⚠️ SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026).
Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
Implements the decisions ticked in #328, and the behaviour specified in https://github.com/msberends/AMR/pull/339#issuecomment-6577438074: `include_screening` now defaults to NULL, using screening breakpoints for screening agents only. With TRUE, a regular agent also takes these breakpoints, and with FALSE a screening agent gives NA with a note.
- antimicrobials gains 13 screening agents, e.g. GEN-S, ERY-S and STR1-S
- GEH and STH rows move to GEN-S and STR1-S, and as.sir() keeps accepting both codes
- Topical cut-off values move to -S agents with site "Topical"
- WHONET-based rows move as ticked, including CLSI cefoxitin for staphylococci and pefloxacin for Salmonella, and EUCAST 2012-2018 cefoxitin MIC
- Clinical breakpoints that EUCAST also allows as a screening test get a copy under the -S agent
dr. M.S. (Matthijs) Berends
2c98dac7ae
