Join multiple metabolic models to form a community

Merges multiple metabolic models into one model where each organisms is within an own compartment. Organism compartments are connected by a shared extracellular space (i.e., environment), from where the organisms can take up nutrients an release metabolic by-products. Exchange reactions are attached to the new (shared) extracelluar compartment.

Usage

joinModels(
  models,
  mergeLB = "none",
  mergeUB = "none",
  origExchangeBounds = "open",
  abun = rep(1/length(models), length(models))
)

Arguments

models: A list of objects of class ModelOrg
mergeLB, mergeUB: Method to use in cases where the individual models differ in the lower/upper bound values for the same exchange reactions. Option "min" uses the minimum LB/UB values found among the individual models for the exchange reactions in the final merged model. "max" acts analogously. "none" will cause the method to stop with an error, if boundaries differ between input models. Further options: "median","mean".
origExchangeBounds: Method to keep/open the flux boundaries of organism-specific exchange reactions. "keep" does not alter the lower or upper bounds of the organism exchange reactions, that connect the respective organism to the shared extracellular space. "open" removes any constraints on organism-specific exchange reactions. "open_lb" and "open_ub" removes only bounds for lower or upper limits, respectively.
abun: Numeric vector to define the relative abundance of the model organisms in the community. Entries of the vector should ideally sum up to 1.