Hypothesis Testing in Healthcare: Drug Safety
A pharmaceutical company GlobalXYZ has just completed a randomized controlled drug trial. To promote transparency and reproducibility of the drug's outcome, they (GlobalXYZ) have presented the dataset to your organization, a non-profit that focuses primarily on drug safety.
The dataset provided contained five adverse effects, demographic data, vital signs, etc. Your organization is primarily interested in the drug's adverse reactions. It wants to know if the adverse reactions, if any, are of significant proportions. It has asked you to explore and answer some questions from the data.
The dataset drug_safety.csv was obtained from Hbiostat courtesy of the Vanderbilt University Department of Biostatistics. It contained five adverse effects: headache, abdominal pain, dyspepsia, upper respiratory infection, chronic obstructive airway disease (COAD), demographic data, vital signs, lab measures, etc. The ratio of drug observations to placebo observations is 2 to 1.
For this project, the dataset has been modified to reflect the presence and absence of adverse effects adverse_effects and the number of adverse effects in a single individual num_effects.
The columns in the modified dataset are:
| Column | Description |
|---|---|
sex | The gender of the individual |
age | The age of the individual |
week | The week of the drug testing |
trx | The treatment (Drug) and control (Placebo) groups |
wbc | The count of white blood cells |
rbc | The count of red blood cells |
adverse_effects | The presence of at least a single adverse effect |
num_effects | The number of adverse effects experienced by a single individual |
The original dataset can be found here.
Your organization has asked you to explore and answer some questions from the data collected. See the project instructions.
# Import packages
import numpy as np
import pandas as pd
from statsmodels.stats.proportion import proportions_ztest
import pingouin
import seaborn as sns
import matplotlib.pyplot as plt
# Load the dataset
drug_safety = pd.read_csv("drug_safety.csv")
# Start coding here...
# Count the adverse effects column for each trx group
trx_adverse_effects = drug_safety.groupby("trx")["adverse_effects"].value_counts()
# compute total rows in each group
trx_adv_sum = trx_adverse_effects.groupby("trx").sum()
#create an array of the Yes counts
yes_group = [trx_adverse_effects["Drug"]["Yes"],trx_adverse_effects["Placebo"]["Yes"]]
# create an array of the total number of rows in each group
n= [trx_adv_sum["Drug"],trx_adv_sum["Placebo"]]
# two sided z-test
two_sample_results = proportions_ztest(yes_group, n)
#storing p_value
two_sample_p_value = two_sample_results[1]
# Determine if num_effects and trx are independent
num_effects_groups = pingouin.chi2_independence(data=drug_safety, x="num_effects", y="trx")
#Extracting the p_value from the chi2 independence test
num_effects_p_value = num_effects_groups[2]["pval"][0]
# Creating a histogram
sns.histplot(data=drug_safety,x="age",hue="trx")
# normality test
normality_t = pingouin.normality(data=drug_safety, dv="age", group="trx", method="shapiro",alpha=0.05)
# Age of the Drug group
age_trx = drug_safety.loc[drug_safety["trx"]=="Drug","age"]
# Select the age of the Placebo group
age_placebo = drug_safety.loc[drug_safety["trx"] == "Placebo", "age"]
#Two sided Mann-Whitney U test
age_group_effects = pingouin.mwu(age_trx,age_placebo)
# Extract the p-value
age_group_effects_p_value = age_group_effects["p-val"]