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piLaboratory / GillesCom

Gillespie Simulation of Ecological Communities Dynamics
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Add argument to give/read elapsed time in cycles or clock time #16

Closed andrechalom closed 7 years ago

andrechalom commented 8 years ago

Currently, bdm() uses number of cycles but the plots and results are given in terms of elapsed simulated time. We need to implement a function to give the simulated cycles, and add arguments for bdm to accept final elapsed time.

andrechalom commented 8 years ago

Implemented the time argument to bdm as "time to simulate in this command" as opposed to "run simulation until specified time"; the other option would be inconsistent with the "cycles" argument, which is interpreted as "cycles to be run at this step".

andrechalom commented 8 years ago

Currently, we don't save the "current cycle" of the snapshot in the trajectories(). This is needed if we want to be able to reconstruct the history of the simulation in terms of cycles instead of simulated time. Is this needed? If we don't think so, this issue is solved by 3c8d002

Lobz commented 8 years ago

We need to add recording of simulated time to trajectories as well.

andrechalom commented 8 years ago

Working on this on branch rcpp_trajectories, which is based on rcpp_module