[R] [cph] Error in [.default (y, , 3) : subscript out of bounds

[Huy Nguyen]

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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