Covid_19_DINN/datasets/transform_SIR.py

import numpy as np
import pandas as pd
import matplotlib.pylab as plt
from matplotlib import rcParams

dataset_path = 'datasets/COVID-19-Todesfaelle_in_Deutschland/'

FONT_COLOR = '#595959'
SUSCEPTIBLE = '#6399f7'
INFECTIOUS = '#f56262'
REMOVED = '#83eb5e'

def transform_general_data(plot_name: str, plot_title: str, exclude=[], plot_size=(12,6), yscale_log=False, plot_legend=True):
    """Function to generate the SIR split from the data in the COVID-19-Todesfaelle_in_Deutschland dataset.
    """
    # read the data
    df = pd.read_csv(dataset_path + 'COVID-19-Todesfaelle_Deutschland.csv')

    df = df.drop(df.index[1200:])

    # population of germany at the end of 2019
    N = 83100000
    S, I, R = np.zeros(df.shape[0]), np.zeros(df.shape[0]), np.zeros(df.shape[0])

    # S_0 = N - I_0
    S[0] = N - df['Faelle_gesamt'][0]
    # I_0 = overall cases at the day - overall death cases at the day
    I[0] = df['Faelle_gesamt'][0] - df['Todesfaelle_gesamt'][0]
    # R_0 = overall death cases at the day
    R[0] = df['Todesfaelle_gesamt'][0]

    # the recovery time is 14 days
    recovery_queue = np.zeros(14)
    
    for day in range(1, df.shape[0]):
        infections = df['Faelle_gesamt'][day] - df['Faelle_gesamt'][day-1]
        deaths = df['Todesfaelle_neu'][day]
        recoveries = recovery_queue[0]

        S[day] = S[day-1] - infections
        I[day] = I[day-1] + infections - deaths - recoveries
        R[day] = R[day-1] + deaths + recoveries

        # update recovery queue
        if I[day] < 0:
            recovery_queue[-1] -= I[day] 
            I[day] = 0

        recovery_queue[:-1] = recovery_queue[1:]
        recovery_queue[-1] = infections

    # plot graphs
    t = np.arange(0, df.shape[0], 1)
    rcParams['font.family'] = 'Comfortaa'
    rcParams['font.size'] = 12

    rcParams['text.color'] = FONT_COLOR
    rcParams['axes.labelcolor'] = FONT_COLOR
    rcParams['xtick.color'] = FONT_COLOR
    rcParams['ytick.color'] = FONT_COLOR

    slide3 = plt.figure(figsize=plot_size)
    ax = slide3.add_subplot(111, facecolor='#dddddd', axisbelow=True)
    ax.set_facecolor('xkcd:white')

    if 'S' not in exclude:
        ax.plot(t, S, label='Susceptible', c=SUSCEPTIBLE, lw=3)
    
    if 'I' not in exclude:
        ax.plot(t, I, label='Infectious', c=INFECTIOUS, lw=3)

    if 'R' not in exclude:
        ax.plot(t, R, label='Removed', c=REMOVED, lw=3)

    if yscale_log:
        plt.yscale('log')

    plt.ylabel('amount of poeple')
    plt.xlabel('time / days')
    plt.title(plot_title)
    ax.yaxis.set_tick_params(length=0)

    if plot_legend:
        plt.legend()

    ax.yaxis.set_tick_params(length=0, which='both')
    ax.xaxis.set_tick_params(length=0, which='both')
    ax.grid(which='major', c='black', lw=0.2, ls='-')

    for spine in ('top', 'right', 'bottom', 'left'):
        ax.spines[spine].set_visible(False)

    slide3.savefig(f'visualizations/{plot_name}.png', transparent=True)