Is there any particular reason to use infomap to detect communities in ecological networks?

[mar-iana]

What is the point of using infomap when I don't have a hierarchical network, but rather a bipartite one, such as species occurrence in communities, with each layer being a time period?
I was trying to adapt the code to use the output of another community detection algorithm in unipartite networks (example: maximizing Modularity with Simulated Annealing- Guimera & Amaral 2005), and connecting modules between layers in relation to their similarity in species composition. However, I wanted to know if this is conceptually correct. Thanks in advance.