[BUG] Error when `ggsurvplot` is used inside function.

[zzawadz]

Expected behavior

ggsurvplot should be able to be used inside other functions.

Actual behavior

Error is thrown when ggsurvplot is used inside function.

Steps to reproduce the problem

library(survminer)
require("survival")

tmp <- function(dt) 
{
  lung2 <- dt
  fit<- survfit(Surv(time, status) ~ sex, data = lung2)
  ggsurvplot(fit)
}

tmp(lung) #error!

session_info()

Session info ----------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, linux-gnu           
 ui       RStudio (1.0.44)            
 language (EN)                        
 collate  pl_PL.UTF-8                 
 tz       Europe/Warsaw               
 date     2017-01-26                  

Packages --------------------------------------------------------------------------------------
 package    * version   date       source                               
 assertthat   0.1       2013-12-06 CRAN (R 3.3.1)                       
 broom        0.4.1     2016-06-24 cran (@0.4.1)                        
 colorspace   1.3-2     2016-12-14 CRAN (R 3.3.1)                       
 DBI          0.5-1     2016-09-10 CRAN (R 3.3.1)                       
 devtools     1.12.0    2016-06-24 CRAN (R 3.3.1)                       
 digest       0.6.11    2017-01-03 cran (@0.6.11)                       
 dplyr        0.5.0     2016-06-24 CRAN (R 3.3.1)                       
 foreign      0.8-67    2016-09-13 CRAN (R 3.3.1)                       
 ggplot2    * 2.2.1     2016-12-30 cran (@2.2.1)                        
 gtable       0.2.0     2016-02-26 CRAN (R 3.3.1)                       
 lattice      0.20-34   2016-09-06 CRAN (R 3.3.1)                       
 lazyeval     0.2.0     2016-06-12 CRAN (R 3.3.1)                       
 magrittr     1.5       2014-11-22 CRAN (R 3.3.1)                       
 Matrix       1.2-7.1   2016-09-01 CRAN (R 3.3.1)                       
 memoise      1.0.0     2016-01-29 CRAN (R 3.3.1)                       
 mnormt       1.5-5     2016-10-15 CRAN (R 3.3.1)                       
 munsell      0.4.3     2016-02-13 CRAN (R 3.3.1)                       
 nlme         3.1-128   2016-05-10 CRAN (R 3.3.1)                       
 plyr         1.8.4     2016-06-08 CRAN (R 3.3.1)                       
 psych        1.6.12    2017-01-08 CRAN (R 3.3.1)                       
 R6           2.2.0     2016-10-05 CRAN (R 3.3.1)                       
 Rcpp         0.12.9    2017-01-16 Github (RcppCore/Rcpp@f57467b)       
 reshape2     1.4.2     2016-10-22 CRAN (R 3.3.1)                       
 scales       0.4.1     2016-11-09 CRAN (R 3.3.1)                       
 stringi      1.1.2     2016-10-01 CRAN (R 3.3.1)                       
 stringr      1.1.0     2016-08-19 CRAN (R 3.3.1)                       
 survival   * 2.40-1    2016-10-30 CRAN (R 3.3.1)                       
 survminer  * 0.2.4.999 2017-01-26 Github (kassambara/survminer@0f036ed)
 tibble       1.2       2016-08-26 CRAN (R 3.3.1)                       
 tidyr        0.6.1     2017-01-10 cran (@0.6.1)                        
 withr        1.0.2     2016-06-20 CRAN (R 3.3.1) 

[zzawadz]

One possible (and very simple solution) is to add parameter data which should be used only inside other functions. I will think about better solutions, but for now nothing comes to my mind;)

[kassambara]

Using the function do.call()should fix this issue.

For example:

library(survminer)
require("survival")

tmp <- function(dt) 
{
  lung2 <- dt
  fit <- do.call(survfit,
                 list(formula = Surv(time, status) ~ sex, data = lung2))
  ggsurvplot(fit)
}

tmp(lung)

[MarcinKosinski]

I think this is related to survift itselft, and not to the ggsurvplot.
@zzawadz this solution was also mentioned here #9 and RTCGA/RTCGA#48

[MarcinKosinski]

I think we might create a FAQ because issues became repeatable :)

[kassambara]

Absolutely for the FAQ!!

[ghowoo]

think this is related to survift itselft, and not to the ggsurvplot.
@zzawadz this solution was also mentioned here #9 and RTCGA/RTCGA#48

I agree. The survfit function's formula construction seems not quite conventional.