From d69e7fa7405252feb25c5e0b36e5320c2af17102 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Thu, 15 Oct 2026 12:13:56 +0200 Subject: [PATCH] (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 --- DESCRIPTION | 2 +- NEWS.md | 2 +- .../reproduction_of_clinical_breakpoints_eucast.R | 5 +---- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a9c128e0c..5779e990b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ 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) diff --git a/NEWS.md b/NEWS.md index e58ba1725..92267a543 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9138 +# AMR 3.0.1.9146 Planned as v3.1.0, mid October 2026. diff --git a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R index 8388548c0..f1810db6c 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R +++ b/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints_eucast.R @@ -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 }