I am using the ovarian dataset from the survival package using the following standard code:
ovarian$rx <- factor(ovarian$rx, levels = c("1", "2"), labels = c("A", "B"))
ovarian$resid.ds <- factor(ovarian$resid.ds, levels = c("1", "2"), labels = c("no", "yes"))
ovarian$ecog.ps <- factor(ovarian$ecog.ps, levels = c("1", "2"), labels = c("good", "bad"))
ovarian <- ovarian %>% mutate(age_group = ifelse(age >=50, "old", "young"))
ovarian$age_group <- factor(ovarian$age_group)
surv_object <- Surv(time = ovarian$futime, event = ovarian$fustat)
fit1 <- survfit(surv_object ~ rx, data = ovarian)
ggsurvplot(fit1, data = ovarian, pval = TRUE)
fit2 <- survfit(surv_object ~ resid.ds, data = ovarian)
ggsurvplot(fit2, data = ovarian, pval = TRUE)
fit.coxph <- coxph(surv_object ~ rx + resid.ds + age_group + ecog.ps, data = ovarian)
ggforest(fit.coxph, data = ovarian)
I'm able to plot the survival curves but for some reason I am getting the error below when trying to forest plot the cox hazard model with the 4 parameters
Error in `[.data.frame`(cbind(allTermsDF, coef[inds, ]), , c("var", "level", :
undefined columns selected
Am I missing something? I got the code off the datacamp tutorial so it should be working. Would really appreciate any suggestions for a solution to this.
Thanks!
It's likely due to broom version 0.7.0 which has been reported to cause that error with survminer ggforest, see here. Hopefully survminer will be updated soon to fix.