ggforest returns error Error in `[.data.frame`(cbind(allTermsDF, coef[inds, ]), , c("var", "level", : undefined columns selected

Question

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!

Answer 1

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.

Answer 2

I had the same problem which resolved when I installed an older version of R (R version 3.6.3) then installed an older version of Broom (0.5.6).