Code for modelling estimated deaths and cases for COVID19.
This is the release related to our upcoming peer-reviewed age paper, where we use age-specific mobility data to estimate the epidemic in the USA by accounting for age-specific heterogeneity. All other code is still the same for previous releases.
To run this code you need to follow the steps listed in the age-specific model here.
The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results.
The instructions for European, Italy, Brazil, USA, Nature, and IFR code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, and version 8). This release is specific to upcoming peer-reviewed age paper.
This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.
This is the release related to our usa-paper (soon to be out) and medRxiv paper, where we use mobility data to estimate the situation in all states of the USA. All other code is still the same.
To run this code you can directly run the base-usa.r file or from the command line after setting the current directory as the repository directory run the following command Rscript base-usa-cases.r
The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results.
The instructions for European, Italy, Brazil, USA, Nature, IFR, USA age-specific code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, version 8, and version 9). This release is specific to [ usa-paper (soon to be out) and medRxiv paper.
This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.
Bugfix in post-processing: deprecated temporary directory in save-posterior-samples, a table that was not in a data.table format in post-processing-summarise-antibody.R, files not correctly called if re-run in post-processing-plot-age-newcases.R and incorrect file name spelling in post-processing-etas.R.
Rest everything remains the same as version 9.
This is the release related to report 32 and medRxiv paper, where we use age-specific mobility data to estimate the epidemic in the USA by accounting for age-specific heterogeneity. All other code is still the same for previous releases.
To run this code you need to follow the steps listed in the age-specific model here.
The code should be run in full mode to obtain credible results. Not running a full run to estimate anything is not recommended and discouraged. Only a full run should be used to get results.
The instructions for European, Italy, Brazil, USA, Nature, and IFR code are the same as earlier (Look at version 3, version 4, version 5, version 6, version 7, and version 8). This release is specific to report 32.
This release has been checked on macOS Catalina version 10.15.6/7 and Ubuntu version 18.04.2.
The code for running models remains unchanged in the release. We provide scripts to calculate ifr for European countries and USA states. We hope the release of ifr computation code will enable the researchers to adapt the ifr calculations as per their requirements. The two files to run are compute-ifr-europe.r and compute-ifr-usa.r.
The code for ifr calculation for a new country will need changes if you have different age-specific bands. The code provided is not a universal code that will work for each country, the intention is to help researchers to modify the code easily for their setup.
The code for ifr needs an additional package named socialmixr, which is not specified in the environment file as it doesn't exist with conda. You will need to download it via CRAN.
This code is the exact code that was used in Flaxman, Mishra, Gandy et al. "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe," Nature, 2020. https://www.nature.com/articles/s41586-020-2405-7
To run the code from the main folder in Rstudio source("base-nature.r") or from the command line Rscript base-nature.r.
The code should be run in full mode to obtain results---debug mode is only to check that your environment has the required libraries; results will not be reliable as the MCMC chains will not have converged.
The repository with posterior draws of the model in Flaxman, Mishra, Gandy et al. "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe," Nature, 2020. https://www.nature.com/articles/s41586-020-2405-7 is here.
This code doesn't supersede our earlier model, it is here for everyone to have direct access to code used in Flaxman, Mishra, Gandy et al. "Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe," Nature, 2020.https://www.nature.com/articles/s41586-020-2405-7.
The instructions for European, Italy, Brazil, and USA code are the same as earlier (Look at version 3, version 4, version 5, version 6).
This is the release related to report 23, where we use mobility data to estimate the situation in all states of the USA. All other code is still the same.
To run this code you can directly run the base-usa.r file or from the command line after setting the current directory as the repository directory run the following command Rscript base-usa.r
The code should be run in full mode to obtain any results. Not running a full run of the model to estimate anything is not recommended and discouraged. Only and only full run should be used to get results.
The instructions for European, Italy, and Brazil code are the same as earlier (Look at version 3, version 4, and version 5). This release is specific to USA report
This is the release related to report 21, where we use mobility data to estimate situation in Brazil. All other code is still the same.
To run this code you can directly run the base-Brazil.r file or from command line after seting the current directory as the repository directory run the following command Rscript base-Brazil.r
The code shold be run in full mode to obtain any results. Not running full model to estimate anything is not recommended and discouraged. Only full run should be used to get results.
The instructions for European and Italy code are same as earlier (Look at version 3 and version 4). This release is specific to Brazil report
This is the release related to report 20, where we use mobility data to estimate situation in Italy. All other code is still the same.
To run this code you can directly run the base-italy.r file or from command line after seting the current directory as the repository directory run the following command Rscript base-italy.r base-italy google interventions '~ -1 + residential + transit + averageMobility' '~ -1 + residential + transit + averageMobility'
The code for scenarios runs only in full mode not in short run or debug mode. Not running full model to estimate anything is not recommended and discouraged. Only full run should be used to get results.
The instructions for European code are same as Version 3. This release is specific to Italy report