On Oct 6, 2017, at 7:58 PM, Ted (Beginner) 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 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$stage, data = df) --------- Se if this works: model <- coxph( Surv(time = start, time2 = stop, event = censor)~ treatment + age + sex + stage, data = df) R regression functions allow you to use column names. The tokens in the formula get handled with evaluation inside the `data` argument's environment. ------------ > plot(survfit(model), > las=1, > xscale = 1.00, > xlab = "Months after diagnosis", > ylab = "Proportion survived", > main = "Baseline Hazard Curve") > > # BEFORE NOW everything works, but then ERROR > treat <- with(colon, > data.frame( > treatment = levels(df$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 > [[alternative HTML version deleted]] In this instance you got away with posting in html, but it might not always be effective. > David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law ______________________________________________ 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.
