#' Calculates performance across resamples
#'
#' Given two numeric vectors of data, the mean squared error and
#'  R-squared are calculated. For two factors, the overall agreement
#'  rate and Kappa are determined.
#'
#' \code{postResample} is meant to be used with \code{apply}
#'  across a matrix. For numeric data the code checks to see if the
#'  standard deviation of either vector is zero. If so, the
#'  correlation between those samples is assigned a value of zero.
#'  \code{NA} values are ignored everywhere.
#'
#' Note that many models have more predictors (or parameters) than
#'  data points, so the typical mean squared error denominator (n -
#'  p) does not apply. Root mean squared error is calculated using
#'  \code{sqrt(mean((pred - obs)^2}. Also, \eqn{R^2} is calculated
#'  wither using as the square of the correlation between the
#'  observed and predicted outcomes when \code{form = "corr"}. when
#'  \code{form = "traditional"}, \deqn{ R^2 = 1-\frac{\sum (y_i -
#'  \hat{y}_i)^2}{\sum (y_i - \bar{y}_i)^2} }. Mean absolute error
#'  is calculated using \code{mean(abs(pred-obs))}.
#'
#' \code{defaultSummary} is the default function to compute
#'  performance metrics in \code{\link{train}}. It is a wrapper
#'  around \code{postResample}. The first argument is \code{data},
#'  which is \code{data.frame} with columns named \code{obs} and
#'  \code{pred} for the observed and predicted outcome values
#'  (either numeric data for regression or character values for
#'  classification). The second argument is \code{lev}, a character
#'  string that has the outcome factor levels or NULL for a
#'  regression model. The third parameter is \code{model}, which can
#'  be used if a summary metric is specific to a model function. If
#'  other columns from the data are required to compute the summary
#'  statistics, but should not be used in the model, the
#'  \code{recipe} method for \code{\link{train}} can be used.
#'
#' \code{twoClassSummary} computes sensitivity, specificity and
#'  the area under the ROC curve. \code{mnLogLoss} computes the
#'  minus log-likelihood of the multinomial distribution (without
#'  the constant term): \deqn{ -logLoss = \frac{-1}{n}\sum_{i=1}^n
#'  \sum_{j=1}^C y_{ij} \log(p_{ij}) } where the \code{y} values are
#'  binary indicators for the classes and \code{p} are the predicted
#'  class probabilities.
#'
#' \code{prSummary} (for precision and recall) computes values for
#'  the default 0.50 probability cutoff as well as the area under
#'  the precision-recall curve across all cutoffs and is labelled as
#'  \code{"AUC"} in the output. If assumes that the first level of
#'  the factor variables corresponds to a relevant result but the
#'  \code{lev} argument can be used to change this.
#'
#' \code{multiClassSummary} computes some overall measures of for
#'  performance (e.g. overall accuracy and the Kappa statistic) and
#'  several averages of statistics calculated from "one-versus-all"
#'  configurations. For example, if there are three classes, three
#'  sets of sensitivity values are determined and the average is
#'  reported with the name ("Mean_Sensitivity"). The same is true
#'  for a number of statistics generated by
#'  \code{\link{confusionMatrix}}. With two classes, the basic
#'  sensitivity is reported with the name "Sensitivity".
#'
#' To use \code{twoClassSummary} and/or \code{mnLogLoss}, the
#'  \code{classProbs} argument of \code{\link{trainControl}} should
#'  be \code{TRUE}. \code{multiClassSummary} can be used without
#'  class probabilities but some statistics (e.g. overall log loss
#'  and the average of per-class area under the ROC curves) will not
#'  be in the result set.
#'
#' Other functions can be used via the \code{summaryFunction}
#'  argument of \code{\link{trainControl}}. Custom functions must
#'  have the same arguments as\code{defaultSummary}.
#'
#' The function \code{getTrainPerf} returns a one row data frame
#'  with the resampling results for the chosen model. The statistics
#'  will have the prefix "\code{Train}" (i.e. "\code{TrainROC}").
#'  There is also a column called "\code{method}" that echoes the
#'  argument of the call to \code{\link{trainControl}} of the same
#'  name.
#'
#' @aliases postResample defaultSummary twoClassSummary prSummary
#'  getTrainPerf mnLogLoss R2 RMSE multiClassSummary MAE
#' @param pred A vector of numeric data (could be a factor)
#' @param obs A vector of numeric data (could be a factor)
#' @param data a data frame with columns \code{obs} and
#'  \code{pred} for the observed and predicted outcomes. For metrics
#'  that rely on class probabilities, such as
#'  \code{twoClassSummary}, columns should also include predicted
#'  probabilities for each class. See the \code{classProbs} argument
#'  to \code{\link{trainControl}}.
#' @param lev a character vector of factors levels for the
#'  response. In regression cases, this would be \code{NULL}.
#' @param model a character string for the model name (as taken
#'  from the \code{method} argument of \code{\link{train}}.
#' @return A vector of performance estimates.
#' @author Max Kuhn, Zachary Mayer
#' @seealso \code{\link{trainControl}}
#' @references Kvalseth. Cautionary note about \eqn{R^2}. American Statistician
#' (1985) vol. 39 (4) pp. 279-285
#' @keywords utilities
#' @examples
#'
#' predicted <-  matrix(rnorm(50), ncol = 5)
#' observed <- rnorm(10)
#' apply(predicted, 2, postResample, obs = observed)
#'
#' classes <- c("class1", "class2")
#' set.seed(1)
#' dat <- data.frame(obs =  factor(sample(classes, 50, replace = TRUE)),
#'                   pred = factor(sample(classes, 50, replace = TRUE)),
#'                   class1 = runif(50))
#' dat$class2 <- 1 - dat$class1            
#'
#' defaultSummary(dat, lev = classes)
#' twoClassSummary(dat, lev = classes)
#' prSummary(dat, lev = classes)
#' mnLogLoss(dat, lev = classes)
#'
#' @export postResample
postResample <- function(pred, obs)
{

