mappeR (version 2.4.0)

create_ball_mapper_object: Ball Mapper

Description

Run Mapper using the identity function as a lens and an \(\varepsilon\)-net cover, greedily generated using a distance matrix.

Usage

create_ball_mapper_object(data, dists, eps)

Value

A list of two data frames, nodes and edges, which contain information about the Mapper graph constructed from the given parameters.

The node data frame consists of:

• id: vertex ID

• cluster_size: number of data points in cluster

• medoid: the name of the medoid of the vertex

• mean_dist_to_medoid: mean distance to medoid of cluster

• max_dist_to_medoid: max distance to medoid of cluster

• cluster_width: maximum pairwise distance within cluster

• wcss: sum of squares of distances to cluster medoid

• data: names of data points in cluster

The edge data frame contains consists of:

• source: vertex ID of edge source

• target: vertex ID of edge target

• weight: Jaccard index of edge; this is the size of the intersection between the vertices divided by the union

• overlap_data: names of data points in overlap

• overlap_size: number of data points overlap

Arguments

data

A data frame.

dists

A distance matrix for the data frame. Can be a dist object or a matrix.

eps

A positive real number for the desired ball radius.

Examples

# Create noisy cirle data set
data = data.frame(x = sapply(1:1000, function(x) cos(x)) + runif(1000, 0, .25),
y = sapply(1:1000, function(x) sin(x)) + runif(1000, 0, .25))

# Set ball radius
eps = .25

# Create Mapper object
create_ball_mapper_object(data, dist(data), eps)