Passing the list of strings as input to a function - r

Question

I am trying automate a simple task in R using a function.
C is list of character variables. mydata- is the dataset.
Basically, I need to give each of the strings in vector C as an input to the function.
dataset:
mydata <- structure(list(a = c(1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L), b = c(4L,3L, 1L, 2L, 1L, 5L, 2L, 2L), c = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,1L), d = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), t = c(42L, 34L, 74L,39L, 47L, 8L, 36L, 39L), s = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L)), .Names = c("a", "b", "c", "d", "t", "s"), row.names = c(NA,8L), class = "data.frame")
code:
c<-c("a","b","c","d")
plot<-function()
for (i in c)
{
fit<-survfit(Surv(s,t)~paste(i), dat=mydata)
ggsurvplot(fit, pval = TRUE)
}
plot()
I m facing the following error:
Error in model.frame.default(formula = Surv(mydata$s, mydata$t) ~
paste(i), : variable lengths differ (found for 'paste(i)')
I have tried the reformulate as well:
plot<-function()
for (i in c)
{
survfit(update(Surv(s,t)~., reformulate(i)), data=mydata)
ggsurvplot(fit, pval = TRUE)
}
plot()
but this code also gives this error:
Error in reformulate(i) : object 'i' not found
Any help to make this code work?
Thanks

Answer 1

Building formulas dynamically can be tricky. Rather than
fit(Surv(mydata$s,mydata$t)~paste(i), dat=mydata)
use
fit(update(Surv(s,t)~., reformulate(i)), data=mydata)
You should avoid using $ with formulas. Here reformualte() helps to build a formula from a string and update combines parts of formulas. See the help pages for these functions if you would like more details.
Here's the full working version with the sample inout
#sample input
mydata <- structure(list(a = c(1L, 1L, 1L, 1L, 0L, 0L, 1L, 0L), b = c(4L,3L, 1L, 2L, 1L, 5L, 2L, 2L), c = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,1L), d = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L), t = c(42L, 34L, 74L,39L, 47L, 8L, 36L, 39L), s = c(0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L)), .Names = c("a", "b", "c", "d", "t", "s"), row.names = c(NA,8L), class = "data.frame")
c<-c("a","b","c","d")
and the code
library(survival)
library(survminer)
plot <- function() {
for (i in c) {
fit <- survfit(update(Surv(t,s)~., reformulate(i)), data=mydata)
ggsurvplot(fit)
}
}
plot()
When I copy/paste that into R I do not get any errors. You must be doing something different than the sample code you've posted.