User-defined parameters handling - Githubissues

ramses-antibiotics / ramses-package

R Package for Data-Driven Antimicrobial Stewardship & Surveillance in Hospitals

https://ramses-antibiotics.web.app/

GNU General Public License v3.0

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User-defined parameters handling #10

Open peterdutey opened 4 years ago

peterdutey commented 4 years ago

Users need to set environment variables

Environment variables

AMR::mdro() arguments
database connection AND/OR server name, username, password etc.
controlled vocabularies

Setting of environment variables (see CRAN startup)

function (options(),
R_ENVIRON
R_ENVIRON_USER
.Renviron files
.Rprofile files
yml (see config)

Note: some of those are not secure ways to do this (need to draft acceptable architecture for the typical hospital).