Creating Survival Plots Diagnostics of Cox Model Summary of Cox Model

Informative and Elegant The function cox.zph() from survival package may be used to test the
proportional hazards assumption for a Cox regression model fit. The
The function ggforest() from the survminer package creates a forest plot
for a Cox regression model fit. Hazard ratio estimates along with confiden-

with survminer graphical verification of this assumption may be performed with the
function ggcoxzph() from the survminer package. For each covariate it
ce intervals and p-values are plotter for each variable.
library("survival")
produces plots with scaled Schoenfeld residuals against the time. library("survminer")
lung$age <- ifelse(lung$age > 70, ">70","<= 70")

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library("survival")
Survival Curves fit <- coxph(Surv(time,
ftest <- cox.zph(fit)
status) ~ sex + age, data = lung)
fit <- coxph( Surv(time, status) ~ sex + ph.ecog + age, data = lung)
fit
ftest . ## Call:
The ggsurvplot() function creates ggplot2 plots from survfit objects. ## rho chisq p ## coxph(formula = Surv(time, status) ~ sex+ph.ecog+age, data=lung)
## sex 0.1236 2.452 0.117 ##
Strata + sex=1 + sex=2 ## age -0.0275 0.129 0.719

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library("survival")

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## coef exp(coef) se(coef) z p
fit <- survfit(Surv(time,status) ## GLOBAL NA 2.651 0.266 ## sex -0.567 0.567 0.168 -3.37 0.00075
~ sex, data = lung) 1.00 library("survminer") ## ph.ecog 0.470 1.600 0.113 4.16 3.1e-05
++ ggcoxzph(ftest) ## age>70 0.307 1.359 0.187 1.64 0.10175

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++
class(fit) ++++ ##
Survival probability

0.75 + Global Schoenfeld Test p: 0.2656 Forest plot for coxph model
## [1] "survfit" + ++++ + ## Likelihood ratio test=31.6 on
++ ++ Schoenfeld Individual Test p: 0.1174 Schoenfeld Individual Test p: 0.7192 ## n= 227, number of events= 164
+
+++ ++
library("survminer")

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+++ ++
0.50 + 0.3
3 0.57 (p.value 0.00075***)
sex
ggsurvplot(fit, data = lung) +
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+ ggforest(fit)
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0.1
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Beta(t) for age

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Beta(t) for sex

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+
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1.6 (p.value 0.000031***)

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ph.ecog
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age>70
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Use the fun argument to set the transformation of the survival curve.
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E.g. "event" for cumulative events, "cumhaz" for the cumulative 55 130 180 270 340 430 560 730 55 130 180 270 340 430 560 730 10−0.4 10−0.2 100 100.2
Time Time
hazard function or "pct" for survival probability in percentage. Hazard ratio

ggsurvplot(fit, data = lung, fun = "event") The function ggcoxadjustedcurves() from the survminer package plots
ggsurvplot(fit, data = lung, fun = "cumhaz")
The function ggcoxdiagnostics() plots different types of residuals as a
Adjusted Survival Curves for Cox Proportional Hazards Model. Adjusted

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function of time, linear predictor or observation id. The type of residual is
Survival Curves show how a selected factor influences survival estimated
+ + Strata + sex=1 + sex=2 selected with type argument. Possible values are "martingale",. "devian-
Strata sex=1 sex=2
from a Cox model.
ce", "score", "schoenfeld", "dfbeta"', "dfbetas", and "scaledsch".
1.00
++ ++ Note that these curves differ from Kaplan Meier estimates since they
+++ + The ox.scale argument defines what shall be plotted on the OX axis.
+ 3 + present expected ssurvival based on given Cox model.
+ + Possible values are "linear.predictions", "observation.id", "time".
0.75
+++ + + library("survival")
Cumulative hazard

Logical arguments hline and sline may be used to add horizontal line or variable Male Female
Cumulative event

+++++ +
library("survminer")
+ + 2 smooth line to the plot.
+++ 1.00
0.50 ++ ++ residuals
lung$sex <- ifelse(lung$sex == 1,
++ ++ + library("survival")
++ ++ +++ "Male", "Female")
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+ ++++ + +++ library("survminer") 2

+++
1 0.75
+
0.25 ++++ +++ fit <- coxph(Surv(time, status) ~ fit <- coxph(Surv(time, status) ~
++ +++ ++++

Survival rate
++
++++++++++++ sex + age, data = lung)
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sex + ph.ecog + age,

Residuals (type = deviance)

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data = lung)
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Group Cases
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ggcoxdiagnostics(fit, ggcoxadjustedcurves(fit, data=lung,
Time Time 0 0.25
type = "deviance", ●

variable=lung$sex)
ox.scale = "linear.predictions")
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With lots of graphical parame-

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ters you have full control over
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Survival probability (%)

look and feel of the survival ++++ ggcoxdiagnostics(fit, time

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+ ++++ + type = "schoenfeld", −2
Note that it is not necessary to include the grouping factor in the Cox
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plots; position and content of ++ ++ ox.scale = "time") −2 −1 0 1 2 3

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+++ ++ Linear Predictions
model. Survival curves are estimated from Cox model for each group
the legend; additional annota- 50 +++ ++
+
tions like p-value, title, subtitle. + +
+++++ age ecog.ps rx defined by the factor independently. variable (35,55] (55,65] (65,85]
1.0
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ggsurvplot(fit, data = lung, 25 + 20
lung$age3 <- cut(lung$age, 1.00
1
conf.int = TRUE, + 0.5 c(35,55,65,85))
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pval = TRUE,
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p = 0.0013 ++
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Residuals (type = schoenfeld)

0 10
fun = "pct", ggcoxadjustedcurves(fit, data=lung, 0.75
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risk.table = TRUE, 0 250 500 750 1000 0.0

variable=lung$age3)
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Survival rate
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Time 0
size = 1,
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linetype = "strata",
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+ + −0.5
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Sex Male Female ●

palette = c("#E7B800",
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"#2E9FDF"), Number at risk ●

0.25
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legend = "bottom",
Male 138 62 20 7 2
legend.title = "Sex",
Sex

Female 90 53 21 3 0
legend.labs = c("Male",
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"Female")) 200 400 600 200 400 600 200 400 600 0 250 500 750 1000
Time Time time

This onepager presents the survminer package [Alboukadel Kassambara, Marcin Kosinski 2017] in version 0.3. CC BY Przemysław Biecek http://github.com/pbiecek
See https://github.com/kassambara/survminer/ for more details. https://creativecommons.org/licenses/by/4.0/