Working example - parameters for the simulation of a trait

Working example - parameters for the simulation of a trait#

import fwdpy11

N = 1000
rho = 1000.0
mu_neutral = 0.0
mu_selected = 1e-3

GSSmo = fwdpy11.GaussianStabilizingSelection.single_trait(
    [
        fwdpy11.Optimum(when=0, optimum=0.0, VS=1.0),
        fwdpy11.Optimum(when=10 * N - 200, optimum=1.0, VS=1.0),
    ]
)

p = {
    "nregions": [],
    "gvalue": fwdpy11.Additive(2.0, GSSmo),
    "sregions": [fwdpy11.GaussianS(0, 1., 1, 0.1)],
    "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * N))],
    "rates": (mu_neutral, mu_selected, None),
    # Keep mutations at frequency 1 in the pop if they affect fitness.
    "prune_selected": False,
    "demography": fwdpy11.ForwardDemesGraph.tubes([N], burnin=1),
    "simlen": 10 * N,
}
params = fwdpy11.ModelParams(**p)

print(params)

ModelParams(nregions=[], sregions=[fwdpy11.GaussianS(beg=0, end=1.0, weight=1.0, sd=0.1, h=1.0, coupled=True, label=0, scaling=1.0)], recregions=[PoissonInterval(beg=0, end=1.0, mean=0.25, discrete=False)], rates=MutationAndRecombinationRates(neutral_mutation_rate=0.0, selected_mutation_rate=0.001, recombination_rate=None), gvalue=Additive(scaling=2.0, gvalue_to_fitness=GaussianStabilizingSelection(is_single_trait=True, optima=[fwdpy11.Optimum(optimum=0.0, VS=1.0, when=0), fwdpy11.Optimum(optimum=1.0, VS=1.0, when=9800)]), noise=None, ndemes=1), demography=ForwardDemesGraph(yaml='time_units: generations\ngeneration_time: 1\ndemes:\n- name: deme0\n  epochs:\n  - {end_time: 0, start_size: 1000}\n', burnin=1, burnin_is_exact=False, round_non_integer_sizes=False), simlen=10000, prune_selected=False, allow_residual_selfing=True)

Modifying model parameters#

Instances of fwdpy11.ModelParams are immutable. To change them, either:

  • Modify the original dict

  • Or, do a round trip through a temporary dict.

The first option is straightforward. Let’s see the second in action. We’ll change the simulation length.

temp_dict = params.asdict()
temp_dict["simlen"] *= 2
params = fwdpy11.ModelParams(**temp_dict)
print(params.simlen)

20000