COVID_LIC (impacts of COVID-19 in Low & Middle Income Countries)
Description and Background
This repository is a collection of my work analyzing and integrating data mostly from these two sources of COVID-19 impacts in Low and Middle Income Countries.
- https://github.com/cmmid/covidm_reports. Described in more detail here: https://cmmid.github.io/topics/covid19/LMIC-projection-reports.html. This is a collection of country-specific projected COVID-19 epidemics with and without interventions.
- https://github.com/CSSEGISandData/COVID-19. Lots of data here, we were mostly using the dates for each country in which they reported > 50 COVID cases.
Draft output website
The draft output is being published here: https://paultanger.github.io/COVID_LIC/
Prerequisites
Outlined in load_libs.R and described in more detail below.
Installation
For now, the best way is clone or fork the repo. The data files have not been uplodated yet, so please contact the author for assistance.
How to use
The data files required for this project are being hosted here: https://drive.google.com/file/d/1naUVZuKa61fosltkoIjhIQJ8XeKROcnO/view?usp=sharing You will need to update the relative directories for these files in the scripts based on where you unzip the data.
This is a work in progress and some files need to be cleaned up but the key places to start are these files:
-
These capture and consolidate data:
- ConsolidateQSfiles.R
- organize_crop_calendar.R
- Organize_JHU_50confirmedcase.R
- Organize_USAID_sorting_cols.R
-
These produce various outputs (summary and graphics):
- get_stats.R
- plot_crop_cal_v1.R
- plot_v1.R
- Combine_Peak_Crop_Plots.R
- plot_regions.R
Development is in progress for a markdown output (rather than pdf outputs):
- Combined_Plots_Md.Rmd
Supporting files (best to just source them):
- load_libs.R
- functions.R
- plot_crop_cal_function.R
- plot_function.R
For the webpages, there is three 3 Rmd files:
- index.Rmd builds the main page
- nationalregions.Rmd builds the nationalregions.html using CountryTemplate.Rmd
- subnationalregions.Rmd builds the subnationalregions.html using CountryTemplateSubRegions.Rmd
For testing of the website, there is a test repo, to pull from that: git pull test master
Future plans
Improve documentation and add additional analysis
How to contribute
If you have any questions or would like to contribute, please let me know, paultangercoder@gmail.com.
License
To be updated later