Post on 25-Feb-2016
description
Survival Models in SAS
Learning ObjectivesWhat type of data merits these?What tools does SAS have?How do I do descriptive analysis?How do I do modelling?Is the model appropriate?A.Pope - Essay on Criticism Part ii Line 15
My Data Stops in the Middle
• Outcome is typically a time duration until an event
• Outcome is not observed for some proportion of the population
• Often the outcome is death of a patient– Other examples
• Failure of an electronic component• Divorce• Change cell phone provider
SAS to the rescue
• Exploratory– FREQ– UNIVARIATE– MEANS/SUMMARY– GPLOT
• Time-to-event most commonly analysed using– LIFETEST– PHREG
Baby’s First Dataset
• NSAPD: Mum’s and babes since 1980• All NS births since 1988• Comprehensive clinical and demographic data• Includes gestational age at birth/delivery• Spontaneous / Induced / No Labour• Question: What factors associated with
premature birth?
How is this ‘time-to-event’?
• Birth is the event• When birth would have happened is censored
– Induced labour– Straight to Caesarean Section
• Measured in weeks since LMP• A (large) set of known risk factors• Many captured in Atlee
The Usual Suspects
• Previous preterm delivery• Multiples• < 6 mos since last preg• Surgery on cervix• IVF• Uterine abnormalities• Smoking
A Long Line-Up• Chorioamnionitis• Weight Gain• UTI• BP• (G)DM• Maternal Weight• Previous Loss• Antepartum Trauma• A/P Bleeding• Polyhydramnios
This LIFE is a TESTThis life is a test-it is only a test.
If it had been an actual life, you would have received furtherinstructions on where to go and what to do.
Remember, this life is only a test.
• proc lifetest• data = Work.ForSHRUG• plots = (s,ls,lls)• maxtime = 45;• time GA_Best * Spontaneous_Labour ( 0 );• id Labour /* censoring = Induced / None */;• strata DLNumFet;• test Prev_PTD Overweight AdmitSmk;• /* latter two most interesting from population health perspective */
• run;
The LIFETEST Procedure
Stratum 4: # of Foetuses = Twins
Product-Limit Survival Estimates
GA_BEST Survival FailureSurvival StandardError
NumberFailed
NumberLeft LABOUR
32.0000 0.9075 0.0925 0.00324 743 7111 S
33.0000 0.8837 0.1163 0.00359 927 6819 S
34.0000 0.8465 0.1535 0.00407 1210 6383 S
35.0000 0.7884 0.2116 0.00466 1638 5761 S
36.0000 0.7119 0.2881 0.00525 2176 4918 S
37.0000 0.6154 0.3846 0.00582 2784 3717 S
38.0000 0.4864 0.5136 0.00651 3417 2145 S
39.0000 0.3550 0.6450 0.00745 3821 861 S
40.0000 0.2125 0.7875 0.00837 4076 325 S
41.0000 0.0999 0.9001 0.00868 4186 76 S
42.0000 0.0543 0.9457 0.00859 4210 22 S
43.1430 0.0339 0.9661 0.00979 4214 6 S
More Babies Arrive Sooner - DuhTest of Equality over Strata
Test Chi-Square DF Pr >Chi-Square
Log-Rank 12814.4469 3 <.0001
Wilcoxon 17518.2974 3 <.0001
-2Log(LR) 184.4172 3 <.0001
Lots of Data = Tiny p-values
Univariate Chi-Squares for the Wilcoxon Test
Variable Test Statistic
StandardError Chi-Square Pr >
Chi-Square Label
PREV_PTD -512.1 21.2544 580.5 <.0001# Previous Preterm Deliveries
Overweight 1074.1 58.7622 334.1 <.0001
ADMITSMK -18207.7 1727.7 111.1 <.0001# Cigarettes / Day @ Admission
Rank Tests for the Association of GA_BEST with Covariates Pooled over Strata
Apply the “C” test
Make the punishment fit the crime
Smoking and weight matter … how much?
