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#' Adds ellipses to an existing plot for each of your groups
#'
#' This function loops over each community and group within, and plots an
#' ellipse around the data. 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
#' [addEllipse()]. See [addEllipse()] for details of the
#' options, and you can also pass additional arguments such as line widths and
#' styles. 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 Ellipses, drawn as lines on an existing figure.
#' @export
plotGroupEllipses <- function(siber, plot.args = list(), iso.order = c(1,2),
...) {
# iso.order is used to relocate and reorientate the covariance matrix
# in the call to addEllipse below.
x <- iso.order[1]
y <- iso.order[2]
for (i in 1:siber$n.communities){
for (j in 1:siber$n.groups[2,i]){
do.call('addEllipse',
c(list(mu = siber$ML.mu[[i]][,c(x,y),j],
sigma = siber$ML.cov[[i]][c(x,y),c(x,y),j]),
m = siber$sample.sizes[i,j],
plot.args,
col = siber$group.names[[i]][j],
...))
} # end loop over groups
}# end loop over communities
} # end function
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