This folder contains individual workflow steps as makefiles. See the overall Makefile for orchestration of these components.
makefile |
Purpose |
|---|---|
support.makefile |
Defines helper tools and constructs directories required for storing results. |
inputs.makefile |
Defines helper tools and constructs directories required for storing results. |
rt.makefile |
Estimates the reproduction number for each variant of interest, combines them into a single object, and then calculates the ratios between them and Omicron. |
mobility.makefile |
Downloads and formats Google mobility data, and data from the Oxford COVID-19 government response tracker. |
susceptible.makefile |
Compute NGM principle eigenvalue ratio for Omicron / Delta, assuming varying levels of immune escape for Omicron, including ratio for a shorter Omicron GI |
threshold.makefile |
Use Rt ratios and estimates of susceptible population to calculate thresholds for transmissibility vs immune escape. |
local.makefile |
Not provided by default this makefile can be used to override settings given in support.makefile`. |