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@@ -7,8 +7,8 @@ which is an ordered
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[factor](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
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levels `S`, `SDD`, `I`, `R`, `NI`.
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Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI
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2011-2025, see *Details*. All breakpoints used for interpretation are
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Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI
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2011-2026, see *Details*. All breakpoints used for interpretation are
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available in our
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[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
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data set.
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@@ -80,29 +80,29 @@ For interpretations of minimum inhibitory concentration (MIC) values and
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disk diffusion diameters:
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- **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial
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Susceptibility Test Data**, 2011-2025, *Clinical and Laboratory
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Susceptibility Test Data**, 2011-2026, *Clinical and Laboratory
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Standards Institute* (CLSI).
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<https://clsi.org/standards/products/microbiology/documents/m39/>.
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- **CLSI M100: Performance Standard for Antimicrobial Susceptibility
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Testing**, 2011-2025, *Clinical and Laboratory Standards Institute*
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Testing**, 2011-2026, *Clinical and Laboratory Standards Institute*
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(CLSI).
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<https://clsi.org/standards/products/microbiology/documents/m100/>.
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- **CLSI VET01: Performance Standards for Antimicrobial Disk and
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Dilution Susceptibility Tests for Bacteria Isolated From Animals**,
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2019-2025, *Clinical and Laboratory Standards Institute* (CLSI).
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2019-2026, *Clinical and Laboratory Standards Institute* (CLSI).
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<https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.
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- **EUCAST Breakpoint tables for interpretation of MICs and zone
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diameters**, 2011-2025, *European Committee on Antimicrobial
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diameters**, 2011-2026, *European Committee on Antimicrobial
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Susceptibility Testing* (EUCAST).
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<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.
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- **WHONET** as a source for machine-reading the clinical breakpoints
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([read more
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here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)),
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1989-2025, *WHO Collaborating Centre for Surveillance of Antimicrobial
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1989-2026, *WHO Collaborating Centre for Surveillance of Antimicrobial
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Resistance*. <https://whonet.org/>.
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## Arguments
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@@ -162,12 +162,12 @@ disk diffusion diameters:
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- guideline:
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A guideline name (or column name) to use for SIR interpretation.
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Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in
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Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in
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the
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[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
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data set), but can be set with the package option
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[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
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Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see
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Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see
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*Details*. Using a column name allows for straightforward
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interpretation of historical data, which must be analysed in the
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context of, for example, different years.
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@@ -457,15 +457,15 @@ interpretation, and the exact input and output values.
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For interpreting MIC values as well as disk diffusion diameters,
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currently implemented guidelines are:
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- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
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- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;
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- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
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- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;
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- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
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CLSI 2022-2025.
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- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
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CLSI 2022-2026.
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The `guideline` argument must be set to e.g., `"EUCAST 2025"` or
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`"CLSI 2025"`. By simply using `"EUCAST"` (the default) or `"CLSI"` as
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The `guideline` argument must be set to e.g., `"EUCAST 2026"` or
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`"CLSI 2026"`. By simply using `"EUCAST"` (the default) or `"CLSI"` as
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input, the latest included version of that guideline will automatically
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be selected. Importantly, using a column name of your data instead,
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allows for straightforward interpretation of historical data that must
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@@ -660,10 +660,10 @@ sir_interpretation_history()
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#> # A tibble: 4 × 18
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#> datetime index method ab_given mo_given host_given input_given
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#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
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#> 1 2026-03-24 12:30:17 1 MIC amoxicillin Escherich… human 8
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#> 2 2026-03-24 12:30:17 1 MIC cipro Escherich… human 0.256
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#> 3 2026-03-24 12:30:18 1 DISK tobra Escherich… human 16
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#> 4 2026-03-24 12:30:18 1 DISK genta Escherich… human 18
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#> 1 2026-03-30 08:14:10 1 MIC amoxicillin Escherich… human 8
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#> 2 2026-03-30 08:14:10 1 MIC cipro Escherich… human 0.256
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#> 3 2026-03-30 08:14:10 1 DISK tobra Escherich… human 16
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#> 4 2026-03-30 08:14:11 1 DISK genta Escherich… human 18
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#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
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#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
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#> # breakpoint_S_R <chr>, site <chr>
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