Additional data= argument in survminer functions

[kassambara]

I'm updating survminer functions to use the .get_data() [ by @pbiecek ] function instead of eval(fit$call$data) .

[kassambara]

Should be ok now!

ggsurvplot() should be used as follow:

require("survival")
fit<- survfit(Surv(time, status) ~ sex, data = lung)

# Drawing survival curves
ggsurvplot(fit, data = lung)

[MarcinKosinski]

I am having such varning right now when I use survminer

code

devtools::install_github('kassambara/survminer')
library(survminer)
library(survival)
fit <- survfit(Surv(time, status) ~ sex, data = lung)

ggsurvplot(fit, data = lung,
  main = "Survival curves", submain = "Based on Kaplan-Meier estimates",
  caption = "created with survminer",
  font.main = c(16, "bold", "darkblue"),
  font.submain = c(15, "bold.italic", "purple"),
  font.caption = c(14, "plain", "orange"),
  font.x = c(14, "bold.italic", "red"),
  font.y = c(14, "bold.italic", "darkred"),
  font.tickslab = c(12, "plain", "darkgreen"),
  ########## risk table #########,
  risk.table = TRUE,
  risk.table.title = "Note the risk set sizes",
  risk.table.subtitle = "and remember about censoring.",
  risk.table.caption = "source code: website.com",
  risk.table.height = 0.35,
  font.risk.table.title = c(13, "bold.italic", "green"),
  font.risk.table.sutitle = c(15, "bold", "pink"),
  font.risk.table.caption = c(11, "plain", "darkgreen"),
  font.risk.table.x = c(8, "bold.italic", "orange"),
  font.risk.table.y = c(11, "bold.italic", "darkgreen"),
  font.risk.table.tickslab = c(9, "bold", "red"),
  ######### ncensor plot ###################
  ncensor.plot = TRUE,
  ncensor.plot.title = "Number of censorings",
  ncensor.plot.subtitle = "over the time.",
  ncensor.plot.caption = "data available at data.com",
  ncensor.plot.height = 0.35,
  font.ncensor.plot.title = c(13, "bold.italic", "green"),
  font.ncensor.plot.sutitle = c(15, "bold", "pink"),
  font.ncensor.plot.caption = c(11, "plain", "darkgreen"),
  font.ncensor.plot.x = c(8, "bold.italic", "orange"),
  font.ncensor.plot.y = c(11, "bold.italic", "darkgreen"),
  font.ncensor.plot.tickslab = c(9, "bold", "red"))

results

> library(survminer)
Loading required package: ggplot2
> ?ggsurvplot
> fit <- survfit(Surv(time, status) ~ sex, data = lung)
Error: could not find function "survfit"
> library(survival)
> fit <- survfit(Surv(time, status) ~ sex, data = lung)
> ggsurvplot(fit, data = lung,
+   main = "Survival curves", submain = "Based on Kaplan-Meier estimates",
+   caption = "created with survminer",
+   font.main = c(16, "bold", "darkblue"),
+   font.submain = c(15, "bold.italic", "purple"),
+   font.caption = c(14, "plain", "orange"),
+   font.x = c(14, "bold.italic", "red"),
+   font.y = c(14, "bold.italic", "darkred"),
+   font.tickslab = c(12, "plain", "darkgreen"),
+   ########## risk table #########,
+   risk.table = TRUE,
+   risk.table.title = "Note the risk set sizes",
+   risk.table.subtitle = "and remember about censoring.",
+   risk.table.caption = "source code: website.com",
+   risk.table.height = 0.35,
+   font.risk.table.title = c(13, "bold.italic", "green"),
+   font.risk.table.sutitle = c(15, "bold", "pink"),
+   font.risk.table.caption = c(11, "plain", "darkgreen"),
+   font.risk.table.x = c(8, "bold.italic", "orange"),
+   font.risk.table.y = c(11, "bold.italic", "darkgreen"),
+   font.risk.table.tickslab = c(9, "bold", "red"),
+   ######### ncensor plot ###################
+   ncensor.plot = TRUE,
+   ncensor.plot.title = "Number of censorings",
+   ncensor.plot.subtitle = "over the time.",
+   ncensor.plot.caption = "data available at data.com",
+   ncensor.plot.height = 0.35,
+   font.ncensor.plot.title = c(13, "bold.italic", "green"),
+   font.ncensor.plot.sutitle = c(15, "bold", "pink"),
+   font.ncensor.plot.caption = c(11, "plain", "darkgreen"),
+   font.ncensor.plot.x = c(8, "bold.italic", "orange"),
+   font.ncensor.plot.y = c(11, "bold.italic", "darkgreen"),
+   font.ncensor.plot.tickslab = c(9, "bold", "red"))
Warning messages:
1: In if (value %in% columns) { :
  the condition has length > 1 and only the first element will be used
2: In if (value %in% columns) { :
  the condition has length > 1 and only the first element will be used

[kassambara]

In your R code, you used :

font.risk.table.sutitle and font.ncensor.plot.sutitle instead of font.risk.table.subtitle and font.ncensor.plot.subtitle.

It should work after updating the names of the two arguments in your script...