Description Usage Arguments Details Value Author(s) See Also
This function builds a graph using a dist
object and a cut-off distance beyond which individuals are no longer connected. It also identifies clusters of connected individuals from the graph. If no cut-off is provided, a histogram is displayed for interactive selection.
1 | vimes_prune(x, cutoff = NULL, graph_opt = vimes_graph_opt(), ...)
|
x |
pairwise distances stored as a |
cutoff |
a cutoff distance beyond which individuals will not be connected in the graph. |
graph_opt |
a list of graphical options for the graphs, as
returned by |
... |
further arguments to be passed to |
The cutoff is inclusive: only cases strictly further away
than the cutoff distance will be disconnected on the graph. Note
that this differs from the original gengraph
implementation
in the package adegenet
.
a list containing:
a graph connecting individuals, weighted with the
input distances, with igraph
class (from the igraph
package).
a list providing cluster information: group membership, cluster sizes, and the number of clusters (K)
Thibaut Jombart thibautjombart@gmail.com
the function gengraph
in the package adegenet
, which
was an initial implementation of the same idea in a genetics
context.
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