Generate Synthetic Consortium Metabolism

Creates a synthetic metabolic network with biologically realistic structure: hub metabolites (Zipf-distributed degree), log-normal species degrees, cyclic cross-feeding backbone for connectivity, approximate mass balance, and no dead-end species by default.

Usage

synCM(name, n_species, max_met, seed = FALSE, dead_ends = FALSE, cm = TRUE)

Arguments

name

Character string. Name for the consortium.

n_species

Integer. Number of species in the consortium.

max_met

Integer. Size of the metabolite pool to sample from.

seed

Integer or FALSE. Random seed for reproducibility. If FALSE (default), a random seed is chosen.

dead_ends

Logical. If FALSE (default), ensures each species has both consumed and produced metabolites by flipping one flux value when all fluxes share the same sign.

cm

Logical. If TRUE (default), returns a ConsortiumMetabolism object. If FALSE, returns the raw edge list as a tibble.

Value

A ConsortiumMetabolism object when cm = TRUE, or a tibble with columns species, metabolites, and fluxes when cm = FALSE.

Examples

synCM("Ex. Community", n_species = 5, max_met = 10)
#> 
#> ── ConsortiumMetabolism 
#> Name: "Ex. Community"
#> Weighted metabolic network: 5 species, 6 metabolites, 10 pathways.
#> Pathways per species: min 1, mean 2.2, max 6.

# Return raw edge list instead
synCM("Test", n_species = 3, max_met = 8, cm = FALSE)
#> # A tibble: 8 × 3
#>   species  metabolites fluxes
#>   <chr>    <chr>        <dbl>
#> 1 OQZ8515G met4        -0.713
#> 2 APF6467H met4        -0.888
#> 3 APF6467H met2         0.886
#> 4 UOH9021W met2        -0.886
#> 5 UOH9021W met4         1.60 
#> 6 UOH9021W met8        -2.57 
#> 7 UOH9021W met3         4.64 
#> 8 UOH9021W met6        -3.19