  isNA <- is.na(pred)
  pred <- pred[!isNA]
  obs <- obs[!isNA]

  if (!is.factor(obs) && is.numeric(obs))
    {
      if(length(obs) + length(pred) == 0)
        {
          out <- rep(NA, 3)
        } else {
          if(length(unique(pred)) < 2 || length(unique(obs)) < 2)
            {
              resamplCor <- NA
            } else {
              resamplCor <- try(cor(pred, obs, use = "pairwise.complete.obs"), silent = TRUE)
              if(class(resamplCor) == "try-error") resamplCor <- NA
            }
          mse <- mean((pred - obs)^2)
          mae <- mean(abs(pred - obs))

          out <- c(sqrt(mse), resamplCor^2, mae)
        }
      names(out) <- c("RMSE", "Rsquared", "MAE")
    } else {
      if(length(obs) + length(pred) == 0)
        {
          out <- rep(NA, 2)
        } else {
          pred <- factor(pred, levels = levels(obs))
          requireNamespaceQuietStop("e1071")
          out <- unlist(e1071::classAgreement(table(obs, pred)))[c("diag", "kappa")]
        }
      names(out) <- c("Accuracy", "Kappa")
    }
  if(any(is.nan(out))) out[is.nan(out)] <- NA
  out
}


#' @rdname postResample
#' @importFrom ModelMetrics auc
#' @export
twoClassSummary <- function (data, lev = NULL, model = NULL)
{
  lvls <- levels(data$obs)
  if(length(lvls) > 2)
    stop(paste("Your outcome has", length(lvls),
               "levels. The twoClassSummary() function isn't appropriate."))
  requireNamespaceQuietStop('ModelMetrics')
  if (!all(levels(data[, "pred"]) == lvls))
    stop("levels of observed and predicted data do not match")
  rocAUC <- ModelMetrics::auc(ifelse(data$obs == lev[2], 0, 1), data[, lvls[1]])
  out <- c(rocAUC,
           sensitivity(data[, "pred"], data[, "obs"], lev[1]),
           specificity(data[, "pred"], data[, "obs"], lev[2]))
  names(out) <- c("ROC", "Sens", "Spec")
  out
}

