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3.0.1 | Jul 20, 2023 |
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1.0.1 | Apr 7, 2023 |
#673 in Algorithms
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The stochastic simulation algorithm (SSA) with a Monte-Carlo generating method.
Example
sosa
allows using the SSA with agents that carry some individual
proprieties evolving over time.
Consider for example human cells which reproduce asexually and are thought
to acquire new point mutations in their genome upon cell division.
We could be interested in tracking the evolution in the number of mutations
over time, as cells reproduce.
Moreover, cells can reproduce at different rates on average, e.g. cells
carrying special mutations can reproduce faster compared to other cells.
In this case, we can use sosa
to perform SSA and at the same time track
those mutations over time taking into account the different proliferation
rates.
Note that if we are just interested in tracking the number of individuals
over time, without taking into consideration the indiviual proprities of
the agents, then rebop
should be used
instead of sosa
.
Find the next reaction in the system according to a
Monte-Carlo generating method.
Returns
None
if the maximal number of iterations have been reached or
there aren't any individuals left in the total population, see
SimState
.
Panics
If no inidividuals left or all computed times are not normal. Compute the Gillepsie-time for all reactions. The Gillespie-time is defined as:
-ln(1 - r) / (population[i] * rates[i]) for i 0..N
where r
is a random number and rates is self.0
.
Returns
- error when all computed times are infinity or 0
- array of computed times otherwise
Generates a random waiting time using the exponential waiting time with
parameter
lambda
of Poisson StochasticProcess.
Returns
- a waiting time of
0
iflambda
is infinity, - a random exponential waiting time if
lambda
f32::is_normal
, - infinity otherwise.
use rand_chacha::{ChaCha8Rng, rand_core::SeedableRng};
let mut rng = ChaCha8Rng::seed_from_u64(1u64);
let lambda_gr_than_zero = 0.1_f32;
assert!(exprand(lambda_gr_than_zero, &mut rng).is_sign_positive());
let lambda_zero = 0_f32;
assert!(exprand(lambda_zero, &mut rng).is_infinite());
let lambda_inf = f32::INFINITY;
assert!((exprand(lambda_inf, &mut rng) - 0.).abs() < f32::EPSILON);
Panics
When lambda
is negative.
use rand_chacha::{ChaCha8Rng, rand_core::SeedableRng};
let mut rng = ChaCha8Rng::seed_from_u64(1u64);
let lambda_neg = -0.1_f32;
exprand(lambda_neg, &mut rng);
Write vector of float into new file with a precision of 4 decimals. Write NAN if the slice to write to file is empty.
Dependencies
~1.7–2.7MB
~56K SLoC