Error in ggsurvplot when log-rank weight specified for some data sets

[kassambara]

The following example from the vignette (http://www.sthda.com/english/rpkgs/survminer/articles/Specifiying_weights_in_log-rank_comparisons.html) works:

library("survival")
library(survminer)
data("kidney", package="KMsurv")
fit1 <- survfit(Surv(time=time, event=delta) ~ type, data=kidney)
ggsurvplot(fit1, data = kidney, pval = TRUE, log.rank.weights = "S1")

P-values from survMisc

library(survMisc)
tenfit <- ten(Surv(time=time, event=delta) ~ type, data=kidney)
capture.output(comp(tenfit)) -> null_dev
attributes(tenfit)$lrt -> tests
tests

                     Q         Var         Z     pNorm   
1             -3.96355     6.23675 -1.587104 0.1124892   
n              9.00000 38919.18761  0.045621 0.9636127   
sqrtN        -13.20293   433.84450 -0.633875 0.5261626   
S1            -2.46920     4.37254 -1.180837 0.2376674   
S2            -2.31343     4.20869 -1.127672 0.2594583   
FH_p=1_q=1    -1.02064     0.10661 -3.125846 0.0017729 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Observation: The pNorm column is present

But, the example below, using another dataset, doesn't work:

library(survival)
library(survminer)
data("larynx", package="KMsurv")
fit2 <- survfit(Surv(time, delta) ~ stage, data=larynx)
ggsurvplot(fit2, data = larynx, log.rank.weights = "S1", pval = TRUE)

Error message:

Error in round(tests$pNorm[tests$W == method], 4) : 
  argument non numérique pour une fonction mathématique

P-values from survMisc

library(survMisc)
tenfit <- ten(Surv(time, delta) ~ stage, data=larynx)
capture.output(comp(tenfit)) -> null_dev
attributes(tenfit)$lrt -> tests
tests

           chiSq df     pChisq    
1          22.763  3 4.5252e-05 ***
n          23.177  3 3.7093e-05 ***
sqrtN      23.141  3 3.7746e-05 ***
S1         23.171  3 3.7199e-05 ***
S2         23.170  3 3.7213e-05 ***
FH_p=1_q=1 16.661  3 0.00082967 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Observation: The pNorm column is not present

[kassambara]

We should update the surv_pvalue() function.

I'm working on this...
We should update the surv_pvalue() function.

I'm working on this...

[kassambara]

fixed now!