AMR/data at e7077081b9011d85bc7696e74a74697c048b29fd - AMR

P281424/AMR

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dr. M.S. (Matthijs) Berends e7077081b9 Set the order of sites in as.sir(), and add the veterinary sites

Sites now go from systemic, IV, meningitis, endocarditis, pneumonia and mastitis to UTI, topical and screen. A breakpoint without a site takes the position of "other", as both mean any site that is not listed next to it. A second site breaks a tie on the first one.

The veterinary sites are now fixed codes as well: mastitis (includes Mammary gland), respiratory, metritis, genital, soft tissue and wounds (includes Abscesses). Sites that are part of each other do not contradict.

site = "other" now leaves out every breakpoint limited to an indication, and prefers a breakpoint without a site.

A rebuild of clinical_breakpoints with this order gives the same data, so the same blocking rows stay.

2026-11-02 20:20:05 +01:00

antibiotics.rda

Set the order of sites in as.sir(), and add the veterinary sites

2026-11-02 20:20:05 +01:00

antimicrobials.rda

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328 )

2026-11-02 17:31:46 +01:00

antivirals.rda

prepare for CRAN

2023-10-20 14:51:48 +02:00

clinical_breakpoints.rda

Rebuild clinical_breakpoints, and add the NEWS entries and version bump for this PR