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EPI 5344:Survival Analysis in

EpidemiologySAS Code for Cox models

March 17, 2015

Dr. N. Birkett,School of Epidemiology, Public Health &

Preventive Medicine,University of Ottawa

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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

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libname allison 'C:/allison_2010/data_sets';

PROC PHREG DATA=allison.recid; MODEL week*arrest(0)=fin age race wexp mar paro prio;RUN;

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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;

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Breslow

Efron

Exact

901/2015

Breslow

Efron

Exact

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Breslow

Efron &Exact

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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;

1201/2015

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:

01/2015

Category Format Order1 low 2

2 in-between 1

3 most 3

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;

01/2015

1501/2015

Effect coding

16

Three-level class variable

• Just for test purposes, define a 3 level variable– combines race and financial aid:

01/2015

Race Financial aid Racefin0 0 1

0 1 1

1 0 2

1 1 3

1701/2015

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;

1801/2015

Reference coding

1901/2015

Effect coding

2001/2015

Ortho-polynomial coding

2101/2015