hamishgibbs/ghana_rt_npi_mobility

Analysis of the impact of COVID-19 interventions in Ghana ## Ghana NPI Analysis Repository for the analysis of the impact of Non-pharmaceutical Interventions in Ghana. *Estimating the relationship between mobility, non-pharmaceutical interventions, and COVID-19 transmission in Ghana* #### Usage This analysis is conducted in the EpiNow2 Docker image, based on the rocker/verse Docker image. To start developing in this container, follow the instructing in the EpiNow2 Wiki. Start the docker container for development: ``` docker run -d -p 8787:8787 --name epinow2 -e USER=epinow2 -e PASSWORD=epinow2 epinow2 ``` You can mount a volume with the `--mount` argument to specify the location of input datasets. The `Makefile` includes convenience commands for interacting with the Docker container. To download the latest EpiNow2 image (requires authentication with GitHub Packages): ``` make build ``` To run a container based on the EpiNow2 image (remember to alter volume mounts in the `Makefile`): ``` make up ``` To stop and remove the Docker container (tagged as `epinow2`): ``` make down ``` #### Environment Variables Environment variables are stored in a project configuration `.env` file stroed in the project root. This file is not tracked in version control. Environment variables: `MOB_DIR`: Directory where mobility data is located `DATA_DIR`: Directory where remaining data is located `OUTPUT_DIR`: Directory for output of figures #### Data Requirements **Line List Data** Line list data is provided by Ghana Health Service. Terms of data use do not permit redistribution of the data. Original data was provided in 15 district-specific line lists. Initial data cleaning was conducted manually. Key data was extracted to standard format `.csv` files (`region`, `district`, `epi_week`, `specimen_date`). Lookups were produced to transform coded (`district` and `epi_week`) values to standard format. Coded value lookup files are included in version control: `config/cases/spatial_lookups` - Lookup files assigning original a …