netgen {EcoNetGen}

netgen

Description

Randomly generate a wide range of interaction networks

Usage

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?

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.

Value

an igraph object

Examples

library(EcoNetGen)

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