#' Inverted Generational Distance (IGD and IGD+) and Averaged Hausdorff Distance
#'
#' Functions to compute the inverted generational distance (IGD and IGD+) and
#' the averaged Hausdorff distance between nondominated sets of points.
#'
#' @rdname igd
#' @export
#' @concept metrics
#' 
#' @template arg_data
#'
#' @template arg_refset
#'
#' @template arg_maximise
#' 
#' @return  (`numeric(1)`) A single numerical value.
#'
#' @author Manuel \enc{López-Ibáñez}{Lopez-Ibanez}
#'
#' @details
#'
#' The generational distance (GD) of a set \eqn{A} is defined as the distance
#' between each point \eqn{a \in A} and the closest point \eqn{r} in a
#' reference set \eqn{R}, averaged over the size of \eqn{A}. Formally,
#' 
#' \deqn{GD_p(A,R) = \left(\frac{1}{|A|}\sum_{a\in A}\min_{r\in R} d(a,r)^p\right)^{\frac{1}{p}} }{GD(A,R) = (1/|A|) * ( sum_{a in A} min_{r in R} d(a,r)^p )^(1/p)}
#' where the distance in our implementation is the Euclidean distance:
#' \deqn{d(a,r) = \sqrt{\sum_{k=1}^M (a_k - r_k)^2} }{d(a,r) = sqrt( sum_{k=1}^M (a_k - r_k)^2)}
#'
#' The inverted generational distance (IGD) is calculated as \eqn{IGD_p(A,R) = GD_p(R,A)}.
#'
#' The modified inverted generational distanced (IGD+) was proposed by
#' \citet{IshMasTanNoj2015igd} to ensure that IGD+ is weakly Pareto compliant,
#' similarly to [epsilon_additive()] or [epsilon_mult()]. It modifies the
#' distance measure as:
#'
#' \deqn{d^+(r,a) = \sqrt{\sum_{k=1}^M (\max\{r_k - a_k, 0\})^2}}{d^+(r,a) = sqrt(sum_{k=1}^M (max {r_k - a_k, 0 })^2)}
#'
#' The average Hausdorff distance (\eqn{\Delta_p}) was proposed by
#' \citet{SchEsqLarCoe2012tec} and it is calculated as:
#'
#' \deqn{\Delta_p(A,R) = \max\{ IGD_p(A,R), IGD_p(R,A) \}}
#'
#' IGDX \citep{ZhoZhaJin2009igdx} is the application of IGD to decision vectors
#' instead of objective vectors to measure closeness and diversity in decision
#' space. One can use the functions `igd()` or `igd_plus()` (recommended)
#' directly, just passing the decision vectors as `data`.
#'
#' 
#' There are different formulations of the GD and IGD metrics in the literature
#' that differ on the value of \eqn{p}, on the distance metric used and on
#' whether the term \eqn{|A|^{-1}} is inside (as above) or outside the exponent
#' \eqn{1/p}.  GD was first proposed by \citet{VelLam1998gp} with \eqn{p=2} and
#' the term \eqn{|A|^{-1}} outside the exponent. IGD seems to have been
#' mentioned first by \citet{CoeSie2004igd}, however, some people also used the
#' name D-metric for the same concept with \eqn{p=1} and later papers have
#' often used IGD/GD with \eqn{p=1}. \citet{SchEsqLarCoe2012tec} proposed to
#' place the term \eqn{|A|^{-1}} inside the exponent, as in the formulation
#' shown above.  This has a significant effect for GD and less so for IGD given
#' a constant reference set. IGD+ also follows this formulation.  We refer to
#' \citet{IshMasTanNoj2015igd} and \citet{BezLopStu2017emo} for a more detailed
#' historical perspective and a comparison of the various variants.
#'
#' Following \citet{IshMasTanNoj2015igd}, we always use \eqn{p=1} in our
#' implementation of IGD and IGD+ because (1) it is the setting most used in
#' recent works; (2) it makes irrelevant whether the term \eqn{|A|^{-1}} is
#' inside or outside the exponent \eqn{1/p}; and (3) the meaning of IGD becomes
#' the average Euclidean distance from each reference point to its nearest
#' objective vector). It is also slightly faster to compute.
#'
#' GD should never be used directly to compare the quality of approximations to
#' a Pareto front, as it often contradicts Pareto optimality. We 
#' recommend IGD+ instead of IGD, since the latter contradicts Pareto
#' optimality in some cases (see examples below), but we implement IGD here
#' because it is still popular due to historical reasons. We are not aware of
#' any proof of whether \eqn{\Delta_p(A,R)} contradicts or not Pareto
#' optimality, thus it must be used with care.
#' 
#' @references
#'
#' \insertAllCited{}
#' 
#' @examples
#' # Example 4 from Ishibuchi et al. (2015)
#' ref <- matrix(c(10,0,6,1,2,2,1,6,0,10), ncol=2, byrow=TRUE)
#' A <- matrix(c(4,2,3,3,2,4), ncol=2, byrow=TRUE)
#' B <- matrix(c(8,2,4,4,2,8), ncol=2, byrow=TRUE)
#' plot(ref, xlab=expression(f[1]), ylab=expression(f[2]),
#'      panel.first=grid(nx=NULL), pch=23, bg="gray", cex=1.5)
#' points(A, pch=1, cex=1.5)
#' points(B, pch=19, cex=1.5)
#' legend("topright", legend=c("Reference", "A", "B"), pch=c(23,1,19),
#'        pt.bg="gray", bg="white", bty = "n", pt.cex=1.5, cex=1.2)
#' cat("A is better than B in terms of Pareto optimality,\n however, IGD(A)=",
#'     igd(A, ref), "> IGD(B)=", igd(B, ref),
#'     ", which contradicts it.\nBy contrast, IGD+(A)=",
#'     igd_plus(A, ref), "< IGD+(B)=", igd_plus(B, ref), ", which is correct.\n")
#'
#' # A less trivial example.
#' extdata_path <- system.file(package="eaf","extdata")
#' path.A1 <- file.path(extdata_path, "ALG_1_dat.xz")
#' path.A2 <- file.path(extdata_path, "ALG_2_dat.xz")
#' A1 <- read_datasets(path.A1)[,1:2]
#' A2 <- read_datasets(path.A2)[,1:2]
#' ref <- filter_dominated(rbind(A1, A2))
#' igd(A1, ref)
#' igd(A2, ref)
#' 
#' @aliases IGDX
igd <- function(data, reference, maximise = FALSE)
{
  data <- check_dataset(data)
  nobjs <- ncol(data) 
  npoints <- nrow(data)
  if (is.null(reference)) {
    stop("reference cannot be NULL")
  }
  reference <- check_dataset(reference)
  if (ncol(reference) != nobjs)
    stop("data and reference must have the same number of columns")
  reference_size <- nrow(reference)
  
