Dear CRAN support team,
I have been facing with an error when using the package *cph* to construct
nomogram! Let me clarify what exactly I have been encountered.
Firstly, this is a summary of my data:
> str(train)
'data.frame': 1323 obs. of 25 variables:
$ LYMPH_NODES_EXAMINED_POSITIVE: Factor w/ 3 levels "<=3","<=9",">10": 3
NA 1 2 NA 1 NA 1 3 1 ...
$ CELLULARITY : Factor w/ 3 levels
"High","Low","Moderate": NA 1 3 1 3 3 1 3 NA 1 ...
$ MENOPAUSAL_STATE : Factor w/ 2 levels "Post","Pre": 1 2 2 1
1 1 1 1 NA 2 ...
$ ER_STATUS : Factor w/ 2 levels
"Negative","Positive": 2 2 2 2 2 2 1 2 2 1 ...
$ OS_MONTHS : num 718 425 822 186 16 816 77 514 NA
821 ...
$ OS_STATUS : Factor w/ 2 levels "DECEASED","LIVING": 2
2 2 1 1 2 1 1 NA 2 ...
$ LATERALITY : Factor w/ 2 levels "Left","Right": 2 2 2
2 1 2 1 1 NA 2 ...
and this is my code:
> attach(train);d <- datadist(CELLULARITY, MENOPAUSAL_STATE, ER_STATUS,
LATERALITY, LYMPH_NODES_EXAMINED_POSITIVE)
> options(datadist = 'd')
> mod.cox <- cph(formula(Surv(OS_MONTHS, OS_STATUS) ~ CELLULARITY +
MENOPAUSAL_STATE + ER_STATUS + LATERALITY +LYMPH_NODES_EXAMINED_POSITIVE),
data=train, x= TRUE, y= TRUE, surv = TRUE)
Right there, I got the error when running mod.cox:
*Error in [.default (y, , 3) : subscript out of bounds*
I did some researches and found this previous issue
<https://github.com/harrelfe/rms/issues/31> and this
<https://github.com/harrelfe/rms/issues/25> related, which solved by
Prof.Harrelfe. But, It seems not working to me.
Any helps would be appreciated.
The example data that produces the same error:
https://drive.google.com/open?id=1Bi9nfg34eByc5H1Bmmq43dz6O8lEaj5O
Best regards,
Huy Nguyen
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