COVID10k

Estimating time to 1k and 10k COVID-19 cases

Running Analysis

This project uses gnu make to define dependencies between inputs. The basic flow of the analysis is:

0. get latest data (updateWHO.R)
1. generate analysis parameters (by-country json files) from WHO SITREP data (WHOprocess.R)
2. from analysis parameters, simulate branching process time series (bpsamples.R)
3. consolidate those results (bpconsolidate.R)
4. various summaries outputs
5. using the branching process series + hospitalization parameters, generate hospital trajectories (by-country)
6. consolidate hospitalization results
7. various summary outputs

Generate Analysis Parameters

There are shared parameter files (inputs/SCENARIO.json), and country specific (*-par.json) parameter files. The country specific ones are made from the latest data:

make params

Generate HPC slurm reference

Generate the list of branching process jobs to do:

make R2.txt R3.txt

then use R2-bps.slurm R3-bps.slurm to run the jobs.

Consolidate Results, Summarize & Visualize