netgen function

netgen

Randomly generate a wide range of interaction networks

netgen(net_size = 50, ave_module_size = 10, min_module_size = 6,
  min_submod_size = 1, net_type = c("mixed", "random", "scalefree",
  "nested", "bi-partite nested", "bi-partite random",
  "tri-trophic bipartite nested-random",
  "tri-trophic bipartite nested-bipartite nested", "bn", "br", "tt-bn-r",
  "tt-bn-bn"), ave_degree = 5, rewire_prob_global = 0.2,
  rewire_prob_local = 0, mixing_probs = c(0.2, 0.2, 0.2, 0.2, 0.2, 0,
  0), verbose = FALSE)

Arguments

• net_size: network size (number of nodes)
• ave_module_size: average module size
• min_module_size: cutoff for the minimum modules size
• min_submod_size: cutoff for submodules, used only for bipartite and tripartite networks
• net_type: network type, see details
• ave_degree: average degree of connection
• rewire_prob_global: probability any given edge should be rewired
• rewire_prob_local: probability that edges within a module should be rewire locally (within the module)
• mixing_probs: module probabilities for first 7 types, used for constructing mixed networks
• verbose: logical, default TRUE. Should a message report summary statistics?

Returns

an igraph object

Details

network type is one of

• mixed
• random
• scalefree
• nested
• bi-partite nested (or short-hand "bn")
• bi-partite random (or short-hand "br")
• tri-trophic bipartite nested-random. (Can use short-hand "ttbnr")
• tri-trophic bipartite nested-bipartite nested (Can use short-hand "ttbnbn")

Valid Parameter Ranges

Please note that not all combinations of parameters will create valid networks. If an invalid combination is requested, netgen() will error with an informative message. A list of these constraints is provided below for reference.

1. net_size \>= ave_module_size. If `net_size = ave_module_size`` the program generates a network with a single module.
2. ave_module_size \> min_module_size
3. ave_degree \>= 1. Preferably larger than 4, to ensure single component modules.
4. rewire_prob_global = 0 produces completely uncoupled modules. To ensure a single component network use rewire_prob_global \> 0 and sufficiently large.
5. rewire_prob_local = 0 produces idealized modules. Use rewire_prob_local \> 0 to add stochasticity to the modules.
6. For tripartite networks min_module_size \> min_submod_size. This also implies min_module_size \>= 2.
7. For scalefree networks (or mixed networks involving scalefree modules) ave_degree \< min_module_size
8. For mixed networks mixing_probs need to sum to 1. If the sum is larger than one, only the first types, corresponding to sum \<=1, will be sampled.

Examples

library(EcoNetGen)

set.seed(12345)
net <- netgen()
adj_plot(net)