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kassambara / survminer

Survival Analysis and Visualization
https://rpkgs.datanovia.com/survminer/
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Wrongly looking ggsurvplot with facet.by #304

Open dmiftakhutdinov opened 6 years ago

dmiftakhutdinov commented 6 years ago

Expected behavior

Two survival plots, one with step for X = 1, and one without step for X = 2

Actual behavior

First two commands: "Error in allf[[1]] : subscript out of bounds" occurs in strata function Third command: the second plot looks wrongly: only censoring symbol @ (20, 1.0) displayed.

It should be noted that the following works perfect:

ggsurvplot(npsurv(Surv(Time, Dead) ~ X, x))

Steps to reproduce the problem

x <- data.frame(Time = c(10, 20, 20, 20), Dead = c(TRUE, FALSE, FALSE, FALSE), X = c(1, 1, 2, 2), Q = c(1, 1, 1, 1))
ggsurvplot(npsurv(Surv(Time, Dead) ~ 1, x), facet.by = "X")
ggsurvplot(npsurv(Surv(Time, Dead) ~ X, x), facet.by = "X")
ggsurvplot(npsurv(Surv(Time, Dead) ~ Q, x), facet.by = "X")

session_info()

Session info ------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.3 (2017-03-06)
 system   x86_64, mingw32             
 ui       RStudio (1.0.136)           
 language (EN)                        
 collate  English_United States.1252  
 tz       America/New_York            
 date     2018-04-30                  

Packages ----------------------------------------------------------------------------------------------------------------
 package      * version  date       source        
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 base         * 3.3.3    2017-03-06 local         
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 graphics     * 3.3.3    2017-03-06 local         
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 SparseM      * 1.76     2017-03-09 CRAN (R 3.3.3)
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 survival     * 2.40-1   2016-10-30 CRAN (R 3.3.3)
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 TH.data        1.0-8    2017-01-23 CRAN (R 3.3.3)
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 xtable         1.8-2    2016-02-05 CRAN (R 3.3.3)
 zoo            1.8-1    2018-01-08 CRAN (R 3.3.3)
dmiftakhutdinov commented 6 years ago

Seems to be the same as #254

dmiftakhutdinov commented 6 years ago

Things seems to be connected to .connect2origin: it doesn't fill variables columns when fit parameter is not supplied. The only thing here, I was studying ggsurvplot without facet.by as I needed this for particular task and wanted to use ggsurvplot()$plot + facet_wrap() instead. ggsurvplot()$plot$data contains wrong values for time = 0 because .connect2origin doesn't fill values when fit parameter is not supplied.

BingxinS commented 5 years ago

You are right, it was with the function .connect2origin() Here is a quick fix: https://github.com/BingxinS/survminer-fix

slyrus commented 3 years ago

The link to the quick fix above doesn't seem to point at anything useful and I'm seeing both the problem described and possibly a similar problem in my own code.

irenerlover commented 1 year ago

I also encountered a similar problem as slyrus...

alansz commented 10 months ago

I also have the same problem.