vimes_prune: Builds a graph from pairwise distances

In reconhub/vimes: VIsualisation and Monitoring of EpidemicS

Description

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.

Usage

vimes_prune(x, cutoff = NULL, graph_opt = vimes_graph_opt(), ...)

Arguments

x	pairwise distances stored as a dist object.
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 vimes_graph_opt.
...	further arguments to be passed to hist.

Details

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.

Value

a list containing:

graph

a graph connecting individuals, weighted with the input distances, with igraph class (from the igraph package).

clusters

a list providing cluster information: group membership, cluster sizes, and the number of clusters (K)

Author(s)

Thibaut Jombart [e-mail]

See Also

the function gengraph in the package adegenet, which was an initial implementation of the same idea in a genetics context.

reconhub/vimes documentation built on May 27, 2019, 4:03 a.m.