#' @rdname postResample
#' @importFrom stats complete.cases
#' @export
mnLogLoss <- function(data, lev = NULL, model = NULL){
  if(is.null(lev)) stop("'lev' cannot be NULL")
  if(!all(lev %in% colnames(data)))
    stop("'data' should have columns consistent with 'lev'")
  if(!all(sort(lev) %in% sort(levels(data$obs))))
    stop("'data$obs' should have levels consistent with 'lev'")

  dataComplete <- data[complete.cases(data),]
  probs <- as.matrix(dataComplete[, lev, drop = FALSE])

  logLoss <- ModelMetrics::mlogLoss(dataComplete$obs, probs)
  c(logLoss = logLoss)
}

#' @rdname postResample
#' @export
multiClassSummary <- function(data, lev = NULL, model = NULL){
  #Check data
  if (!all(levels(data[, "pred"]) == levels(data[, "obs"])))
    stop("levels of observed and predicted data do not match")

  has_class_probs <- all(lev %in% colnames(data))

  if(has_class_probs) {
    ## Overall multinomial loss
    lloss <- mnLogLoss(data = data, lev = lev, model = model)

    requireNamespaceQuietStop("ModelMetrics")
    requireNamespaceQuietStop("MLmetrics")

    #Calculate custom one-vs-all ROC curves for each class
    prob_stats <-
      lapply(levels(data[, "pred"]),
             function(x){
               #Grab one-vs-all data for the class
               obs  <- ifelse(data[,"obs"] == x, 1, 0)
               prob <- data[,x]
               roc_auc <- try(ModelMetrics::auc(obs, data[,x]), silent = TRUE)
               # browser()
               pr_auc <- try(MLmetrics::PRAUC(y_pred = data[,x], 
                                              y_true = obs),
                             silent = TRUE)
               if(inherits(pr_auc, "try-error"))
                 pr_auc <- NA
               res <- c(ROC = roc_auc, AUC = pr_auc)
               return(res)
               })
    prob_stats <- do.call("rbind", prob_stats)
    prob_stats <- colMeans(prob_stats, na.rm = TRUE)
  }

  #Calculate confusion matrix-based statistics
  CM <- confusionMatrix(data[, "pred"], data[, "obs"],
                        mode = "everything")

  #Aggregate and average class-wise stats
  #Todo: add weights
  # RES: support two classes here as well
  if (length(levels(data[, "pred"])) == 2) {
    class_stats <- CM$byClass
  } else {
    class_stats <- colMeans(CM$byClass)
    names(class_stats) <- paste("Mean", names(class_stats))
  }

  # Aggregate overall stats
  overall_stats <-
    if (has_class_probs)
      c(CM$overall,
        logLoss = as.numeric(lloss),
        AUC = unname(prob_stats["ROC"]),
        prAUC = unname(prob_stats["AUC"]))
  else
    CM$overall


  # Combine overall with class-wise stats and remove some stats we don't want
  stats <- c(overall_stats, class_stats)
  stats <- stats[! names(stats) %in% c('AccuracyNull', "AccuracyLower", "AccuracyUpper",
                                       "AccuracyPValue", "McnemarPValue",
                                       'Mean Prevalence', 'Mean Detection Prevalence')]

  # Clean names
  names(stats) <- gsub('[[:blank:]]+', '_', names(stats))

  # Change name ordering to place most useful first
  # May want to remove some of these eventually
  stat_list <- c("Accuracy", "Kappa", "Mean_F1", 
                 "Mean_Sensitivity", "Mean_Specificity",
                 "Mean_Pos_Pred_Value", "Mean_Neg_Pred_Value", 
                 "Mean_Precision", "Mean_Recall",
                 "Mean_Detection_Rate",
                 "Mean_Balanced_Accuracy")
  if(has_class_probs) stat_list <- c("logLoss", "AUC", "prAUC", stat_list)
  if (length(levels(data[, "pred"])) == 2) stat_list <- gsub("^Mean_", "", stat_list)

  stats <- stats[c(stat_list)]

  return(stats)
}
