rsetse (version 0.5.0)

prepare_continuous_force: Prepare continuous features for embedding

Description

This function prepares a continuous network for SETSe projection. The function works for networks with a single feature or high-dimensional features. The network takes in an igraph object and produces an undirected igraph object that can be used with the embedding functions.

Usage

prepare_continuous_force(
  g,
  node_names,
  k = NULL,
  force_var,
  sum_to_one = TRUE,
  distance = 1
)

Arguments

g

an igraph object

node_names

a character string. A vertex attribute which contains the node names.

k

The spring constant. This value is either a numeric value giving the spring constant for all edges or NULL. If NULL is used the k value will not be added to the network. This is useful k is made through some other process.

force_var

A character vector. This is the vector of node attributes to be used as the force variables. All the attributes must be a numeric or integer value, and cannot have NA's. On a single variable embedding this is usually "force"

sum_to_one

Logical. whether the total positive force sums to 1, if FALSE the total is the sum of the positive cases

distance

a positive numeric value. The default is 1

Value

A network with the correct edge and node attributes for the embeddings process.

Details

The function subtracts the mean from all the values so that the system is balanced. If sum_to_one is true then everything is divided by the absolute sum over two

The function adds the node attribute 'force' and the edge attribute 'k' unless k=NULL. The purpose of the function is to easily be able to project continuous networks using SETSe.

The function creates several variables

• force: a vertex attribute representing the force produced by each node. The sum of this variable will be 0

• k: The spring constant representing the stiffness of the spring.

• edge_name: the name of the edges. it takes the form "from_to" where "from" is the origin node and "to" is the destination node using the as_data_frame function from igraph

See Also

setse_auto_hd

Other prepare_setse: prepare_categorical_force(), prepare_edges()

Examples

# NOT RUN {
embeddings <- biconnected_network %>%
#prepare the network for a binary embedding
#k is already present in the data so is left null in the preparation function
prepare_edges(k = NULL, distance = 1) %>%
prepare_continuous_force(., node_names = "name", force_var = "force") %>%
#embed the network using auto_setse
#in the biconnected_network dataset the edge weights are used directly as k values
setse_auto(k = "weight")
# }