Change the columns into factors before you give them to the coxph function, e.g.
df$treatment <- factor( df$treatment ) -- Sent from my phone. Please excuse my brevity. On October 7, 2017 5:01:19 PM GMT+01:00, "Ted Beginner (RStudio) via R-help" <r-help@r-project.org> wrote: > >For adjusted survival curves I took the sample code from here: >https://rpubs.com/daspringate/survival >and adapted for my date, but ... have a QUESTION. > >library(survival) >library(survminer) >df<-read.csv("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 > ># THANKS, DAVID WINSEMIUS for remark!!! ("R regression functions allow >you to use column names.") >model <- coxph( Surv(time = start, >time2 = stop, >event = censor) ~ treatment + age + sex + stage, data = df) > >plot(survfit(model), >las=1, >xscale = 1.00, >xlab = "Months after diagnosis", >ylab = "Proportion survived", >main = "Baseline Hazard Curve") > >#HOW TO EXPLAIN TO R, THAT treatment, age, sex and stage ARE FACTORS, >AND NOT CONTINUOUS VAR? >treat <- with (df, >data.frame ( >treatment = levels(treatment), >age = rep(levels(age)[1], 2), >sex = rep(levels(sex)[1], 2), >stage = rep(levels(stage)[1], 2))) > >str(treat) > [[alternative HTML version deleted]] > >______________________________________________ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
