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89 lines
3.1 KiB
Markdown
89 lines
3.1 KiB
Markdown
# Data Set Denoting Bacterial Intrinsic Resistance
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Data set containing 'EUCAST Expected Resistant Phenotypes' of *all*
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bug-drug combinations between the
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md) and
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[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
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sets.
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## Usage
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``` r
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intrinsic_resistant
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```
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
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079 observations and 3 variables:
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- `mo`
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Microorganism ID which occurs in
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[`microorganisms$mo`](https://amr-for-r.org/reference/microorganisms.md).
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Names can be retrieved using
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[`mo_name()`](https://amr-for-r.org/reference/mo_property.md).
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- `ab`
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Antimicrobial ID which occurs in
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[`antimicrobials$ab`](https://amr-for-r.org/reference/antimicrobials.md).
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Names can be retrieved using
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[`ab_name()`](https://amr-for-r.org/reference/ab_property.md).
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- `version`
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Guideline name and version.
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## Details
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This data set is currently strictly follows ['EUCAST Expected Resistant
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Phenotypes'
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v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
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(2023). The
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This data set is internally used by:
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- [`not_intrinsic_resistant()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
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(an [antimicrobial
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selector](https://amr-for-r.org/reference/antimicrobial_selectors.md))
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- [`mo_is_intrinsic_resistant()`](https://amr-for-r.org/reference/mo_property.md)
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- [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) to model
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\\\beta(1, 9999)\\ for resistant bug-drug combinations, per
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[doi:10.1093/jac/dkv397](https://doi.org/10.1093/jac/dkv397)
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## Download Our Reference Data
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All reference data sets in the AMR package - including information on
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microorganisms, antimicrobials, and clinical breakpoints - are freely
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available for download in multiple formats: R, MS Excel, Apache Feather,
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Apache Parquet, SPSS, and Stata.
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For maximum compatibility, we also provide machine-readable,
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tab-separated plain text files suitable for use in any software,
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including laboratory information systems.
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Visit [our website for direct download
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links](https://amr-for-r.org/articles/datasets.html), or explore the
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actual files in [our GitHub
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repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
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## Examples
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``` r
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intrinsic_resistant
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#> # A tibble: 294,079 × 3
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#> mo ab version
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#> <mo> <ab> <chr>
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#> 1 B_GRAMP ATM 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 2 B_GRAMP COL 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 3 B_GRAMP NAL 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 4 B_GRAMP PLB 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 5 B_GRAMP TEM 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 6 B_ANAER-POS ATM 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 7 B_ANAER-POS COL 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 8 B_ANAER-POS NAL 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 9 B_ANAER-POS PLB 'EUCAST Expected Resistant Phenotypes' v1.2
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#> 10 B_ANAER-POS TEM 'EUCAST Expected Resistant Phenotypes' v1.2
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#> # ℹ 294,069 more rows
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```
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