match_running.py

import pandas as pd
from osmatching import match


covid_df = pd.read_csv(
    "output/input_covid.csv", parse_dates=["patient_index_date", "died_date_ons"]
)
covid_df = covid_df.loc[covid_df["patient_index_date"].notnull()]
covid_df = covid_df.loc[covid_df["patient_index_date"] <= "2021-02-01"]
covid_df = covid_df.loc[~(covid_df["died_date_ons"] <= covid_df["patient_index_date"])]
covid_df.to_csv("output/input_covid_with_exclusions.csv", index=False)


gen_pop_df = pd.read_csv("output/input_general_population.csv")
gen_pop_df["patient_index_date"] = "2019-02-01"
gen_pop_df.to_csv("output/input_general_population_with_index_date.csv", index=False)

match(
    case_csv="input_covid_with_exclusions",
    match_csv="input_general_population_with_index_date",
    matches_per_case=5,
    match_variables={
        "sex": "category",
        "age": 1,
        "stp": "category",
    },
    closest_match_variables=["age"],
    index_date_variable="patient_index_date",
    output_suffix="_general_population",
    output_path="output",
)