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get_relative_volume <- function(hv_list, tol = 1e-10){
# check if the object is an HypervolumeList
# calculation makes no sense for a single hypervolume
if(! inherits(hv_list, "HypervolumeList")){
stop("hv_list must be an HypervolumeList")
}
if(length(hv_list@HVList) < 2){
stop("At least two hypervolumes are needed for a relative volume")
}
# check if hypervolumes method were built within the occupancy routine
hyper_methods <- sapply(hv_list@HVList, function(x) x@Method)
if(any(! hyper_methods %in% c("n_occupancy", "n_occupancy_test", "n_occupancy_permute",
"occupancy_to_union", "occupancy_to_ushared", "occupancy_to_intersection"))){
stop("Construction method must be one of n_occupancy, n_occupancy_test, n_occupancy_permute,
occupancy_to_union, occupancy_to_unshared or occupancy_to_intersection")
}
# get volume of the hyper list and try to reconstruct the volume of the union
# the reconstruction is made for each hypervolume in the hypervolume list
vols <- get_volume(hv_list)
#all_length <- length(hv_list@HVList[[1]]@ValueAtRandomPoints)
combine_vrp <- lapply(hv_list@HVList, function(x) x@ValueAtRandomPoints)
combine_vrp <- do.call(cbind, combine_vrp)
zeroes_check <- apply(combine_vrp, 1, function(x) sum(abs(x)))
all_length <- sum(zeroes_check != 0)
i_length <- unlist(lapply(hv_list@HVList, function(z) sum(z@ValueAtRandomPoints != 0)))
all_vol <- vols*all_length/i_length
# if reconstructed volume differs above a certain threshold stop the function
if(any(dist(all_vol) > tol)){
stop("The reconstruction of the total volume failed. Try to: \n
\t 1. Increase the tolerance if results satisfy your needs. \n
\t 2. Check the accuracy of the results of hypervolume_n_occupancy. \n
Contact the maintener if none of the above applies to you.")
}
# # get the relative volume
# if(identical(method, "entire")){
# res <- vols / all_vol[[1]]
# }
# # get the relative volume of
# if(identical(method, "unique_fraction")){
# all_occupancy <- do.call(cbind, lapply(hv_list@HVList, function(z) z@ValueAtRandomPoints))
# all_occupancy[all_occupancy != 0] <- 1
# res <- rep(NA, length(vols))
#
# for(i in 1:length(vols)){
# res_temp <- all_occupancy[, i] - apply(all_occupancy[, -i, drop = FALSE], 1, function(z) sum(any(z > 0)))
# res_temp <- sum(res_temp[res_temp > 0])*all_vol[[1]]/all_length
# res[i] <- res_temp / all_vol[[1]]
# }
#
# names(res) <- names(vols)
#
# }
res <- vols / all_vol[[1]]
res
}
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