CS9 Example

Core Surveillance 9 ("cs9") is a free and open-source framework for real-time analysis and disease surveillance.

Read the introduction vignette, or run help(package="cs9").

No .Renviron is needed

library(cs9example) runs on a bare machine. When CS9_DBCONFIG_ACCESS is empty, the package configures itself against SQLite files under file.path(tempdir(), "cs9example"). It then needs no database server and no .Renviron.

Pointing it at your own database

A .Renviron always wins. The package applies the defaults only when CS9_DBCONFIG_ACCESS is empty. The override is all or nothing. Set CS9_DBCONFIG_ACCESS and you own the whole configuration. The package supplies none of the other defaults, and a partial configuration fails to load. Open the file with:

usethis::edit_r_environ("project")

Then add these environment variables to keep SQLite but choose the two file paths yourself:

CS9_AUTO=0
CS9_PATH='/cs9path'

CS9_DBCONFIG_ACCESS='config/anon'
CS9_DBCONFIG_DRIVER='SQLite'

CS9_DBCONFIG_DB_CONFIG='/cs9path/config.sqlite'
CS9_DBCONFIG_DB_ANON='/cs9path/anon.sqlite'

SQLite reads none of CS9_DBCONFIG_SERVER, CS9_DBCONFIG_PORT, CS9_DBCONFIG_USER, CS9_DBCONFIG_PASSWORD or any CS9_DBCONFIG_SCHEMA_*. For a PostgreSQL configuration instead, see vignette("installation", package = "cs9").

After you add these variables, restart your R session. The changes take effect then.