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Stratification in The Cox Model: Patrick Breheny
Stratification in The Cox Model: Patrick Breheny
Patrick Breheny
November 17
Introduction
Covariates
A number of covariates which potentially affect survival were also
recorded:
karno: The Karnofsky score, a way of quantifying the
patient’s overall baseline status, with ≥ 70 denoting that the
patient is able to care for themselves, 40 − 60 meaning that
the patient requires assistance and regular medical care, and
10 − 30 meaning that the patient is hospitalized
diagtime: Time in months from diagnosis to randomization
age: Age in years at randomization
prior: Indicator for whether the patient had received prior
therapy
celltype: Type of tumor (small cell, large cell, squamous,
adenocarcinoma)
Kaplan-Meier
Standard Test
1.0
0.8
0.6
Survival
0.4
0.2
0.0
Time (years)
Cox results
Treatment ● 0.16
Prior ● 0.76
Age ● 0.35
Hazard ratio
Patrick Breheny Survival Data Analysis (BIOS 7210) 6/20
Introduction
Checking the proportional hazards assumption
Fitting stratified Cox models
Treatment (Version 1)
Standard Test
0
log(Λ(t))
−1
−2
−3
−4
Time (years)
0.6
0.4
logΛ1(t) − logΛ2(t)
0.2
0.0
−0.2
Time (years)
4
Λ2(t)
0 1 2 3 4
Λ1(t)
Cell type
0
log(Λ(t))
−1
−2
−3
−4
Time (years)
Karnofsky
0
log(Λ(t))
−1
−2
−3
−4
Time (years)
Remarks
Furthermore,
X
`(β) = `j (β)
j
X
u(β) = uj (β)
j
X
I(β) = Ij (β),
j
R code
Predictions
Standard treatment, wait 12 months, age 40, no prior treatment
1.0
0.8
0.6
Survival
0.4
0.2
0.0
Time (years)
Final remarks