T2 - Infectious Challenge Time Series

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt

from emodlib.malaria import IntrahostComponent, create_config

duration = 300

asexuals = np.zeros(duration)
gametocytes = np.zeros(duration)

config = create_config()
ic = IntrahostComponent.create(config)
ic.challenge()

for t in range(duration):
    ic.update(dt=1)
    asexuals[t] = ic.parasite_density
    gametocytes[t] = ic.gametocyte_density

df = pd.DataFrame({'days': range(duration),
                   'parasite_density': asexuals,
                   'gametocyte_density': gametocytes}).set_index('days')

df.head(10)

	parasite_density	gametocyte_density
days
0	0.000000	0.0
1	0.000000	0.0
2	0.000000	0.0
3	0.000000	0.0
4	0.000000	0.0
5	0.000000	0.0
6	0.003000	0.0
7	0.003000	0.0
8	0.047676	0.0
9	0.047676	0.0

fig, ax = plt.subplots(1, 1, figsize=(8, 3))
df.plot(ax=ax, color=dict(parasite_density='navy', gametocyte_density='darkgreen'))
ax.set(yscale='log')
fig.set_tight_layout(True)