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#' Computes sensitivity measures
#'
#' Computes sensitivity measures: TP, FP, TN, FN, Sensitivity, Specificity,
#' Accuracy
#'
#'
#' @param all.data A data matrix containing predicted and real risk groups
#' @return A vector containing TP, FP, TN, FN, Sensitivity, Specificity,
#' Accuracy
#' @author Syed Haider
#' @keywords Sensitivity Specificity
#' @export calculate.sensitivity.stats
calculate.sensitivity.stats <- function(all.data = NULL) {
# to store output of this method
sen.spe <- rep(NA, 7);
names(sen.spe) <- c("TP", "FP", "TN", "FN", "Sensitivity", "Specificity", "Accuracy");
# TP
sen.spe["TP"] <- nrow(
all.data[
all.data[, "riskgroup"] == "1"
&
all.data[, "real.survival.group"] == "high",
]
);
# FP
sen.spe["FP"] <- nrow(
all.data[
all.data[, "riskgroup"] == "1"
&
all.data[, "real.survival.group"] == "low",
]
);
# TN
sen.spe["TN"] <- nrow(
all.data[
all.data[, "riskgroup"] == "0"
&
all.data[, "real.survival.group"] == "low",
]
);
# FN
sen.spe["FN"] <- nrow(
all.data[
all.data[, "riskgroup"] == "0"
&
all.data[, "real.survival.group"] == "high",
]
);
# Sensitivity
sen.spe["Sensitivity"] <- sen.spe["TP"] / (sen.spe["TP"] + sen.spe["FN"]) * 100;
# Specificity
sen.spe["Specificity"] <- sen.spe["TN"] / (sen.spe["TN"] + sen.spe["FP"]) * 100;
# Overall accuracy
sen.spe["Accuracy"] <- (sen.spe["TP"] + sen.spe["TN"]) / (sen.spe["TP"] + sen.spe["TN"] + sen.spe["FP"] + sen.spe["FN"]) * 100;
return (sen.spe);
}
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