BacArena: consume – R documentation

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consume

Function to account for the consumption and production of substances

The generic function consume implements the consumption and production of substances based on the flux of exchange reactions of organisms

consume(object, sublb, cutoff = 1e-06, bacnum, fbasol)

## S4 method for signature 'Organism'
consume(object, sublb, cutoff = 1e-06, bacnum, fbasol)

`object`	An object of class Organisms.
`sublb`	A vector containing the substance concentrations in the current position of the individual of interest.
`cutoff`	A number giving the cutoff value by which value of objective function is considered greater than 0.
`bacnum`	Integer indicating the number of bacteria individuals per gridcell
`fbasol`	Problem object according to the constraints and then solved with `optimizeProb`.

The consumption is implemented by adding the flux of the exchange reactions to the current substance concentrations.

Returns the updated vector containing the substance concentrations in the current position of the individual of interest.

NULL

Modeling Framework for Cellular Communities in their Environments

v1.8.2

GPL-3 | file LICENSE

Authors

Eugen Bauer [aut], Johannes Zimmermann [aut, cre]

Initial release