11 May 2015

Steppe plot

Steppe plots show the interval between two dates for each case in a line list. Common examples include the time betweet onset and death, or onset and report. The steppe plot function works best when NaNs or NaTs are removed.

import epipy
import pandas as pd

df = epipy.get_data('mers_line_list')
df['death_date'] = df['Approx death date'].apply(epipy.date_convert)
df = df.dropna(how='any', subset=['onset_date', 'death_date'])
df = df.tail(15) #select out last 15 cases

fig, ax = epipy.stripe_plot(df, 'Case #', 'onset_date', 'death_date', 'Sex', legend=True)
ax.set_ylabel('Case number')
ax.set_title('Onset to death range (MERS-CoV)')

The result is a nice visualization of the individual case histories across time.

Steppe plot of selected MERS-CoV cases

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