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R-tutorial: survival analysis

Open R-markdown version of this file

This tutorial shows some basic tools for survival analysis using R. In particular, how to obtain the Kaplan-Meier graph and how to fit a
univariate and a multiple Cox regression model. It is also shown how to export the results in a publishable table format.

For the purpose of illustration we use the German breast cancer data which are for example shipped with the R-package pec:

Loading data for tutorial

We load the data from the 'pec' package:

library(data.table)
library(pec)
data(GBSG2,package="pec")
setDT(GBSG2)
GBSG2

horTh age menostat tsize tgrade pnodes progrec estrec time cens
1: no 70 Post 21 II 3 48 66 1814 1
2: yes 56 Post 12 II 7 61 77 2018 1
3: yes 58 Post 35 II 9 52 271 712 1
4: yes 59 Post 17 II 4 60 29 1807 1
5: no 73 Post 35 II 1 26 65 772 1
---
682: no 49 Pre 30 III 3 1 84 721 0
683: yes 53 Post 25 III 17 0 0 186 0

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 684: no 51 Pre 25 III 5 43 0 769 1 TABLE OF CONTENTS
685: no 52 Post 23 II 3 15 34 727 1
686: no 55 Post 23 II 9 116 15 1701 1

Then, we make sure that tumor grade is a factor:

GBSG2$tgrade <- as.factor(as.character(GBSG2$tgrade))

GBSG2$Age <- cut(GBSG2$age,c(0,40,60,81),labels=c("21-40","41-60","61-80"))

and we categorize age into 4 categories:

GBSG2$Age <- cut(GBSG2$age,c(-Inf,40,50,65,Inf),labels=c("<40","40-50","51-65",">65"))

We also load the R-packages survival and prodlim and Publish

library(prodlim)
library(survival)
library(Publish)

Estimation of the median follow-up time

When reporting the length of follow-up usually the aim is to describe how long the study was able to observe the enrolled
subjects. Naive estimates using e.g., the observed times of all subjects tend to underestimate follow-up because of early events.
Schemper and Smith (Control Clin Trials, 1996,17:343–346) suggested to estimate potential follow-up based on the Kaplan-
Meier for the censored times. An approximation of this so-called reverse Kaplan-Meier can be obtained by reversing the event
indicator so that the outcome of interest becomes being censored. However, when there are ties in the data in the sense that some
subjects have exactly the same event times then this would not be exactly correct. Here is how to calculate the reverse Kaplan-
Meier estimate which is always exactly correct and how to obtain median follow-up with 95% confidence limits and inter quartile
range (IQR):

quantile(prodlim(Hist(time,cens)~1,data=GBSG2,reverse=TRUE))

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 TABLE OF CONTENTS

Quantiles of the potential follow up time distribution based on the Kaplan-Meier method
applied to the censored times reversing the roles of event status and censored.

Table of quantiles and corresponding confidence limits:

q quantile lower upper
1 0.00 NA NA NA
2 0.25 1976 1869 2027
3 0.50 1645 1570 1714
4 0.75 1100 974 1195
5 1.00 8 8 17
Median time (IQR):1645.00 (1100.00;1976.00)

The median potential follow-up time of the GBSG2 study was 1645 days (IQR: [1100 days;1714 days]). This means that 50% of
the patients would have been observed for at least 1645 days had there been no events.

Kaplan-Meier

Kaplan-Meier graph

km0 <- prodlim(Hist(time,cens)~1,data=GBSG2)

plot(km0)

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 TABLE OF CONTENTS

after some fine tuning:

km0 <- prodlim(Hist(time,cens)~1,data=GBSG2)

par(mar=c(7,7,5,5), # margin of figure

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 mgp=c(4,1,0)) # move axis label away from figure TABLE OF CONTENTS
plot(km0,
xlab="Years", # label for x-axis
ylab="Absolute risk of death", # label for y-axis
type="cuminc", # increasing risks = 1-survival instead of
axis1.at=seq(0,2900,365.25), # time grid for x-axis
axis1.labels=0:7, # time labels for x-axis
axis2.las=2, # rotate labels of y-axis
atrisk.dist=1, # adjust numbers below the figure
atrisk.labels="Number of \npatients: ") # labels for numbers below figure

