validation/parameter_calculation/Time_to_death_calculation.py

# Import libraries
import pandas as pd
import numpy as np

# Set file paths
file_path = '<YOUR_DATA_PATH>/'
input_file_path = file_path + 'data_for_model_e_columns/'


def read_data(file):
    """
    Read in data source
    --------
    :param file: string filename
    :return: dataframe
    """
    df = pd.read_csv(file)
    return df


def format_data(onboard, IDs):
    """
    Convert datetime columns to datetime format, filter to only include RECEIVER and scale up IDs,
    and add Date of death column
    --------
    :param onboard: dataframe containing onboarding dates
    :param IDs: dataframe containing IDs of interest
    :return: formatted dataframe
    """
    onboard['OB_date'] = pd.to_datetime(onboard['OB_date'])
    onboard['censor'] = pd.to_datetime(onboard['censor'])
    onboard = pd.merge(IDs, onboard, on="Study_ID", how="left")
    conditions_DOD = [onboard['censor'] != '2021-08-31']
    values_DOD = [onboard['censor'].dt.date]
    onboard['DOD'] = np.select(conditions_DOD, values_DOD, default=None)
    onboard['DOD'] = pd.to_datetime(onboard['DOD'])
    return onboard


def calculate_suvival(onboard, date_of_death, OB_date):
    """
    Calculate days from onboarding to date of death for those who died over the course of the RECEIVER study
    and save the dataframe
    --------
    :param onboard: dataframe containing onboarding and date of death data
    :param date of death: datetime column showing date of death
    :param OB_date: datetime column showing onboarding date
    """
    onboard['days'] = (onboard[date_of_death] - onboard[OB_date]).dt.days
    onboard.to_csv(file_path + 'Time_to_death_for_cohorts.csv')


def main():
    # Read in data
    onboard_file = input_file_path + "onboarding_dates.csv"
    RC_SU1_IDs_file = input_file_path + "RC_SU1_IDs.csv"
    
    onboard = read_data(onboard_file)
    RC_SU1_IDs = read_data(RC_SU1_IDs_file)

    # Format data
    onboard = format_data(onboard, RC_SU1_IDs)

    # Calculate days alive following onboarding and save the dataframe
    calculate_suvival(onboard, 'DOD', 'OB_date')

    
main()