R/performance.R

In OmicsMarkeR: Classification and Feature Selection for 'Omics' Datasets

#' @title Performance Statistics (Internal for \code{perf.calc})
#' @description Calculates confusion matrix and ROC statistics comparing the 
#' results of the fitted models to the observed groups.
#' @param pred vector of groups predicted by a fitted classification model
#' @param obs vector of groups from the original dataset
#' @return Returns confusion matrix and ROC performance statistics including
#' Accuracy, Kappa, ROC.AUC, Sensitivity, Specificity, Positive Predictive 
#' Value, and Negative Predictive Value
#' @seealso caret function \code{\link{confusionMatrix}}
#' @import caTools
#' @importFrom caret confusionMatrix


performance.stats <- function(pred, obs)
{
    isNA <- is.na(pred)
    pred <- pred[!isNA]
    obs <- obs[!isNA]
    
    if(length(obs) + length(pred) == 0)
    {
        out <- rep(NA, 2)
    } else {
        #library(caTools)
        tmp.auc <- colMeans(colAUC(order(pred), obs, 
                                   plotROC = FALSE, alg = "ROC"))
        pred <- factor(pred, levels = levels(obs))  
        
        tmp <- caret::confusionMatrix(pred, obs)
        
        overall.stats <- c("Accuracy", "Kappa")
        byclass.stats <- c("Sensitivity", "Specificity", 
                           "Pos Pred Value", "Neg Pred Value")
        
        colnames(tmp$byClass)
        
        overall.index <- which(names(tmp$overall) %in% overall.stats)
        if(nlevels(obs) == 2){
            byclass.index <- which(names(tmp$byClass) %in% byclass.stats)
        }else{
            byclass.index <- which(colnames(tmp$byClass) %in% byclass.stats)
        }
        
        out <- c(tmp$overall[overall.index], 
                 dim(tmp$table)[1], 
                 tmp$byClass[byclass.index], tmp.auc)
    }
    names(out) <- c("Accuracy", "Kappa", "Table", "Sensitivity",
                    "Specificity", "Pos Pred Value", "Neg Pred Value",
                    "ROC.AUC")
    out <- out[c("Accuracy", "Kappa", "ROC.AUC", "Sensitivity", 
                 "Specificity", "Pos Pred Value", "Neg Pred Value",
                 "Table")]
    
    # correct negative predictive NaN to 0
#     out[which(is.nan(out["Neg Pred Value"]))] <- 0
# #     print(out)
# #     print(which(is.na(out["Pos Pred Value"])))
#     out[which(is.nan(out["Pos Pred Value"]))] <- 0
#     print(out["Pos Pred Value"])
#     print()
#     if(any(is.nan(out))){ stop("NaN FOUND!!!")}
    if(any(is.nan(out))) out[is.nan(out)] <- 0
    out
}

#' @title Performance Statistics Calculations
#' @description Calculates confusion matrix and ROC statistics comparing 
#' the results of the fitted models to the observed groups.
#' @param data dataframe of predicted (pred) and observed (obs) groups
#' @param lev Group levels
#' @param model String indicating which model was initially run
#' @return Returns confusion matrix and ROC performance statistics including
#' Accuracy, Kappa, ROC.AUC, Sensitivity, Specificity, Positive Predictive 
#' Value, and Negative Predictive Value
#' @seealso caret function \code{\link{confusionMatrix}}
# ' @export

perf.calc <- function(data,          
                      lev = NULL, 
                      model = NULL)     
{
    if(is.character(data$obs)){
        data$obs <- factor(data$obs, levels = lev)
        data$pred <- factor(data$pred, levels = lev)
    } 
    out <- performance.stats(data[,"pred"], data[,"obs"])
    out <- out[!names(out) == "Table"]
    out
}