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 TABLE OF CONTENTS

Stratified Kaplan-Meier

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 km1 <- prodlim(Hist(time,cens)~tgrade,data=GBSG2) TABLE OF CONTENTS
par(mar=c(7,7,5,5), mgp=c(3,1,0))
plot(km1,
atrisk.labels=paste("Tumor grade: ",c("I","II","III"),": "),
atrisk.title="",
xlab="Years", # label for x-axis
axis1.at=seq(0,2900,365.25), # time grid for x-axis
axis1.labels=0:7, # time labels for x-axis
legend.x="bottomleft", # positition of legend
legend.cex=0.8, # font size of legend
legend.title="Tumor Grade\n", #
logrank=TRUE) # show log-rank p-value

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 TABLE OF CONTENTS

Log-rank test

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 survdiff(Surv(time,cens)~horTh,data=GBSG2) TABLE OF CONTENTS

Call:
survdiff(formula = Surv(time, cens) ~ horTh, data = GBSG2)

N Observed Expected (O-E)^2/E (O-E)^2/V

horTh=no 440 205 180 3.37 8.56
horTh=yes 246 94 119 5.12 8.56

Chisq= 8.6 on 1 degrees of freedom, p= 0.003

Median survival

overall Kaplan-Meier

km0 <- prodlim(Hist(time,cens)~1,data=GBSG2)

quantile(km0)

Quantiles of the event time distribution based on the method.

Table of quantiles and corresponding confidence limits:

q quantile lower upper
1 0.00 NA NA NA
2 0.25 NA 2456 NA
3 0.50 1807 1528 2018
4 0.75 727 612 801
5 1.00 72 72 120
Median time (IQR):1807.00 (727.00;--)

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 stratified Kaplan-Meier TABLE OF CONTENTS

km1 <- prodlim(Hist(time,cens)~tgrade,data=GBSG2)

quantile(km1)

Quantiles of the event time distribution based on the method.

Table of quantiles and corresponding confidence limits:

tgrade=I

q quantile lower upper 1 0.00 NA NA NA 2 0.25 NA NA NA 3 0.50 NA 1990 NA 4 0.75 1459 991 NA 5 1.00
476 476 662 Median time (IQR):– (1459.00;–)

Table of quantiles and corresponding confidence limits:

tgrade=II

q quantile lower upper 1 0.00 NA NA NA 2 0.25 NA 2456 NA 3 0.50 1730 1481 2018 4 0.75 745 646 842 5 1.00
72 72 171 Median time (IQR):1730.00 (745.00;–)

Table of quantiles and corresponding confidence limits:

tgrade=III

q quantile lower upper 1 0.00 NA NA NA 2 0.25 NA 2034 NA 3 0.50 1337 956 2034 4 0.75 476 403 571 5 1.00
98 98 177 Median time (IQR):1337.00 (476.00;–)

Quantiles of event time distribution

tgrade=I

Median time (lower.95; upper.95): – (1990;–) IQR (time): (1459;–)

tgrade=II

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 Median time (lower.95; upper.95): 1730 (1481;2018) IQR (time): (745;–) TABLE OF CONTENTS

tgrade=III

Median time (lower.95; upper.95): 1337 (956;2034) IQR (time): (476;–)

Tabulate results

Overall Kaplan-Meier

km0 <- prodlim(Hist(time,cens)~1,data=GBSG2)

publish(km0,times=seq(0,2900,365.25),org=TRUE)

Interval No. at risk No. of events No. lost to follow-up Survival probability CI.95
0.0– 0.0 686 0 0 100.0 0.0–100.0
0.0– 365.2 686 56 28 91.6 89.4– 93.7
365.2– 730.5 602 109 35 74.6 71.3– 78.0
730.5–1095.8 458 59 68 64.3 60.5– 68.1
1095.8–1461.0 331 39 64 55.9 51.8– 60.0
1461.0–1826.2 228 22 85 49.2 44.7– 53.7
1826.2–2191.5 121 11 74 41.9 36.3– 47.4
2191.5–2556.8 36 3 30 34.3 24.7– 43.8

