```
#' Calculate overlaps between all pairs of a hypervolume list
#'
#' Find all pairwise intersections, unions, etc., between elements in a hypervolume list.
#'
#' @param hv.list Object of class 'HypervolumeList'.
#' @param what Options are "jaccard" or "sorensen".
#' @param cores The number of cores to use for parallel processing.
#'
#' @details Makes the assumption that the hv.list was loaded in with loadHypervolumes,
#' and that the Name elements in the list are of the form 'Genus_species.RDS'. Function
#' only calculates the set of {i,j}, not {j,i}. Because of the way
#' hypervolume_set works, these values can change slightly, so some precision is
#' lost here. Prints progress to screen.
#'
#' @return Matrix with rownames and colnames corresponding to the input hv.list, and
#' the elements filled in according to the specified 'what'.
#'
#' @export
#'
#' @references Blonder, B., C. Lamanna, C. Violle, and B. J. Enquist. 2014.
#' The n-dimensional hypervolume. Global Ecology and Biogeography 23:595-609.
hypervolumeOverlaps <- function(hv.list, what, cores)
{
#because hypervolume is just a suggests, use this to ensure people have it installed
if(!requireNamespace("hypervolume", quietly = TRUE))
{
stop("The hypervolume package is needed for this. Install it.", call. = FALSE)
}
registerDoParallel(cores)
#define j here to avoid notes during devtools check
j <- 1
#set up a blank matrix, give it names
overlaps <- matrix(nrow=length(hv.list@HVList), ncol=length(hv.list@HVList))
#pull the names from the hv.list
tempNames <- sub(".RDS", "", unlist(lapply(hv.list@HVList, function(x) x@Name)))
rownames(overlaps) <- tempNames
colnames(overlaps) <- tempNames
for(i in 1:length(hv.list@HVList))
{
#concatenate the results of each inner loop into a vector
toInsert <- foreach(j = 1:i, .combine='c') %dopar%
{
#find the various sets of i with j
sets <- hypervolume::hypervolume_set(hv.list@HVList[[i]],
hv.list@HVList[[j]], verbose=FALSE, check.memory=FALSE)
#calculate overlap statistics
temp <- hypervolume::hypervolume_overlap_statistics(sets)
#set the relevant element in the matrix to the requested overlap stat
temp[what]
}
#now set that concatenated vector to be the correct elements in overlaps
overlaps[i,1:length(toInsert)] <- toInsert
#print the progress
numerator <- sum(!is.na(overlaps))
denominator <- ((1+dim(overlaps)[1])*dim(overlaps)[1])/2
print(numerator/denominator)
}
overlaps
}
```

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