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10
reference/AMR-options.md
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@@ -63,14 +63,14 @@ the `AMR` package. Set them using the
[`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
and many plotting functions. **While unset**, the AMR package uses the
latest implemented EUCAST guideline (currently EUCAST 2025).
latest implemented EUCAST guideline (currently EUCAST 2026).
- For [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), this
determines which clinical breakpoint guideline is used to interpret
MIC values and disk diffusion diameters. It can be either the
guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including
a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011
to 2025, and CLSI 2011 to 2025.
to 2026, and CLSI 2011 to 2026.
- For [`resistance()`](https://amr-for-r.org/reference/proportion.md)
and
@@ -92,7 +92,7 @@ the `AMR` package. Set them using the
interpretative colouring. These colours are derived from
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
background and therefore depend on the active `guideline` setting,
which again uses EUCAST 2025 if not set explicitly.
which again uses EUCAST 2026 if not set explicitly.
- `AMR_guideline`
A [character](https://rdrr.io/r/base/character.html) to set the
@@ -101,8 +101,8 @@ the `AMR` package. Set them using the
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md). Can be only
the guideline name (e.g., `"CLSI"`) or the name with a year (e.g.
`"CLSI 2019"`). The default to the latest implemented EUCAST
guideline, currently `"EUCAST 2025"`. Supported guideline are
currently EUCAST (2011-2025) and CLSI (2011-2025).
guideline, currently `"EUCAST 2026"`. Supported guideline are
currently EUCAST (2011-2026) and CLSI (2011-2026).
- `AMR_ignore_pattern`
A [regular expression](https://rdrr.io/r/base/regex.html) to ignore