vimes_prune: Builds a graph from pairwise distances
In thibautjombart/vimes: VIsualisation and Monitoring of EpidemicS

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 `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`.

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:

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)

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.

thibautjombart/vimes documentation built on May 31, 2019, 10:38 a.m.