Run the agent- and FBA-based simulation.
Usage
run_simulation(
object,
niter,
verbose = 1,
lim_cells = 1e+05,
lim_time = 300,
convergence.e = 1e-04,
record = NULL,
n.cores = NULL,
live.plot = F,
on.iteration = NULL,
...
)Arguments
- object
An object of class growthSimulation
- niter
Number of rounds to simulate
- verbose
Control the 'chattiness' of the simulation logs. 0 - no logs, 1 - only main logs, 2 - chaffinch.
- lim_cells
Simulation terminates of total number of cells exceed this value.
- lim_time
Simulation terminated after the first iteration that finished after this time limit (in minutes).
- convergence.e
Numeric indicating when community growth (pg) is considered to have reached convergence
- record
Character vector that indicates, which simulation variables should be recorded after each simulation iteration. See Details.
- n.cores
Number of CPUs to use for parallelisation. If NULL (default), it will use the number of detectable cores minus 1 and in maximum 10 cores.
- live.plot
Logical. If TRUE, positions of cells are plotted at each iteration. Caution: May reduce performance of simulation. Default: FALSE
- on.iteration
An optional function that is performed at the end of each iteration and returns again an object of class growthSimulation.
- ...
Additional arguments to `on.iteration`
Details
Recording: The cells' positions, masses, sizes, and metabolite exchanges are always recorded. Also recorded are the global metabolite concentrations. Due to memory considerations, local metabolite concentrations are not recorded by default. However, users can specify which concentrations are tracked during the simulation using the `record` option. E.g.
record = c("compound_cpd00029_e0","compound_cpd00211_e0")
records the concentration fo the to two metabolites `cpd00029_e0` and `cpd00211_e0`. All compound concentration can be recorded with
record = "compounds" ,
yet, is not advised as this could be storage- and time-consuming. Compound
concentrations are not stored in memory but on the hard drive in a file
within the working directory. Tracked concentrations can also be plotted with
plot_environment.
Exoenzyme concentrations cannot be recorded in the current version.
Convergence is checked by calculating the ratio: $$c := | a_i / min(a_{i-1},...,a_{i-5}) - 1 |$$ \(a_i\) is the total biomass at iteration \(i\). The simulation terminates if \(c\) is below `convergence.e`. Thus, one can expect longer simulations when reducing `convergence.e`.