a problem about error in cph of R code: object 'n' not found"

Question

I am trying to generate a nomogram with the following R code and keep on getting error for the last line. The error message says "Error in cph(Surv(futime, fustat) ~ ., x = T, y = T, surv = T, data = rt, : object 'n' not found". Could anyone please help? Thanks in advance.

library(rms)
setwd("C:\\Users\\yue\\Desktop\\04.diff")                  
rt=read.table("risk.txt",sep="\t",header=T,row.names=1,check.names=F)   
rt=rt[c(1:(ncol(rt)-2))] 

dd <- datadist(rt)
options(datadist="dd")

f <- cph(Surv(futime, fustat) ~ ., x=T, y=T, surv=T, data=rt, time.inc=1)

Hi, I put the "risk.txt" in the google drive link: https://drive.google.com/file/d/1CzohRmkz4mfiEJtESWiv3tHAMBrqSQKS/view?usp=sharing — Thea, May 31 '21 at 05:02
＾This is the only input file I have in the path I include in the code — Thea, May 31 '21 at 05:05
Have you tried `s1 <- Surv(rt$futime, rt$fustat);f <- cph(s1 ~ FOXM1 + IGF2BP3, x=TRUE, y=TRUE, surv=TRUE, data=rt, time.inc=1)` — akrun, May 31 '21 at 05:08
There is a `n` argument. But, I tested your data with the code commented above. It is not giving any errors — akrun, May 31 '21 at 05:18
had same problem with shiny... opening a new RStudio session seemed to work it out! — Edgar Alarcón, May 31 '21 at 05:25

score 0 · Accepted Answer · answered May 31 '21 at 05:22

We can create the Surv object as

s1 <- Surv(rt$futime, rt$fustat)
f <- cph(s1 ~ FOXM1 + IGF2BP3, x=TRUE, y=TRUE, surv=TRUE, data=rt, time.inc=1)

-output

f
Cox Proportional Hazards Model
 
 cph(formula = s1 ~ FOXM1 + IGF2BP3, data = rt, x = TRUE, y = TRUE, 
     surv = TRUE, time.inc = 1)
 
                        Model Tests    Discrimination    
                                              Indexes    
 Obs       232    LR chi2     49.90    R2       0.231    
 Events     43    d.f.            2    Dxy      0.550    
 Center 1.0881    Pr(> chi2) 0.0000    g        1.019    
                  Score chi2  70.81    gr       2.771    
                  Pr(> chi2) 0.0000                      
 
         Coef   S.E.   Wald Z Pr(>|Z|)
 FOXM1   0.0812 0.0174 4.65   <0.0001 
 IGF2BP3 0.1426 0.0303 4.70   <0.0001

a problem about error in cph of R code: object 'n' not found"

1 Answers1