Stratified Kaplan-Meier

km1 <- prodlim(Hist(time,cens)~tgrade,data=GBSG2)

publish(km1,times=seq(0,2900,365.25),org=TRUE)

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 TABLE OF CONTENTS
tgrade=I

Interval No. at risk No. of events No. lost to follow-up Survival probability CI.95
0.0– 0.0 81 0 0 100.0 0.0–100.0
0.0– 365.2 81 0 4 100.0 0.0–100.0
365.2– 730.5 77 5 7 93.1 87.2– 98.9
730.5–1095.8 65 6 8 83.8 74.9– 92.6
1095.8–1461.0 51 5 10 74.4 63.4– 85.5
1461.0–1826.2 36 0 15 74.4 63.4– 85.5
1826.2–2191.5 21 2 14 62.0 43.8– 80.2
2191.5–2556.8 5 0 5 NA NA– NA

tgrade=II

Interval No. at risk No. of events No. lost to follow-up Survival probability CI.95
0.0– 0.0 444 0 0 100.0 0.0–100.0
0.0– 365.2 444 33 19 92.3 89.8– 94.8
365.2– 730.5 392 69 19 75.8 71.7– 79.9
730.5–1095.8 304 44 42 64.1 59.4– 68.8
1095.8–1461.0 218 26 37 55.7 50.6– 60.8
1461.0–1826.2 155 20 54 47.0 41.4– 52.6
1826.2–2191.5 81 7 46 40.5 33.9– 47.1
2191.5–2556.8 28 3 22 30.7 18.9– 42.5

tgrade=III

Interval No. at risk No. of events No. lost to follow-up Survival probability CI.95
0.0– 0.0 161 0 0 100.0 0.0–100.0
0.0– 365.2 161 23 5 85.3 79.7– 90.8
365.2– 730.5 133 35 9 62.5 54.9– 70.2
730.5–1095.8 89 9 18 55.3 47.2– 63.4

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 Interval No. at risk No. of events No. lost to follow-up Survival probability CI.95 TABLE OF CONTENTS
1095.8–1461.0 62 8 17 47.2 38.6– 55.9
1461.0–1826.2 37 2 16 43.5 34.0– 53.0
1826.2–2191.5 19 2 14 35.4 22.6– 48.2
2191.5–2556.8 3 0 3 NA NA– NA

Cox regression

Univariate Cox regression

cox1 <- coxph(Surv(time,cens)~tgrade,data=GBSG2)

summary(cox1)

Call:
coxph(formula = Surv(time, cens) ~ tgrade, data = GBSG2)

n= 686, number of events= 299

coef exp(coef) se(coef) z Pr(>|z|)

tgradeII 0.8718 2.3912 0.2460 3.543 0.000395 ***
tgradeIII 1.1537 3.1701 0.2615 4.411 0.0000103 ***
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

tgradeII 2.391 0.4182 1.476 3.873
tgradeIII 3.170 0.3155 1.899 5.293

Concordance= 0.577 (se = 0.015 )

Rsquare= 0.035 (max possible= 0.995 )
Likelihood ratio test= 24.23 on 2 df, p=0.000005

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 Wald test = 19.75 on 2 df, p=0.00005 TABLE OF CONTENTS
Score (logrank) test = 21.1 on 2 df, p=0.00003

Comparison of Kaplan-Meier and Cox regression

library(pec)
km.grade <- prodlim(Surv(time,cens)~tgrade,data=GBSG2)
cox.grade <- coxph(Surv(time,cens)~tgrade,data=GBSG2,x=TRUE,y=TRUE)
newdata <- data.frame(tgrade=c("I","II","III"))
## first show Kaplan-Meier without confidence limits
plot(km.grade, lty=1, lwd=3,
col=c("darkgreen","darkorange","red"), confint=FALSE)
## now add survival estimates based on Cox regression
plotPredictSurvProb(cox.grade, lty=2,
col=c("darkgreen","darkorange","red"),
add=TRUE, sort(unique(GBSG2$time)),
newdata=newdata)
mtext("Comparison of univariate Cox regression and stratified Kaplan-Meier")

