Nothing
#############################################################
#
# getShiftNodesFromIndex (....)
#
# Args: ephy = object of class 'bammdata'
# index = the index of the sample you wish to view, e.g.,
# if index = 5, this will give you the nodes subtending
# all branches with rate shifts for the 5th sample
# from the posterior in your 'bammdata' object.
#
#
# Returns: - a vector of the nodes where shifts occurred, excluding the root.
# Note: if NO shifts occured, this will return a
# numeric object of length zero
#
##' @title Identify nodes associated with rate shifts from \code{bammdata}
##' object
##'
##' @description Find the node numbers associated with rate shifts for a
##' specified sample from the posterior distribution contained in a
##' \code{bammdata} object.
##'
##' @param ephy A \code{bammdata} object.
##' @param index The index value of the posterior sample from which you want
##' to identify shift nodes. This is \emph{not} the same as the actual
##' generation number of the MCMC sample. If your \code{bammdata} object
##' contains 100 samples from the posterior distribution, the value of
##' \code{index} must range from 1 to 100.
##'
##' @return A vector of nodes (excluding the root) that define branches on
##' which shifts occurred for the specified sample from the posterior.
##' Will return a numeric of length 0 if no non-root shifts occur in the
##' specified sample.
##'
##' @author Dan Rabosky
##'
##' @seealso \code{\link{addBAMMshifts}}, \code{\link{plot.bammdata}},
##' \code{\link{maximumShiftCredibility}}
##'
##' @examples
##' data(whales, events.whales)
##' ed <- getEventData(whales, events.whales, burnin=0.1, nsamples=500)
##'
##' # Get the maximum shift credibility configuration:
##' msc <- maximumShiftCredibility(ed)
##'
##' # Get the nodes at which shifts occurred in the
##' # maximum shift credibility configuration:
##'
##' getShiftNodesFromIndex(ed, index=msc$sampleindex)
##' @keywords models
##' @export
getShiftNodesFromIndex <- function(ephy, index) {
if (index > length(ephy$eventData)) {
cat("Error. Attempting to access non-existent element from 'bammdata' object\n");
cat("You have << ", length(ephy$eventData), " >>> samples in your 'bammdata' object\n");
cat("Value of index must be no greater than the number of samples\n\n");
stop();
}
root <- length(ephy$tip.label) + 1;
nodes <- ephy$eventData[[index]]$node;
nodes <- nodes[nodes != root];
return(nodes);
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.