| align | Network Alignment |
| best_fit_optim | Empirical parameterization |
| classify | Mechanistic Network Classification |
| classify_Systematic | Mechanistic Network Classification |
| compare | Compare Networks Many-to-Many |
| compare_Target | Compare Networks One-to-Many |
| gini | Gini coefficient |
| grow_DD | Grow a Duplication and Divergence Network |
| grow_DM | Grow a Duplication and Mutation Network |
| grow_ER | Grow an Erdos-Renyi Random Network |
| grow_NM | Grow a Niche Model Network |
| grow_PA | Grow a Preferential Attachment Network |
| grow_SW | Grow a Small-World Network |
| ics | Induced Conserved Structure (ICS) |
| make_DD | Makes a Duplication and Divergence Network |
| make_DM | Make a Duplication and Mutation Network |
| make_Mixture | Make a Mixture Mechanism Network |
| make_NM | Make a Niche Model network |
| make_Null | Mechanism Null Distributions |
| make_Null_canonical | Mechanism Null Distributions |
| make_Null_mixture | Mechanism Null Distributions |
| make_SW | Makes a Small-World Network |
| make_Systematic | Systematically Make Networks |
| make_Systematic_canonical | Systematically Make Networks |
| make_Systematic_directedCanonicalLike | Systematically Make Networks |
| make_Systematic_mixture | Systematically Make Networks |
| null_fit_optim | Empirical parameterization via null distributions |
| stir_DD | Sitrs a Duplication and Divergence Network |
| stir_DM | Stirs a Duplication and Mutation Network |
| stir_ER | Stir an Erdos-Renyi Random Network |
| stir_NM | Stirs a Niche Model Network |
| stir_PA | Stirs a Preferential Attachment Network |
| stir_SW | Stirs a Small-World Network |