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 TABLE OF CONTENTS

Multiple Cox regression

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 cox2 <- coxph(Surv(time,cens)~tgrade+age+tsize+pnodes+progrec+estrec,data=GBSG2) TABLE OF CONTENTS
summary(cox2)

Call:
coxph(formula = Surv(time, cens) ~ tgrade + age + tsize + pnodes +
progrec + estrec, data = GBSG2)

n= 686, number of events= 299

coef exp(coef) se(coef) z Pr(>|z|)

tgradeII 0.6459107 1.9077236 0.2490306 2.594 0.00949 **
tgradeIII 0.8231461 2.2776542 0.2676730 3.075 0.00210 **
age -0.0028977 0.9971065 0.0061744 -0.469 0.63885
tsize 0.0071504 1.0071760 0.0038631 1.851 0.06417 .
pnodes 0.0496877 1.0509429 0.0075636 6.569 0.0000000000505 ***
progrec -0.0022732 0.9977294 0.0005736 -3.963 0.0000739478425 ***
estrec 0.0001392 1.0001392 0.0004428 0.314 0.75322
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

tgradeII 1.9077 0.5242 1.1710 3.1081
tgradeIII 2.2777 0.4390 1.3479 3.8489
age 0.9971 1.0029 0.9851 1.0092
tsize 1.0072 0.9929 0.9996 1.0148
pnodes 1.0509 0.9515 1.0355 1.0666
progrec 0.9977 1.0023 0.9966 0.9989
estrec 1.0001 0.9999 0.9993 1.0010

Concordance= 0.684 (se = 0.018 )

Rsquare= 0.131 (max possible= 0.995 )
Likelihood ratio test= 95.93 on 7 df, p=<2e-16
Wald test = 104.5 on 7 df, p=<2e-16
Score (logrank) test = 111.2 on 7 df, p=<2e-16

Plotting individualized survival probabilities

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 The following code extracts the survival probabilities for specific combinations of the risk factors: for all three categories ofTABLE OF CONTENTS
tumor grade and fixed age, tumor size and number of positive lymph nodes.

library(pec)
data(GBSG2)
cox2 <- coxph(Surv(time,cens)~tgrade+age+tsize+pnodes,data=GBSG2,x=TRUE,y=TRUE)
newdata <- data.frame(tgrade=c("I","II","III"),age=50,tsize=30,pnodes=8)
plotPredictSurvProb(cox2,
sort(unique(GBSG2$time)),
newdata=newdata,
col=c("darkgreen","darkorange","red"),
legend.title="Tumor grade",
legend.legend=c("I","II","III"))
mtext("Individualized survival curves from multiple Cox regression
age=50, tumor size= 30, no. positive lymph nodes=8",line=1.5,cex=1.3)

multiple-cox-survival-curves.jpg

Stratified

Allowing different baseline hazards between subgroups defined by menopause status:

cox3 <- coxph(Surv(time,cens)~tgrade+age+strata(menostat)+tsize+pnodes+progrec+estrec,d

summary(cox3)

Call:
coxph(formula = Surv(time, cens) ~ tgrade + age + strata(menostat) +
tsize + pnodes + progrec + estrec, data = GBSG2, x = TRUE)

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 TABLE OF CONTENTS
n= 686, number of events= 299

coef exp(coef) se(coef) z Pr(>|z|)

tgradeII 0.6206848 1.8602015 0.2492349 2.490 0.012761 *
tgradeIII 0.8050319 2.2367678 0.2676438 3.008 0.002631 **
age -0.0102152 0.9898368 0.0092931 -1.099 0.271670
tsize 0.0072755 1.0073020 0.0038726 1.879 0.060287 .
pnodes 0.0502917 1.0515778 0.0076171 6.602 0.0000000000404 ***
progrec -0.0022259 0.9977766 0.0005729 -3.885 0.000102 ***
estrec 0.0001704 1.0001704 0.0004505 0.378 0.705218
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

tgradeII 1.8602 0.5376 1.1413 3.0319
tgradeIII 2.2368 0.4471 1.3237 3.7795
age 0.9898 1.0103 0.9720 1.0080
tsize 1.0073 0.9928 0.9997 1.0150
pnodes 1.0516 0.9510 1.0360 1.0674
progrec 0.9978 1.0022 0.9967 0.9989
estrec 1.0002 0.9998 0.9993 1.0011

