF Hyperlinks?
108 291 moveto (Listing 1.3-A) ushow
205 291 moveto (Subjects for whom the blind was broken during the study) show
205 283 moveto (All-Subjects-Randomized group) show
(F-26) Calc Dots
[ /Rect [ 106 581 528 601 ]
/Color [0 0 1]
/Page 25
/View [/XYZ 144 117 null]
/Subtype /Link
/ANN pdfmark
From SAS to Postscript
•
SAS macro %_SAS2PS
•
Parameters:
Author
creator of the appendix
Apptype
type of appendix (STAT, IDL or CRF)
Apptype=stat, sections will be generated.
Apptype=idl, no sections will be generated.
Apptype=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
From SAS to Postscript
•
SAS macro %_SAS2PS
•
Parameters:
Pagetext
text in pagenumber
Filemask
selection of files to include
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) ?
From SAS to Postscript
•
SAS macro %_SAS2PS
•
Parameters:
Firstpag
starting pagenumber in output file.
Inlib
libname of library with input SAS files
Outlib
libname of library where postscript file will be written.
Outfile
name of postscript file.
%_SAS2PS Macro
• Read in all text files
• Sort by section, type and number
• Generate table of contents
• Generate postscript, including:
– Bookmark / hyperlink information
– Graphics
Conclusion
• With SAS/Base and Acrobat Distiller it is
possible to create PDF documents from
SAS output.
• This process is completely automated
Where to Get the Info?
•
First guide to postscript:
http://www.Cs.Indiana.Edu/docproject/
programming/postscript/postscript.Html
•
Pdfmark reference manual:
http://partners.Adobe.Com/asn/developer/
technotes.Html
•
Pdfmark primer by thomas merz:
http://www.Pdflib.Com/pdfmark/index.Html
•
Get ghostscript/ghostview:
http://www.Cs.Wisc.Edu/~ghost/index.Html
Questions ?
PDF ??
Postscript ??
PDFMark ??
SAS ??
Thank
You !!
Contact:
lex.jansen@organon.com