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Analysis Functions

Functions for analyzing relationships between time series

cross_corr()
Find the lag at which cross-correlation between two time series is maximised
rolling_corr()
Calculate rolling (moving-window) correlation between two time series
estimate_rt()
Estimate the effective reproduction number (Rt) over time by group
calc_percent_change()
Convert a count time series to fractional change relative to a baseline period

Visualization

Functions for visualizing results

plot_corr()
Plot time series and rolling correlation over time by group
plot_lag()
Plot a histogram of optimal lags across groups

Data

Example datasets included in the package

china_case_data
Daily confirmed cases of COVID-19 in China
exante_movement_data
Daily within-city movement data for different regions in China
wastewater_data
Weekly SARS-CoV-2 wastewater concentration for three US states
covid_case_data
Weekly reported COVID-19 cases for three US states