From 78faf57be7a1727706b8244a806e7ab9e531db0b Mon Sep 17 00:00:00 2001 From: Swapnil Mishra Date: Thu, 9 Apr 2020 18:25:14 +0100 Subject: [PATCH] Update README.md --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index aaaae55..97743b6 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,10 @@ # covid19model Code for modelling estimated deaths and cases for COVID19 from Report 13 published by MRC Centre for Global Infectious Disease Analysis, Imperial College London: [Estimating the number of infections and the impact of nonpharmaceutical interventions on COVID-19 in 11 European countries](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-13-europe-npi-impact/) +## Version 2 Release +In this update we extend our original [model](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-13-europe-npi-impact/) to include (a) population saturation effects, (b) prior uncertaintyon the infection fatality ratio and (c) a more balanced prior on intervention effects. We also (d) included another3 countries (Greece, the Netherlands and Portugal). The updated technical detail is available [here](https://github.com/ImperialCollegeLondon/covid19model/blob/master/Technical_description_of_Imperial_COVID_19_Model.pdf) + + This repository has code for replication purposes. The bleeding edge code and advancements are done in a private repository. Ask report authors for any collaborations. ## Contributing @@ -41,8 +45,12 @@ package manager please see `environment.yml` for a full list of dependencies. There are two ways to run our code:- * Open the rstudio project covid19model.Rproj file in rstudio and run/source base.r file * To run from commandline please enter the cloned directory and type 'Rscript base.r base' in terminal + +# Results * The results are stored in two folders results and figures. * Results has the stored stan fits and data used for plotting * Figures have the images with daily cases, daily death and Rt for all countries. -## Please note to not make you wait for long we have by default run sampling for short period. To be comparable with report please uncomment the line 212 and comment out line 213. This will run sampling for 4000 iterations with 2000 warmups and 4 chains. +## Notice + * Please note to not make you wait for long we have by default run sampling for short period. For proper estimates please uncomment the line 202 and comment out line 203. This will run sampling for 4000 iterations with 2000 warmups and 4 chains. + * Python code is right now not updated and won't work. Python code is good for only version 1 model and data.