compute_multimodal_mod {CommKern} R Documentation

## Compute multimodal modularity matrix

### Description

Description of the compute multimodal modularity matrix function.

### Usage

compute_multimodal_mod(mod_matrix, net, communities, alpha)


### Arguments

 mod_matrix the modularity matrix output from the compute_modularity_matrix function net a network object in list form (see the matrix_to_df function for more details) communities the vector of node assignments to communities alpha a double parameter balancing the use of the guidance matrix in modularity calculation

### Details

Calculates the multimodal version of the modularity matrix, which is detailed in the accompanying manuscript as the following:

\sum_{i \neq j} M_{ij} \delta(C_i,C_j) - \alpha \sum_{i \neq j} S_{ij} \delta(C_i,C_j).

This function incorporates both the modularity matrix calculated from the compute_modularity_matrix function and adds the additional component of a guidance matrix. The alpha parameter controls the extent to which the guidance matrix influences the modularity, where alpha=0 means the function reverts to the typical modularity calculation and alpha > 0 allows for some influence of the guidance matrix. The guidance matrix will not penalize the modularity if two nodes are not connected within it; it will only decrease the modularity if the two nodes have guidance information. The function takes in a network object, the mod_matrix output from compute_modularity_matrix, a vector of communities, and a parameter alpha and returns the multimodal modularity matrix.

### Value

multimodal modularity matrix

matrix_to_df, compute_modularity_matrix