Allow for survfit(..., conf.type = "none")

[HeidiSeibold]

This works now and did result in an error before:

library("survminer")
#> Loading required package: ggplot2
#> Loading required package: ggpubr
#> Loading required package: magrittr
library("survival")
data("GBSG2", package = "TH.data")


## Cox model
cxmod <- coxph(Surv(time, cens) ~ horTh + tsize, data = GBSG2)

# retrieve survival curve from model
newdat <- expand.grid(horTh = levels(GBSG2$horTh), tsize = quantile(GBSG2$tsize, 
  probs = c(0.25, 0.5, 0.75)))
rownames(newdat) <- letters[1:6]
newdat
#>   horTh tsize
#> a    no    20
#> b   yes    20
#> c    no    25
#> d   yes    25
#> e    no    35
#> f   yes    35


cxsf <- survfit(cxmod, data = GBSG2, newdata = newdat, conf.type = "none")
str(cxsf)
#> List of 10
#>  $ n       : int 686
#>  $ time    : num [1:574] 8 15 16 17 18 29 42 46 57 63 ...
#>  $ n.risk  : num [1:574] 686 685 684 683 681 680 679 678 677 676 ...
#>  $ n.event : num [1:574] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ n.censor: num [1:574] 1 1 1 2 1 1 1 1 1 1 ...
#>  $ surv    : num [1:574, 1:6] 1 1 1 1 1 1 1 1 1 1 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : NULL
#>   .. ..$ : chr [1:6] "a" "b" "c" "d" ...
#>  $ type    : chr "right"
#>  $ cumhaz  : num [1:574, 1:6] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ std.err : num [1:574, 1:6] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ call    : language survfit(formula = cxmod, newdata = newdat, conf.type = "none", data = GBSG2)
#>  - attr(*, "class")= chr [1:2] "survfit.cox" "survfit"

surv_cxmod0 <- surv_summary(cxsf)
str(surv_cxmod0)
#> 'data.frame':    3444 obs. of  9 variables:
#>  $ time    : num  8 15 16 17 18 29 42 46 57 63 ...
#>  $ n.risk  : num  686 685 684 683 681 680 679 678 677 676 ...
#>  $ n.event : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ n.censor: num  1 1 1 2 1 1 1 1 1 1 ...
#>  $ surv    : num  1 1 1 1 1 1 1 1 1 1 ...
#>  $ std.err : num  0 0 0 0 0 0 0 0 0 0 ...
#>  $ upper   : logi  NA NA NA NA NA NA ...
#>  $ lower   : logi  NA NA NA NA NA NA ...
#>  $ strata  : Factor w/ 6 levels "a","b","c","d",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  - attr(*, "table")='data.frame':    6 obs. of  7 variables:
#>   ..$ records   : num  686 686 686 686 686 686
#>   ..$ n.max     : num  686 686 686 686 686 686
#>   ..$ n.start   : num  686 686 686 686 686 686
#>   ..$ events    : num  299 299 299 299 299 299
#>   ..$ *rmean    : num  1671 1910 1617 1865 1507 ...
#>   ..$ *se(rmean): num  41.4 51.4 39.2 49.4 34.9 ...
#>   ..$ median    : num  1814 2456 1684 2372 1388 ...

[kassambara]

Thank you @HeidiSeibold for your contribution

[HeidiSeibold]

I am not sure how you do testing, but adding the above code to the tests might be a good idea. Thanks for the merge @kassambara