paultanger/COVID_LIC

This repository is a collection of my work analyzing and integrating data of COVID-19 impacts in Low and Middle Income Countries. Check out the output here:

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