p.adjust in cuminc_pairs is not working

[chestrad]

p.adjust in cuminc_pairs is not working.
method="BH", method="bonferroni", and method="none" give equal results.

[chestrad]

Thank you very much for the useful R package!!

[raredd]

Thanks for raising the issue! Are you using the upper triangle of the p-value matrix? The lower triangle should remain unchanged with the adjustment being made to the upper:

library('cmprsk2')
cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'none')$p.value$death
#        A     B    AB     O
# A     NA 0.391 0.788 0.201
# B  0.391    NA 0.776 0.877
# AB 0.788 0.776    NA 0.712
# O  0.201 0.877 0.712    NA

cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'bon')$p.value$death
#        A     B    AB  O
# A     NA 1.000 1.000  1
# B  0.391    NA 1.000  1
# AB 0.788 0.776    NA  1
# O  0.201 0.877 0.712 NA

cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'BH')$p.value$death
#        A     B    AB     O
# A     NA 0.877 0.877 0.877
# B  0.391    NA 0.877 0.877
# AB 0.788 0.776    NA 0.877
# O  0.201 0.877 0.712    NA

[chestrad]

Thanks for raising the issue! Are you using the upper triangle of the p-value matrix? The lower triangle should remain unchanged with the adjustment being made to the upper:

library('cmprsk2')
cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'none')$p.value$death
#        A     B    AB     O
# A     NA 0.391 0.788 0.201
# B  0.391    NA 0.776 0.877
# AB 0.788 0.776    NA 0.712
# O  0.201 0.877 0.712    NA

cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'bon')$p.value$death
#        A     B    AB  O
# A     NA 1.000 1.000  1
# B  0.391    NA 1.000  1
# AB 0.788 0.776    NA  1
# O  0.201 0.877 0.712 NA

cuminc_pairs(Surv(futime, event(censored)) ~ abo, transplant, method = 'BH')$p.value$death
#        A     B    AB     O
# A     NA 0.877 0.877 0.877
# B  0.391    NA 0.877 0.877
# AB 0.788 0.776    NA 0.877
# O  0.201 0.877 0.712    NA

Thank you so much for your prompt reply. cmprsk2 is very convenient!!