Estimates of the effective reproduction number for South-West Ontario
--WARNING-- this is a work in progress!
This repo host R scripts to estimate the effective reproduction number ("Re") of reported COVID-19 cases for multiple Public Health Units (PHUs) in Ontario. Currently, there is a focus on the South-West regions. The estimation uses the R package EpiEstim
.
swo-Re.R
: This is the main script that retrieves and filter epidemiological data, estimates Re and plot its evolution over time.utils.R
: Implements utility functions.phus.csv
: Name of the PHUs selected. The names must be consistent with the data source (which is the line list from MoH).phu-group.csv
: Grouping of multiple PHUs (reported cases are aggregated within the group).
- identify importations?
- quantify testing/reporting delays?
- well-identified transmission chains for very low counts settings? (Blumberg's method?)