P9.3.2Tuberculosis rates per head by state in the USA
The populations of each state in the USA over the years 1993–2018 are given in the file US-populations.txt. Read these data into a pandas DataFrame with a suitable index, and analyze them for any interesting trends. Then combine these data with those of Problem P9.3.1 to determine the states with the greatest and least prevalence of tuberculosis per head of population in 2018.
Show solution
Here are some ideas for analysis of the population data.
tuberculosisrates
import pandas as pd
import matplotlib.pyplot as plt
pops = pd.read_csv("US-populations.txt", index_col=0)
pops.columns = pops.columns.astype(int)
print("The most populous states (2018)")
print(pops[2018].sort_values(ascending=False)[:10])
print("The least populous states (2018)")
print(pops[2018].sort_values(ascending=False)[-10:])
print("States with an annual population decrease of greater than 10000")
exodus_states = pops.index[(pops.T.diff() < -10000).any()]
print(exodus_states.tolist())
fig, ax = plt.subplots(figsize=(7, 4))
pops.loc[exodus_states].T.diff().plot(ax=ax)
ax.set_xlabel("Year")
ax.set_ylabel("Population change")
plt.tight_layout()
plt.show()
# Read in the TB data
df = pd.read_csv(
"tb-cases.txt",
sep="\t",
usecols=("State", "Year", "Cases"),
skipfooter=21,
engine="python",
)
# Extract only year 2018 and drop the columns we don't need.
df = df[df["Year"] == 2018]
df = df.set_index(df["State"]).drop(["State", "Year"], axis=1)
df["pops"] = pops[2018]
df["TB prevalence per million"] = df["Cases"] / df["pops"] * 1.0e6
print("Lowest and highest TB prevalence in 2018")
print(df["TB prevalence per million"].sort_values().iloc[[0, -1]])
Output:
The most populous states (2018)
State
California 39461588
Texas 28628666
Florida 21244317
New York 19530351
Pennsylvania 12800922
Illinois 12723071
Ohio 11676341
Georgia 10511131
North Carolina 10381615
Michigan 9984072
Name: 2018, dtype: float64
The least populous states (2018)
State
Maine 1339057
Montana 1060665
Rhode Island 1058287
Delaware 965479
South Dakota 878698
North Dakota 758080
Alaska 735139
District of Columbia 701547
Vermont 624358
Wyoming 577601
Name: 2018, dtype: float64
States with an annual population decrease of greater than 10000
['Illinois', 'Louisiana', 'Massachusetts', 'Michigan', 'New York', 'West Virginia']
Lowest and highest TB prevalence in 2018
State
Wyoming 1.731299
Alaska 85.698079
Name: TB prevalence per million, dtype: float64
The plot of states that have seen a population decrease shows the effect of Hurricane Katrina in 2005, and a variety of more complex changes in states such as Michigan and New York.
