01/20151 EPI 5344: Survival Analysis in Epidemiology SAS Code for Cox models March 17, 2015 Dr. N. Birkett, School of Epidemiology, Public Health & Preventive Medicine, University of Ottawa

01/20152 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 –Current version is 9.4

01/20153 libname allison 'C:/allison_2010/data_sets'; PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio; RUN;

01/20154

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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;

01/20158 Breslow Efron Exact

01/20159 Breslow Efron Exact

01/ Breslow Efron & Exact

01/ 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;

01/ Reference coding

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: 01/ CategoryFormatOrder 1low2 2in-between1 3most3

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; 01/201514

01/ Effect coding

Three-level class variable Just for test purposes, define a 3 level variable –combines race and financial aid: 01/ RaceFinancial aidRacefin

01/ 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;

01/ Reference coding

01/ Effect coding

01/ Ortho-polynomial coding

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