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Creating PDF documents including hyper-links, bookmarks and a table of contents with the SAS  software. Lex Jansen NV Organon Oss, The Netherlands PowerPoint PPT Presentation

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

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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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Presentation in powerpoint 97

Creating PDF documents including

hyper-links, bookmarks and a table of contents with the SAS software.

Lex JansenNV Organon

Oss, The Netherlands


Contents

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

ClinTrial

CRF

Investigator

SAS Clinical Data Warehouse

Data Entry(ClinTrial)

Electronic Submission

Document Management System (Documentum)

The Data Flow


The data flow1

SAS

ClinTrial

CRF

SAS Clinical Data Warehouse

PDF

Document Management System (Documentum)

The Data Flow

Electronic Submission


Why the pdf format

Why the PDF Format ?

  • Independent of environment

  • Easy navigation (hyperlinks, bookmarks)

  • Easy distribution (free acrobat reader)

  • The FDA wants it


Types of appendices

Types of Appendices

  • Statistical analyses (STAT)(different sections with:tables, analyses, graphics, listings)

  • Individual data listings (IDL)

  • Case report form tabulations (CRF)


Statistical analysis

Statistical Analysis


Individual data listing

Individual Data Listing


Case report form tabulation

Case Report Form Tabulation


Environment

Environment

  • Windows NT, SP 4

  • Sas 6.12, TS045, only SAS/base

  • Acrobat distiller 3.02 / 4.05


How do we get from sas to pdf

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!!


How to get from sas to pdf

Postscript

file

Listings

PDF file

How to Get From SAS to PDF

Tables

Analyses

%_sas2ps

Graphics

%_ps2pdf + Acrobat Distiller

SAS output


From postscript to pdf

IN

PS2PDF

AcrobatDistillerwatches

OUT

AcrobatDistillerconverts

From Postscript to PDF

Convert!!

X


Sas output conventions

SAS Output Conventions

  • Portraitlinesize=94pagesize=87landscapelinesize=145pagesize=56

  • Options NOCENTER NODATE NONUMBER

  • Conventions for TITLES and FOOTNOTES

  • Graphic output uses postscript DEVICE=PSL


Sas output conventions titles

<section>-<number>or <number>

Table, Analysis, Listing, Figure

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 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

Table of Contents


Sas output conventions footnotes

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

Postscript file

Text file with title

SAS Output Conventions- Graphics

  • Graphics are generated with a postscript device (PSL)

  • Every graphic has a corresponding text file with the title in it


Sas output conventions graphics1

Postscript file

Text file with title

SAS Output Conventions- Graphics

  • Graphics are generated with a postscript device (PSL)

  • Every graphic has a corresponding text file with the title in it

#Figure 6.1.E ANCOVA model check: normal Q-Q plot of studentized residuals

Outcome variable: (Prothrombin) Fragment 1+2 [nmol/L]

Outliers excluded

Per Protocol group


What is postscript

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

(595,842)

=

8,3 inch x11,7 inch

(0,0)

Postscript - Coordinate System

A4

1 inch

=

72 points


Postscript coordinate system1

(612,792)

=

8,5 inch x11 inch

(0,0)

Postscript - Coordinate System

Letter

1 inch

=

72 points


Postscript adding text

Postscript - Adding Text

Listing 4Dosing Compliance.

Descriptives per Subject and per Cycle.

Intent-to-Treat Group.

Choose fontX-coordinateY-coordinatemoveto(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

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

%%EndProlog

%%BeginSetup

...

%%EndSetup

%%Page: 1

%%Page: 2

%%Trailer

%%DocumentFonts: Courier Helvetica-Bold Helvetica

%%Pages: 474

%%EOF

Define procedures and fonts

Define Hyperlinks and Bookmarks

Describe page 1

Describe page 2


How to use the pdfmark operator

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

How to Define PDF Bookmarks?

[/Title string

/Count int

…action-specific key-value pairs

/OUT pdfmark


How to define pdf bookmarks1

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

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 hyperlinks1

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

From SAS to Postscript

  • SAS macro %_SAS2PS

  • Parameters:

    Authorcreator of the appendix

    Apptypetype 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 postscript1

From SAS to Postscript

  • SAS macro %_SAS2PS

  • Parameters:

Pagetext text in pagenumber

Filemaskselection of files to include

Maketocgenerate table of contents (Y/N) ?

T1, ..., t24 character strings with section titles.

Watermrk generate watermark (Y/N) ?

Wmtextwatermark text in case watermrk=y

Bookmark generate bookmarks (Y/N) ?


From sas to postscript2

From SAS to Postscript

  • SAS macro %_SAS2PS

  • Parameters:

Firstpagstarting pagenumber in output file.

Inliblibname of library with input SAS files

Outliblibname of library where postscript file will be written.

Outfilename of postscript file.


Sas2ps macro

%_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

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

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


Presentation in powerpoint 97

Demo


Questions

Questions ?

PDF ??

Postscript ??

PDFMark ??

SAS ??


Thank you

Thank You !!

Contact:

[email protected]


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