Core Surveillance 9 ("cs9") is a free and open-source framework for real-time analysis and disease surveillance.
Read the introduction vignette here or run help(package="cs9").
If you are running this interactively in Posit Studio/Workbench, you need to set up your environment variables. Run the following command:
usethis::edit_r_environ("project")Then add these environment variables to the .Renviron file:
CS9_DBCONFIG_USER='yourusername'
CS9_DBCONFIG_PASSWORD='yourStrongPassword100'
CS9_AUTO=0
CS9_PATH='/cs9path'
CS9_DBCONFIG_ACCESS='config/anon'
CS9_DBCONFIG_DRIVER='PostgreSQL Unicode'
CS9_DBCONFIG_PORT='5432'
CS9_DBCONFIG_SSLMODE='no'
CS9_DBCONFIG_ROLE_CREATE_TABLE='yourusername'
CS9_DBCONFIG_SERVER='db'
CS9_DBCONFIG_SCHEMA_CONFIG='public'
CS9_DBCONFIG_DB_CONFIG='postgres'
CS9_DBCONFIG_SCHEMA_ANON='public'
CS9_DBCONFIG_DB_ANON='postgres'
After adding these variables, restart your R session for the changes to take effect.