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#' Plots illustrative convex hulls for each group within all communities
#'
#' This function loops over each community and group within, and plots a
#' convex hull around the data. N.B. use of convex hulls to compare isotopic
#' niche width among groups within or between communities is not recommended
#' owing to strong sample size bias. Use of ellipse area is recommended instead.
#' This feature is provided for illustrative purposes only, and because some
#' people have expressed a desire for this feature for figure generation. See
#' demonstration scripts for more examples.
#'
#' @param siber a siber object as created by createSiberObject
#' @param plot.args a list of plotting arguments for passing to
#' [graphics::lines()]. See [graphics::lines()] for
#' details of the options. See also the demonstration scripts for examples of
#' use.
#' @param iso.order a vector of length 2, either `c(1,2)` or`c(2,1)`.
#' The order determines which of the columns of raw data are plotted on the x
#' (1) or y (2) axis. N.B. this will be deprecated in a future release, and
#' plotting order will be achieved at point of data-entry.
#' @param ... additional arguments to be passed to [addEllipse()].
#'
#' @return A series of convex hulls added to an existing plot.
#' @export
plotGroupHulls <- function(siber, plot.args = NULL, iso.order = c(1,2), ...) {
# iso.order used to specify which data goes on which axis.
x <- iso.order[1]
y <- iso.order[2]
for (i in 1:siber$n.communities){
for (j in 1:siber$n.groups[2,i]){
# find the indices for the jth group in the kth community
idx <- siber$raw.data[[i]]$group == siber$group.names[[i]][j]
# calculate the hull around the jth group in the
# ith community
ch <- siberConvexhull( siber$raw.data[[i]][idx, x],
siber$raw.data[[i]][idx, y]
)
# add the lines
do.call('lines', c(list(x = ch$xcoords, y = ch$ycoords), plot.args))
}
}
}
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