Concordance= 0.687 (se = 0.025 )

Rsquare= 0.131 (max possible= 0.99 )
Likelihood ratio test= 96.29 on 7 df, p=<2e-16
Wald test = 105.3 on 7 df, p=<2e-16
Score (logrank) test = 111.7 on 7 df, p=<2e-16

Interaction (effect modification).

Testing if tumor grade effect depends on age:

cox4 <- coxph(Surv(time,cens)~tgrade+Age+strata(menostat)+tsize+pnodes+progrec+estrec,d

cox5 <- coxph(Surv(time,cens)~tgrade*Age+strata(menostat)+tsize+pnodes+progrec+estrec,d
anova(cox4,cox5,test="chisq")

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 Analysis of Deviance Table TABLE OF CONTENTS
Cox model: response is Surv(time, cens)
Model 1: ~ tgrade + Age + strata(menostat) + tsize + pnodes + progrec + estrec
Model 2: ~ tgrade * Age + strata(menostat) + tsize + pnodes + progrec + estrec
loglik Chisq Df P(>|Chi|)
1 -1535.1
2 -1531.0 8.2495 6 0.2204

Possible ways to conclude:

The tumor grade effect on the hazard rate is not significantly different between age groups (p=0.47).
Within the limitations of this study we were not able to identify a significant difference of the tumor grade effect on the the
hazard rate between age groups (p=0.47).

Tabulate results

Multiple Cox regression

Apply publish function to the Cox fit:

cox3 <- coxph(Surv(time,cens)~tgrade+age+strata(menostat)+tsize+pnodes+progrec+estr

publish(cox3,org=TRUE)

Variable Units HazardRatio CI.95 p-value

tgrade I Ref
II 1.86 [1.14;3.03] 0.01276
III 2.24 [1.32;3.78] 0.00263
age 0.99 [0.97;1.01] 0.27167
tsize 1.01 [1.00;1.01] 0.06029

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 Variable Units HazardRatio CI.95 p-value TABLE OF CONTENTS
pnodes 1.05 [1.04;1.07] < 0.001
progrec 1.00 [1.00;1.00] < 0.001
estrec 1.00 [1.00;1.00] 0.70522

With interaction term

cox5 <- coxph(Surv(time,cens)~tgrade * menostat+tsize+age+pnodes+progrec+estrec,dat

publish(cox5,org=TRUE)

Variable Units HazardRatio CI.95 p-value

tsize 1.01 [1.00;1.01] 0.0691
age 0.99 [0.97;1.01] 0.2426
pnodes 1.05 [1.04;1.07] <0.001
progrec 1.00 [1.00;1.00] <0.001
estrec 1.00 [1.00;1.00] 0.7903
tgrade(I): menostat(Pre vs Post) 0.53 [0.19;1.45] 0.2125
tgrade(II): menostat(Pre vs Post) 0.84 [0.57;1.24] 0.3771
tgrade(III): menostat(Pre vs Post) 0.81 [0.47;1.40] 0.4435
menostat(Post): tgrade(II vs I) 1.58 [0.87;2.88] 0.1330
menostat(Post): tgrade(III vs I) 1.92 [1.00;3.67] 0.0483
menostat(Pre): tgrade(II vs I) 2.53 [1.10;5.83] 0.0297
menostat(Pre): tgrade(III vs I) 2.95 [1.23;7.10] 0.0156

Note: the main effects do usually not have an interpretation in the presence of interaction (effect modification).

