asking for help about an error" Error in xy.coords(x, y) : 'x' and 'y' lengths differ "

[Beibei]

I am plotting a calibration during the establishment of the proportional hazards model，but there comes an error after running the last line:

Error in xy.coords(x, y) : 'x' and 'y' lengths differ

code is as follows:

#data reading
seer<-read.table("seer.txt",header=T,sep="\t")

seer$age<-factor(seer$age,labels=c("<50","50-59","60-69","70-79",">=80"))
seer$sex<-factor(seer$sex,labels=c("Female","Male"))
seer$race<-factor(seer$race,labels=c("Black","White","Other"))
seer$stage_T<-factor(seer$stage_T,labels=c("T0","T1","T2","T3a","T3b","T3NOS","T4","TX"))
seer$stage_N<-factor(seer$stage_N,labels=c("N0","N1","NX"))
seer$stage_M<-factor(seer$stage_M,labels=c("M0","M1"))
#establishing the cox model
#3-year
cox1 <- cph(Surv(survival_time,status) ~ age + sex + race +  stage_T + stage_N + stage_M,surv=T,x=T, y=T,time.inc = 1*12*3,data=seer) 

cal <- calibrate(cox1, cmethod="KM", method="boot", u=1*12*3, m= 12000, B=100)

#plotting the calibration curve
pdf("calibrate3.pdf",12,8)
par(mar = c(10,5,3,2),cex = 1.0)
plot(cal,lwd=3,lty=2,errbar.col="black",xlim = c(0,1),ylim = c(0,1),xlab ="Nomogram-Predicted Probability of 3-Year Survival",ylab="Actual 3-Year Survival",col="blue")
lines(cal,c('mean.predicted','KM'),type = 'a',lwd = 3,col ="black" ,pch = 16) #error comes after here

I am very looking forward to your reply！Thank you.

[Beibei]

Thanks for your kindness,and could you please give me you email so I can send you the seer.txt ?
It seems that new users have no right to upload files.
Best wishes.

[nirgrahamuk]

sending seer.txt privately by email would seem to exclude other forum users of the opportunity to help you. Alternatives to consider might be, hosting seer.txt on a file sharing platforming and sharing a link. i.e. github.com
Alternatively, following the reprex guide. a combination of head() and dput() use is usually sufficient. Yarnabrinas link is there if you want to read the guide (recommended).

[Beibei]

Sorry for this late reply.It's a bit difficult for me,a non-English speaker to create a link between my computer and github.Here is the link to my github account and you can get the file seer.txt there.https://github.com/hbb1518/document/tree/0b7f406c2dd78838edf6c32f2dbdd07510bf8e89
Thank you for your help and I'm looking forward to your reply.

[nirgrahamuk]

The last working line of code you have gives:

par(mar = c(10,5,3,2),cex = 1.0)
plot(cal,lwd=3,lty=2,errbar.col="black",xlim = c(0,1),ylim = c(0,1),xlab ="Nomogram-Predicted Probability of 3-Year Survival",ylab="Actual 3-Year Survival",col="blue")

its not exactly clear to me what you intended for

lines(cal,c('mean.predicted','KM'),type = 'a',lwd = 3,col ="black" ,pch = 16) #error comes after here

to do,
but this works and plots a dotted black line over the previous blue line

lines(cal[,'mean.predicted'],cal[,'KM'],lty=3,lwd = 2,col ="black" ,pch = 16)