Error if argument 'data' is not provided.

[dnzmarcio]

Expected behavior

The function .get_data would extract data from the model fit if the argument 'data' is not provided.

Actual behavior

The function .get_data returns NULL.

Steps to reproduce the problem

library(survminer)
library(survival)
fit <- survfit(Surv(ovarian$futime, ovarian$fustat) ~ 1)
ggsurvplot(fit)
fit <- survfit(Surv(ovarian$futime, ovarian$fustat) ~ 1, data = ovarian)
ggsurvplot(fit)

session_info()

# please paste here the result of
devtools::session_info()
Session info -------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, mingw32             
 ui       RStudio (1.0.136)           
 language (EN)                        
 collate  English_United States.1252  
 tz       America/Los_Angeles         
 date     2017-06-23                  

Packages -----------------------------------------------------------------------------------------------------
 package    * version   date       source                               
 assertthat   0.1       2013-12-06 CRAN (R 3.3.1)                       
 base       * 3.3.1     2016-06-21 local                                
 bindr        0.1       2016-11-13 CRAN (R 3.3.3)                       
 bindrcpp     0.2       2017-06-17 CRAN (R 3.3.3)                       
 broom        0.4.2     2017-02-13 CRAN (R 3.3.3)                       
 chron        2.3-50    2017-02-20 CRAN (R 3.3.3)                       
 cmprsk       2.2-7     2014-06-17 CRAN (R 3.3.3)                       
 colorspace   1.2-6     2015-03-11 CRAN (R 3.3.1)                       
 data.table   1.9.6     2015-09-19 CRAN (R 3.3.1)                       
 datasets   * 3.3.1     2016-06-21 local                                
 devtools     1.13.1    2017-05-13 CRAN (R 3.3.3)                       
 digest       0.6.10    2016-08-02 CRAN (R 3.3.1)                       
 dplyr        0.7.1     2017-06-22 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 (R 3.3.3)                       
 ggpubr     * 0.1.3     2017-06-06 CRAN (R 3.3.3)                       
 glue         1.1.0     2017-06-13 CRAN (R 3.3.3)                       
 graphics   * 3.3.1     2016-06-21 local                                
 grDevices  * 3.3.1     2016-06-21 local                                
 grid         3.3.1     2016-06-21 local                                
 gridExtra    2.2.1     2016-02-29 CRAN (R 3.3.1)                       
 gtable       0.2.0     2016-02-26 CRAN (R 3.3.1)                       
 km.ci        0.5-2     2009-08-30 CRAN (R 3.3.2)                       
 KMsurv       0.1-5     2012-12-03 CRAN (R 3.3.2)                       
 knitr        1.14      2016-08-13 CRAN (R 3.3.1)                       
 labeling     0.3       2014-08-23 CRAN (R 3.3.0)                       
 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)                       
 methods    * 3.3.1     2016-06-21 local                                
 mnormt       1.5-4     2016-03-09 CRAN (R 3.3.0)                       
 munsell      0.4.3     2016-02-13 CRAN (R 3.3.1)                       
 nlme         3.1-128   2016-05-10 CRAN (R 3.3.1)                       
 parallel     3.3.1     2016-06-21 local                                
 pkgconfig    2.0.1     2017-03-21 CRAN (R 3.3.3)                       
 plyr         1.8.4     2016-06-08 CRAN (R 3.3.1)                       
 psych        1.6.9     2016-09-17 CRAN (R 3.3.1)                       
 purrr        0.2.2.2   2017-05-11 CRAN (R 3.3.3)                       
 R6           2.1.3     2016-08-19 CRAN (R 3.3.1)                       
 Rcpp         0.12.7    2016-09-05 CRAN (R 3.3.1)                       
 reshape2     1.4.1     2014-12-06 CRAN (R 3.3.1)                       
 rlang        0.1.1     2017-05-18 CRAN (R 3.3.3)                       
 scales       0.4.1     2016-11-09 CRAN (R 3.3.2)                       
 splines      3.3.1     2016-06-21 local                                
 stats      * 3.3.1     2016-06-21 local                                
 stringi      1.1.1     2016-05-27 CRAN (R 3.3.0)                       
 stringr      1.2.0     2017-02-18 CRAN (R 3.3.3)                       
 survival   * 2.41-3    2017-04-04 CRAN (R 3.3.3)                       
 survminer  * 0.4.0.999 2017-06-23 Github (kassambara/survminer@6fe5873)
 survMisc     0.5.4     2016-11-23 CRAN (R 3.3.3)                       
 tibble       1.3.3     2017-05-28 CRAN (R 3.3.3)                       
 tidyr        0.6.3     2017-05-15 CRAN (R 3.3.3)                       
 tools        3.3.1     2016-06-21 local                                
 utils      * 3.3.1     2016-06-21 local                                
 withr        1.0.2     2016-06-20 CRAN (R 3.3.1)                       
 xtable       1.8-2     2016-02-05 CRAN (R 3.3.1)                       
 zoo          1.7-13    2016-05-03 CRAN (R 3.3.1) 

[kassambara]

.get_data() works only when survfit() is used as follow:

fit <- survfit(Surv(futime, fustat) ~ 1, data = ovarian)
ggsurvplot(fit)

If you decide to use survfit() as follow (not recommended):

fit <- survfit(Surv(ovarian$futime, ovarian$fustat) ~ 1)

then, you should specify the argument data in ggsurvplot() as follow:

ggsurvplot(fit, data = ovarian)

[dnzmarcio]

Oh, I see. Thank you. Maybe a cleaner error message would be helpful:

.get_data <- function(fit, data = NULL, complain = TRUE) {
  if(is.null(data)){
    if (complain)
      warning ("The `data` argument is not provided. Data will be extracted from model fit.")
    data <- eval(fit$call$data)
    if (is.null(data))
      stop("The `data` argument should be provided either to ggsurvfit or survfit.")
  }
  data
}

[kassambara]

Ok, we'll clarify this. Thanks

[kassambara]

fixed now, thanks