Code
R console
source("scripts/lineages_public_repo.R")COVID-19 Lineages
Washington State DOH COVID-19 lineage extraction process
This repo contains scripts that will pull lineages of interest from the CDC and transform them.
The repo will output a .csv file called lineages.csv that will be updated whenever new lineages are updated from the CDC. You can refresh/fetch this git repo for new changes and the .csv file will be updated.
To run the process:
- Run lineages script:
- Run the lineages classification script:
Code
R console
source("scripts/lineages_classification_for_test_repo.R")Variables
The variables produced by the scripts are used in the Sequencing and Variants Report. Here’s a list:
| Variables | Description |
|---|---|
| cdc_class | Variable indicating VOC (variant of concern) or VBM (variant being monitored) |
| who_name | Variable indicating the WHO name |
| doh_variant_name | Grouping variable in WA DOH Sequencing and Variant report |
| hex_code | Hex color for doh_variant_name group |
| lineage_reporting_group | Variable indicating reporting group of lineage coded as: 1: Currently monitoring 2: Formerly monitoring 3: Formerly circulating, not monitored |
| report_table_name | Variable name in numerical/pango form for table outputs |