Specificity and sensitivity measures

I have been trying to calculate some measures about specificity and sensitivity.
The SDMTools R package worked great to get the overall estimates.

library(SDMTools)

a <- c(1,1,1,1,0,0,0,1,0,1,1,1) #observed
b <- c(1,1,0,0,1,0,0,1,0,0,1,1) #predicted

accuracy(a, b)
#       threshold       AUC omission.rate sensitivity specificity prop.correct     Kappa
#1            0.5    0.6875         0.375       0.625        0.75    0.6666667 0.3333333

Unfortunately, I was not able to get the raw numbers for TRUE POSITIVE,TRUE NEGATIVE, FALSE POSITIVE, FALSE NEGATIVE. I would like to have them in four different columns. Does anyone know a package or a function that can do that? The result I would like to get is below.

#TP  TN  FP  FN
#5    3   1   3

1 answer

  • answered 2018-10-09 16:46 adviksh

    You could use a custom function like this one below to calculate the true / false classification counts:

    accuracy_table <- function(obs, pred){
      data.frame(TP = sum(obs == 1 & pred == 1),
                 TN = sum(obs == 0 & pred == 0),
                 FP = sum(obs == 0 & pred == 1),
                 FN = sum(obs == 1 & pred == 0))
    }
    
    accuracy_table(a, b)
    

    This function relies on observations and predictions being coded with 0 as the negative case and 1 as the positive case, so it won't work as desired in other cases.