/SWO-Re

Estimates of the effective reproduction number for South-West Ontario

Primary LanguageRMIT LicenseMIT

SWO-Re

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.

Files Description

  • 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).

To investigate

  • identify importations?
  • quantify testing/reporting delays?
  • well-identified transmission chains for very low counts settings? (Blumberg's method?)