Tools for the simulation and analysis of circadian rhythms
Project description
Circadian
Welcome to circadian
, a computational package for the simulation and
analysis of circadian rhythms
Install
circadian
can be installed via pip
:
pip install circadian
Overview
The circadian
package implements key mathematical models in the field
such as:
Forger99
- Forger et al. (1999)Hannay19
andHannay19TP
- Hannay et al. (2019)Jewett99
- Kronauer et al. (1999)
See all the available models at circadian/models.py
Additionally, circadian
provides a set of tools for simulating and
analzying circadian rhythms:
- Define light schedules using the
Light
class and feed directly into the models - Calculate phase response curves using the
PRCFinder
class - Generate actograms and phase plots with the
circadian.plots
module
Finally, the package streamlines the process of reading, processing, and
analyzing wereable data via the circadian.readers
module.
Check out the documentation for a full overview of the package and its features.
Example
The code below shows how to simulate the circadian rhythm of a shift worker for four different models and visualize the results in an actogram plot
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.lines as lines
from circadian.plots import Actogram
from circadian.lights import LightSchedule
from circadian.models import Forger99, Jewett99, Hannay19, Hannay19TP
days_night = 3
days_day = 2
slam_shift = LightSchedule.ShiftWork(lux=300.0, days_on=days_night, days_off=days_day)
total_days = 30
time = np.arange(0, 24*total_days, 0.10)
light_values = slam_shift(time)
f_model = Forger99()
kj_model = Jewett99()
spm_model = Hannay19()
tpm_model = Hannay19TP()
equilibration_reps = 2
initial_conditions_forger = f_model.equilibrate(time, light_values, equilibration_reps)
initial_conditions_kj = kj_model.equilibrate(time, light_values, equilibration_reps)
initial_conditions_spm = spm_model.equilibrate(time, light_values, equilibration_reps)
initial_conditions_tpm = tpm_model.equilibrate(time, light_values, equilibration_reps)
The models are integrated using an explicit Runge-Kutta 4 (RK4) scheme
trajectory_f = f_model(time, initial_conditions_forger, light_values)
trajectory_kj = kj_model(time, initial_conditions_kj, light_values)
trajectory_spm = spm_model(time, initial_conditions_spm, light_values)
trajectory_tpm = tpm_model(time, initial_conditions_tpm, light_values)
The Dim Light Melatonin Onset (DLMO), an experimental measurement of circadian phase, is calculated for each model by
dlmo_f = f_model.dlmos()
dlmo_kj = kj_model.dlmos()
dlmo_spm = spm_model.dlmos()
dlmo_tpm = tpm_model.dlmos()
Lastly, the results of the simulation–DLMOs included– are visualized in
an
Actogram
plot from the circadian.plots
module
acto = Actogram(time, light_vals=light_values, opacity=1.0, smooth=False)
acto.plot_phasemarker(dlmo_f, color='blue')
acto.plot_phasemarker(dlmo_spm, color='darkgreen')
acto.plot_phasemarker(dlmo_tpm, color='red')
acto.plot_phasemarker(dlmo_kj, color='purple')
# legend
blue_line = lines.Line2D([], [], color='blue', label='Forger99')
green_line = lines.Line2D([], [], color='darkgreen', label='Hannay19')
red_line = lines.Line2D([], [], color='red', label='Hannay19TP')
purple_line = lines.Line2D([], [], color='purple', label='Jewett99')
plt.legend(handles=[blue_line, purple_line, green_line, red_line],
loc='upper center', bbox_to_anchor=(0.5, 1.12), ncol=4)
plt.title("Actogram for a Simulated Shift Worker", pad=35)
plt.tight_layout()
plt.show()
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