How do I calculate correlation rate and kappa statistic between two (ordinal) categorical variables (clinical stage and pathologic stage) as in the table in the provided article? https://link.springer.com/article/10.1007/s11605-018-3777-y
This is what I did in R and got results but I am not sure if it is correct:
library(polycor)
library(irr)
polychor(my_dataset$clinical_T, my_dataset$pathologic_T) # calculating overall correlation between clinical stage and pathologic stage
Tstage <- cbind(my_dataset$clinical_T, my_dataset$pathologic_T)
kappa2(Tstage) # calculating cohen's kappa