# ============================================================
# Diagnostic Test Accuracy
# Biostatistics in R — Rverse Analytics
# https://rverseanalytics.com/learn-biostatistics/diagnostic
# ============================================================

# Diagnostic test accuracy from a 2x2 table
# test positive: TP true, FP false ; test negative: FN, TN
TP <- 90; FP <- 10
FN <- 20; TN <- 80
# Sensitivity & specificity
sensitivity <- TP / (TP + FN)
specificity <- TN / (TN + FP)
c(sensitivity = sensitivity, specificity = specificity)
# Predictive values
PPV <- TP / (TP + FP)
NPV <- TN / (TN + FN)
c(PPV = PPV, NPV = NPV)
# Likelihood ratios
c(LR_positive = sensitivity / (1 - specificity),
  LR_negative = (1 - sensitivity) / specificity)