For adjusted survival curves I took the sample code from here:
https://rpubs.com/daspringate/survival
and adapted for my date, but got error.
I would like to understand what is my mistake. Thanks!
#ADAPTATION FOR MY DATA
library(survival)
library(survminer)
df<-read.csv("F:/R/data/base.csv", header = TRUE, sep = ";")
head(df)
ID start stop censor sex age stage treatment
1 1 0 66 0 2 1 3 1
2 2 0 18 0 1 2 4 2
3 3 0 43 1 2 3 3 1
4 4 0 47 1 2 3 NA 2
5 5 0 26 0 1 4 3 NA
S <- Surv(
time = df$start,
time2 = df$stop,
event = df$censor)
head(S)
[1] (0,66+] (0,18+] (0,43] (0,47] (0,26+] (0,29+]
model <- coxph(S ~ df$treatment + df$age + df$sex + df$stage, data = df)
plot(survfit(model),
las=1,
xscale = 1.00,
xlab = "Months after diagnosis",
ylab = "Proportion survived",
main = "Baseline Hazard Curve")
# BEFORE NOW everything works, but then ERROR
treat <- with(colon,
data.frame(
treatment = levels(df$treatment),
age = rep(levels(df$age)[1], 2),
sex = rep(levels(df$sex)[1], 2),
stage = rep(levels(df$stage)[1], 2)))
str(treat)
'data.frame': 0 obs. of 0 variables
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