RLeaping

RLeaping 1 is a solver developed for speeding up the Gillespie (SSA) 2. In the standard stochastic simulation algorithm (SSA), each reaction is simulated individually. In RLeaping, reactions are grouped together and executed at the same time. While leaping methods are approximate, they result in faster simulations.

RLeaping can be supplied with four parameters, but we recommend that you do not change the default values unless there is reason to do so. You can speed up the simulation time by increasing epsilon, but the accuracy of the method will decrease.

Parameter

Data type

Default

Description

solver

string

NA

R and RLeaping are both valid names to run this solver.

epsilon

float

0.01

Determines the error of the approximation; accepts values greater than 0 and much less than 1. A value of close to 0 is equivalent to a standard stochastic simulation and a value close to 1 is the most aggressive speedup (and largest error). We do not recommend changing this value.

theta

float

0

Controls the time step selection; accepts values between 0 and 1. A value of 0 is the most conservative and will limit the occurrence of a negative species value.

sorting interval

float

365

Sorts the reaction propensities according to this time interval; accepts positive values. To disable sorting, set the sorting interval greater than or equal to the simulation time.

verbose

bool

false

If true, extra information is printed to the command line, which can be useful for debugging or testing the solver.