Forest plots: showing hazard ratios with confidence intervals

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 par(cex=4) TABLE OF CONTENTS
cox2 <- coxph(Surv(time,cens)~tgrade+age+tsize+pnodes,data=GBSG2)
rt2 <- do.call("rbind",regressionTable(cox2))
plotConfidence(x=rt2$HazardRatio,
lower=rt2$Lower,
upper=rt2$Upper,
xlim=c(0,5),
factor.reference.pos=1,
labels=c("Tumor grade I",
" II",
" III",
"Age (years)",
"Tumor size (mm)",
"No. positive\nlymph nodes"),
title.labels="Factor",
cex=2,
xlab.cex=1.3,
xlab="Hazard ratio")

forest-cox2.jpg

Competing risks

Visualization of the model

library(riskRegression)
data(Melanoma)

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 levels(Melanoma$event) <- gsub("\\.","\n\n",levels(Melanoma$event)) TABLE OF CONTENTS
with(Melanoma,plot(Hist(time,event,cens.code="censored"),arrowLabelStyle="count"))

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 Aalen-Johansen graph TABLE OF CONTENTS

The graph shows the cumulative incidence of cancer related death since surgery.

library(riskRegression)
data(Melanoma)
aj <- prodlim(Hist(time,status)~1,data=Melanoma)
plot(aj,cause=1)

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 TABLE OF CONTENTS

Stratified Aalen-Johansen

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 library(riskRegression) TABLE OF CONTENTS
data(Melanoma)
aj2 <- prodlim(Hist(time,status)~sex,data=Melanoma)
plot(aj2,cause=1)

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 TABLE OF CONTENTS

Gray's test

library(cmprsk)
with(Melanoma,cuminc(ftime=time,fstatus=status,group=sex))$Tests

stat pv df
1 5.8140209 0.0158989 1
2 0.8543656 0.3553203 1

The Gray test shows a significantly higher risk of cancer related death for males compared to females (p-value= 0.0159).
The Gray test shows no non-significant difference in risks of other cause mortality between males and females (p-value=
0.3553).

Cox regression

The function fits Cox regression models, one for each competing risk.

Same formula for both competing risks

library(riskRegression)
CSC(Hist(time,status)~sex+age+invasion+logthick+ulcer,data=Melanoma)

CSC(formula = Hist(time, status) ~ sex + age + invasion + logthick +

ulcer, data = Melanoma)

Right-censored response of a competing.risks model

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 TABLE OF CONTENTS
No.Observations: 205

Pattern:

Cause event right.censored

1 57 0
2 14 0
unknown 0 134

----------> Cause: 1

Call:
survival::coxph(formula = survival::Surv(time, status) ~ sex +
age + invasion + logthick + ulcer, x = TRUE, y = TRUE)

n= 205, number of events= 57

coef exp(coef) se(coef) z Pr(>|z|)

sexMale 0.416256 1.516273 0.277562 1.500 0.13370
age 0.010690 1.010747 0.008465 1.263 0.20667
invasionlevel.1 0.325882 1.385252 0.386854 0.842 0.39957
invasionlevel.2 0.399668 1.491329 0.536187 0.745 0.45604
logthick 0.422402 1.525621 0.250260 1.688 0.09144 .
ulcerpresent 0.951752 2.590245 0.329443 2.889 0.00386 **
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

sexMale 1.516 0.6595 0.8801 2.612
age 1.011 0.9894 0.9941 1.028
invasionlevel.1 1.385 0.7219 0.6490 2.957
invasionlevel.2 1.491 0.6705 0.5214 4.266
logthick 1.526 0.6555 0.9342 2.492
ulcerpresent 2.590 0.3861 1.3581 4.940

Concordance= 0.767 (se = 0.04 )

Rsquare= 0.199 (max possible= 0.937 )
Likelihood ratio test= 45.44 on 6 df, p=0.00000004
Wald test = 38.67 on 6 df, p=0.0000008
Score (logrank) test = 45.79 on 6 df, p=0.00000003

