Source code for sbmlsim.examples.experiments.covid.experiments.bertozzi2020
from pathlib import Path
from typing import Dict
from sbmlsim.experiment import ExperimentDict, SimulationExperiment
from sbmlsim.model import AbstractModel
from sbmlsim.plot import Axis, Figure
from sbmlsim.simulation import Timecourse, TimecourseSim
from sbmlsim.task import Task
[docs]class Bertozzi2020(SimulationExperiment):
[docs] def models(self) -> Dict[str, AbstractModel]:
Q_ = self.Q_
models = {
"model": AbstractModel(
source=Path(__file__).parent
/ ".."
/ "models"
/ "Bertozzi2020"
/ "Bertozzi2020.xml",
language_type=AbstractModel.LanguageType.SBML,
changes={},
)
}
return ExperimentDict(models)
[docs] def tasks(self) -> Dict[str, Task]:
if self.simulations():
return ExperimentDict(
{
f"task_{key}": Task(model="model", simulation=key)
for key in self.simulations()
}
)
[docs] def simulations(self) -> Dict[str, TimecourseSim]:
Q_ = self.Q_
Ro_CA = 1.9544
Io_CA = [3956, 39.56, 0.3956, 0.003956]
tcsims = {}
for k, io_ca in enumerate(Io_CA):
tcsims[f"sim{k}"] = TimecourseSim(
[
Timecourse(
start=0,
end=215,
steps=281,
changes={
"Ro_CA": Q_(Ro_CA, "dimensionless"),
"Io_CA": Q_(io_ca, "dimensionless"),
},
)
]
)
return tcsims
[docs] def figures(self) -> Dict[str, Figure]:
unit_time = "time"
unit_y = "substance"
fig_1 = Figure(self, sid="plot_1", name=f"{self.sid} (plot_1)")
plots = fig_1.create_plots(Axis("time", unit=unit_time), legend=True)
plots[0].set_yaxis("y", unit_y)
# simulation
task_id = "task_sim0"
colors = ["black", "blue", "red", "green"]
for k, skey in enumerate(["Infected", "Susceptible", "Recovered", "Peak_Time"]):
color = colors[k]
plots[0].add_data(
task=task_id,
xid="time",
yid=skey,
label=skey,
color=color,
linewidth=2,
)
return {"plot_1": fig_1}