compute_multimodal_mod {CommKern}  R Documentation 
Description of the compute multimodal modularity matrix function.
compute_multimodal_mod(mod_matrix, net, communities, alpha)
mod_matrix 
the modularity matrix output from the

net 
a network object in list form (see the 
communities 
the vector of node assignments to communities 
alpha 
a double parameter balancing the use of the guidance matrix in modularity calculation 
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.
multimodal modularity matrix
matrix_to_df
, compute_modularity_matrix