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 TABLE OF CONTENTS

----------> Cause: 2

Call:
survival::coxph(formula = survival::Surv(time, status) ~ sex +
age + invasion + logthick + ulcer, x = TRUE, y = TRUE)

n= 205, number of events= 14

coef exp(coef) se(coef) z Pr(>|z|)

sexMale 0.19618 1.21675 0.55962 0.351 0.725915
age 0.09048 1.09469 0.02554 3.543 0.000396 ***
invasionlevel.1 -1.40328 0.24579 0.73843 -1.900 0.057388 .
invasionlevel.2 -2.08963 0.12373 1.23631 -1.690 0.090987 .
logthick 0.44436 1.55949 0.39440 1.127 0.259884
ulcerpresent 0.12655 1.13491 0.65348 0.194 0.846444
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

sexMale 1.2167 0.8219 0.40630 3.644
age 1.0947 0.9135 1.04125 1.151
invasionlevel.1 0.2458 4.0685 0.05781 1.045
invasionlevel.2 0.1237 8.0819 0.01097 1.396
logthick 1.5595 0.6412 0.71989 3.378
ulcerpresent 1.1349 0.8811 0.31529 4.085

Concordance= 0.835 (se = 0.085 )

Rsquare= 0.097 (max possible= 0.481 )
Likelihood ratio test= 20.88 on 6 df, p=0.002
Wald test = 16.94 on 6 df, p=0.01
Score (logrank) test = 18.36 on 6 df, p=0.005

Different formula for the two competing risks

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 library(riskRegression) TABLE OF CONTENTS
CSC(list(Hist(time,status)~sex+age+invasion+logthick+ulcer,Hist(time,status)~sex+ag

CSC(formula = list(Hist(time, status) ~ sex + age + invasion +

logthick + ulcer, Hist(time, status) ~ sex + age), data = Melanoma)

Right-censored response of a competing.risks model

No.Observations: 205

Pattern:

Cause event right.censored

1 57 0
2 14 0
unknown 0 134

----------> Cause: 1

Call:
survival::coxph(formula = survival::Surv(time, status) ~ sex +
age + invasion + logthick + ulcer, x = TRUE, y = TRUE)

n= 205, number of events= 57

coef exp(coef) se(coef) z Pr(>|z|)

sexMale 0.416256 1.516273 0.277562 1.500 0.13370
age 0.010690 1.010747 0.008465 1.263 0.20667
invasionlevel.1 0.325882 1.385252 0.386854 0.842 0.39957
invasionlevel.2 0.399668 1.491329 0.536187 0.745 0.45604
logthick 0.422402 1.525621 0.250260 1.688 0.09144 .
ulcerpresent 0.951752 2.590245 0.329443 2.889 0.00386 **
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

sexMale 1.516 0.6595 0.8801 2.612
age 1.011 0.9894 0.9941 1.028
invasionlevel.1 1.385 0.7219 0.6490 2.957

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 invasionlevel.2 1.491 0.6705 0.5214 4.266 TABLE OF CONTENTS
logthick 1.526 0.6555 0.9342 2.492
ulcerpresent 2.590 0.3861 1.3581 4.940

Concordance= 0.767 (se = 0.04 )

Rsquare= 0.199 (max possible= 0.937 )
Likelihood ratio test= 45.44 on 6 df, p=0.00000004
Wald test = 38.67 on 6 df, p=0.0000008
Score (logrank) test = 45.79 on 6 df, p=0.00000003

----------> Cause: 2

Call:
survival::coxph(formula = survival::Surv(time, status) ~ sex +
age, x = TRUE, y = TRUE)

n= 205, number of events= 14

coef exp(coef) se(coef) z Pr(>|z|)

sexMale 0.36910 1.44643 0.54712 0.675 0.499914
age 0.07581 1.07876 0.02155 3.518 0.000434 ***
---
codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

exp(coef) exp(-coef) lower .95 upper .95

sexMale 1.446 0.6914 0.495 4.227
age 1.079 0.9270 1.034 1.125

Concordance= 0.821 (se = 0.085 )

Rsquare= 0.076 (max possible= 0.481 )
Likelihood ratio test= 16.22 on 2 df, p=0.0003
Wald test = 13.96 on 2 df, p=0.0009
Score (logrank) test = 14.47 on 2 df, p=0.0007

Last update: 23 Nov 2018 by Thomas Alexander Gerds.

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