(v3.0.1.9146) Correct the comment in the EUCAST reproduction script stating that breakpoints in brackets are excluded from clinical_breakpoints: they are kept as blocking rows without values

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dr. M.S. (Matthijs) Berends committed 2026-10-15 12:13:56 +02:00
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Package: AMR
Version: 3.0.1.9138
Version: 3.0.1.9146
Date: 2026-10-15
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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# AMR 3.0.1.9138
# AMR 3.0.1.9146
Planned as v3.1.0, mid October 2026.
@@ -494,10 +494,7 @@ parse_bp <- function(txt) {
t <- trimws(txt)
# placeholders such as "-" (susceptibility testing not recommended), "IE"
# or "Note" are kept as they are: the cleanup turns them into blocking rows
# Parenthesised values like "(2)" are EUCAST's "breakpoints in brackets"
# (see is_bracketed_bp()). They are preserved as-is in the raw file so
# they remain distinguishable from clinical breakpoints. The cleanup
# section later excludes them from the clinical_breakpoints table.
# Parenthesised values like "(2)" are EUCAST's "breakpoints in brackets" (see is_bracketed_bp()). They are kept as they are in the raw file, so that they remain distinguishable from clinical breakpoints. The cleanup turns them into blocking rows as well: the row stays in clinical_breakpoints, but with breakpoint_S and breakpoint_R set to NA and the bracketed values stated in the note (see "Blocking rows").
t
}