  maximise <- as.logical(rep_len(maximise, nobjs))
    
  return(.Call(igd_C,
               as.double(t(data)),
               as.integer(nobjs),
               as.integer(npoints),
               as.double(t(reference)),
               as.integer(reference_size),
               maximise))
}

#' @rdname igd
#' @export
#' @concept metrics
#' @examples
#' # IGD+ (Pareto compliant)
#' igd_plus(A1, ref)
#' igd_plus(A2, ref)
#' 
igd_plus <- function(data, reference, maximise = FALSE)
{
  data <- check_dataset(data)
  nobjs <- ncol(data) 
  npoints <- nrow(data)
  if (is.null(reference)) {
    stop("reference cannot be NULL")
  }
  reference <- check_dataset(reference)
  if (ncol(reference) != nobjs)
    stop("data and reference must have the same number of columns")
  reference_size <- nrow(reference)
  
  maximise <- as.logical(rep_len(maximise, nobjs))
    
  return(.Call(igd_plus_C,
               as.double(t(data)),
               as.integer(nobjs),
               as.integer(npoints),
               as.double(t(reference)),
               as.integer(reference_size),
               maximise))
}

#' @rdname igd
#' @param p (`integer(1)`) Hausdorff distance parameter (default: `1L`).
#' @concept metrics
#' @examples
#' # Average Haussdorff distance
#' avg_hausdorff_dist(A1, ref)
#' avg_hausdorff_dist(A2, ref)
#' @export
avg_hausdorff_dist <- function(data, reference, maximise = FALSE, p = 1L)
{
  data <- check_dataset(data)
  nobjs <- ncol(data) 
  npoints <- nrow(data)
  if (is.null(reference)) {
    stop("reference cannot be NULL")
  }
  reference <- check_dataset(reference)
  if (ncol(reference) != nobjs)
    stop("data and reference must have the same number of columns")
  reference_size <- nrow(reference)
  
  maximise <- as.logical(rep_len(maximise, nobjs))
    
  return(.Call(avg_hausdorff_dist_C,
               as.double(t(data)),
               as.integer(nobjs),
               as.integer(npoints),
               as.double(t(reference)),
               as.integer(reference_size),
               maximise,
               as.integer(p)))
}