• Hazards – not just for golf any more• Proportional Hazards REGression• Doesn’t assume functional form for baseline
hazard• Does assume that effect of covariate
proportional over time• Manifests itself as, e.g., parallel lines on plot
Deciphering the code
• proc phreg• data = Work.ForSHRUG• plots ( overlay timerange = 24, 44 )=• ( cumhaz survival ) /* interesting weeks */• simple /* compare healthy/unhealthy */;• where Weighted_Ran > 0.9;• /* 10% of 'healthy' + 55% w/ 1 risk factor + */
Modelling – not just for the young and beautiful !
• model GA_Best * Spontaneous_Labour ( 0 ) =• Prev_PTD DLNumFet AdmitSmk
Chorioamnionitis Gest_HT PrexHT Pre_Existing_Diabetes GDM DLAborts Overweight Underweight ;
• assess var = ( Prev_PTD DLNumFet AdmitSmk Chorioamnionitis Gest_HT PrexHT GDM DLAborts Pre_Existing_Diabetes Overweight Underweight )
• ph; /* / resample seed = 19 *//* takes 8 hours to run! */
Odious? NO – ODS – Yes!• ODS GRAPHICS ON; ODS GRAPHICS OFF;
What about plurality?
Transformational Experience
On the other hand …
But what about the question?Analysis of Maximum Likelihood Estimates
Parameter DF ParameterEstimate
StandardError
Chi-Square Pr > ChiSq Hazard
Ratio Label
PREV_PTD 1 0.47499 0.03067 239.8634 <.0001 1.608# Previous Preterm Deliveries
DLNUMFET 1 1.43623 0.05435 698.4233 <.0001 4.205 # of Foetuses
ADMITSMK 1 0.00368 0.0005484 45.1439 <.0001 1.004# Cigarettes / Day @ Admission
Assume makes an ass of u and meChorioamnionitis 1 -0.05611 0.12410 0.2044 0.6512 0.945
Gest_HT 1 -0.88739 0.13010 46.5222 <.0001 0.412 Gestational Hypertension
PrexHT 1 -0.34641 0.10133 11.6869 0.0006 0.707 Pre-existing Hypertension
Pre_Existing_Diabete 1 -0.03388 0.11821 0.0821 0.7744 0.967 Pre-existing Diabetes
GDM 1 -0.08809 0.04698 3.5162 0.0608 0.916 Gestational Diabetes
DLABORTS 1 -0.0002450 0.01265 0.0004 0.9845 1.000# of Pregnancies, Excl. the Present, with Non-viable Foetus
Criticism
A little learning is a dangerous thing;Drink deep, or taste not the Pierian spring:There shallow draughts intoxicate the brain,And drinking largely sobers us again.
Two of 372 rhyming couplets
Competing Risks
• Censoring must be non-informative• Here some covariates are associated with
– Induction– No Labour– Need different models
• Look at cumulative probability of 3 outcomes
One last tidbit• %CIF macro• http://support.sas.com/kb/45/addl/fusion_45997_13_fusion_45997_12_cif.txt
• Crude cumulative incidence function• No covariates• Endpoints (time to spontaneous labour, e.g.) subject to competing
risks– Induction for reason associated with length of pregnancy– No Labour for …
• Comes with confidence limits• Needs Base & IML ( in 9.2 also GRAPH )• No recommendation
Questions?
• SHRUG.President@gmail.com• Ron.Dewar@HowDidIGetInvolved?ca
• http://www.ats.ucla.edu/stat/examples/asa/test_proportionality.htm• http://www4.stat.ncsu.edu/~lu/ST790/homework/Biometrika-1993-LIN-557-72.pdf
• http://escarela.com/archivo/anahuac/03o/residuals.pdf
• SAS is a registered trademark or trademark of SAS Institute Inc. in Canada, the USA and other countries with dysfunctional political institutions.