I have a dataset my_data
for survival analysis with
time
until a certain event of interest,status
coded as 0 and 1, indicating whether the event has occurred or not at time
, andfactor
s (factor1
, factor2
, ...) that might influence the occurrence of the event.I analyze the data in R, using the survival
and survminer
package, à la
surv_object1 <- survfit(Surv(time, status) ~ factor1, data = my_data)
ggsurvplot(surv_object1)
surv_object2 <- survfit(Surv(time, status) ~ factor2, data = my_data)
ggsurvplot(surv_object2)
etc.
Instead of writing multiple lines of code, I would like to write a function that expects a factor
as a variable and returns a survival plot.
So far, I have tried writing
survival_plot <- function(factor) {
survival_object <- survfit(Surv(time, status) ~ factor, data = my_data)
surv_plot <- ggsurvplot(survival_object)
return(surv_plot)
}
However, when running
survival_plot(factor1)
it returns
Error in eval(predvars, data, env) : object 'factor1' not found
I have already double checked the spelling of my factors, made sure, that the columns that I name do exist in my dataframe, and tried !!sym{}, but without any luck.
I also tried the solution pointed out here, but again without any success.
Even though I can write the lines as pointed out above, I am still wondering what I am doing wrong. Any help would be much appreciated!
A minimal working example should be
library(survival)
library(survminer)
survival_plot <- function(factor) {
s_obj <- survfit(Surv(rfstime, status) ~ factor, data = survival::gbsg)
surv_plot <- ggsurvplot(s_obj)
return(surv_plot)
}
survival_plot(meno)
And for the solution of this thread
survival_function <- function(strata_x) {
gbsg$s <- Surv(gbsg$rfstime, gbsg$status)
survFormula <- as.formula(paste("s ~", strata_x))
my_survfit <- survfit(survFormula, data = gbsg)
my_survfit$call$formula <- survFormula
ggsurvplot(my_survfit, data = gbsg)
}
ggsurvplot
will look in s_obj$call$formula
to find what model was fit.
You can e.g. make your own call, and use eval(parse())
, or overwrite the wrong call. These both work:
survival_plot <- function(factor) {
call <- glue::glue('s_obj <- survfit(Surv(rfstime, status) ~ {factor}, data = survival::gbsg)')
eval(parse(text = call))
surv_plot <- ggsurvplot(s_obj)
return(surv_plot)
}
survival_plot2 <- function(factor) {
form <- as.formula(glue::glue('Surv(rfstime, status) ~ {factor}'))
s_obj <- survfit(form, data = survival::gbsg)
s_obj$call$formula <- form
surv_plot <- ggsurvplot(s_obj)
return(surv_plot)
}
Use as
survival_plot('meno')
survival_plot2('meno')