EPI 5344: Survival Analysis in Epidemiology SAS Code for Cox models March 18 , 2014

1. EPI 5344:Survival Analysis in EpidemiologySAS Code for Cox modelsMarch 18, 2014 Dr. N. Birkett, Department of Epidemiology & Community Medicine, University of Ottawa

2. SAS code (1) • Cox models use Proc PHREG • I assume that you all have at least Version 9.2 of SAS • Prior to this version, ‘phreg’ was more limited • An experimental version (tphreg)could be used instead. BUT, I strongly encourage you to upgrade to at least SAS 9.2

3. libname allison 'C:/allison_2010/data_sets'; PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio; RUN;

7. title 'Ties Handling: BRESLOW'; PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio / TIES=BRESLOW; RUN; title 'Ties Handling: EFRON'; PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio / TIES=EFRON; RUN; title 'Ties Handling: EXACT’; PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio / TIES=EXACT; RUN;

8. Breslow Efron Exact

9. Breslow Efron Exact

10. Breslow Efron & Exact

11. PROC PHREG DATA=allison.recid; class fin /param=ref ref=last ; MODEL week*arrest(0)=fin age race wexp mar paro prio / TIES=EFRON; RUN; PROC PHREG DATA=allison.recid; class fin /param=effect ; MODEL week*arrest(0)=fin age race wexp mar paro prio / TIES=EFRON; RUN;

12. Reference coding

13. An issue with ref coding (1) • By default, SAS orders the levels of a categorical variable by the ‘format’ labels if they have been assigned. • Consider:

14. An issue with ref coding (2) • You want to use ‘level=1’ as the reference. • This SAS code won’t do that: class x/param=ref ref=first; • Instead, the reference will be level 2. • You must use this code: class x/param=ref ref=first order=internal;

15. Effect coding

16. Three-level class variable • Just for test purposes, define a 3 level variable • combines race and financial aid:

17. PROC PHREG DATA=njb1; class racefin /param=ref ref=last ; MODEL week*arrest(0)=racefin age / TIES=EFRON; RUN; PROC PHREG DATA=njb1; class racefin /param=effect ; MODEL week*arrest(0)=racefin age / TIES=EFRON; RUN; PROC PHREG DATA=njb1; class racefin /param=orthopoly ; MODEL week*arrest(0)=racefin age / TIES=EFRON; RUN;

18. Reference coding

19. Effect coding

20. Ortho-polynomial coding