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85 lines
3.5 KiB
Markdown
85 lines
3.5 KiB
Markdown
# Data Set with 534 Microorganisms In Species Groups
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A data set containing species groups and microbiological complexes,
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which are used in [the clinical breakpoints
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table](https://amr-for-r.org/reference/clinical_breakpoints.md).
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## Usage
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``` r
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microorganisms.groups
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```
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 534
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observations and 4 variables:
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- `mo_group`
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ID of the species group / microbiological complex
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- `mo`
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ID of the microorganism belonging in the species group /
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microbiological complex
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- `mo_group_name`
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Name of the species group / microbiological complex, as retrieved with
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[`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
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- `mo_name`
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Name of the microorganism belonging in the species group /
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microbiological complex, as retrieved with
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[`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
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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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## See also
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md)
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
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## Examples
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``` r
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microorganisms.groups
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#> # A tibble: 534 × 4
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#> mo_group mo mo_group_name mo_name
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#> <mo> <mo> <chr> <chr>
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#> 1 B_ACNTB_BMNN-C B_ACNTB_BMNN Acinetobacter baumannii complex Acinetobacter ba…
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#> 2 B_ACNTB_BMNN-C B_ACNTB_CLCC Acinetobacter baumannii complex Acinetobacter ca…
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#> 3 B_ACNTB_BMNN-C B_ACNTB_LCTC Acinetobacter baumannii complex Acinetobacter di…
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#> 4 B_ACNTB_BMNN-C B_ACNTB_NSCM Acinetobacter baumannii complex Acinetobacter no…
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#> 5 B_ACNTB_BMNN-C B_ACNTB_PITT Acinetobacter baumannii complex Acinetobacter pi…
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#> 6 B_ACNTB_BMNN-C B_ACNTB_SFRT Acinetobacter baumannii complex Acinetobacter se…
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#> 7 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides frag…
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#> 8 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovat…
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#> 9 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thet…
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#> 10 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex Bacteroides vulg…
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#> # ℹ 524 more rows
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# these are all species in the Bacteroides fragilis group, as per WHONET:
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microorganisms.groups[microorganisms.groups$mo_group == "B_BCTRD_FRGL-C", ]
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#> # A tibble: 5 × 4
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#> mo_group mo mo_group_name mo_name
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#> <mo> <mo> <chr> <chr>
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#> 1 B_BCTRD_FRGL-C B_BCTRD_FRGL Bacteroides fragilis complex Bacteroides fragilis
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#> 2 B_BCTRD_FRGL-C B_BCTRD_OVTS Bacteroides fragilis complex Bacteroides ovatus
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#> 3 B_BCTRD_FRGL-C B_BCTRD_THTT Bacteroides fragilis complex Bacteroides thetaiot…
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#> 4 B_BCTRD_FRGL-C B_PHCCL_VLGT Bacteroides fragilis complex Bacteroides vulgatus
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#> 5 B_BCTRD_FRGL-C B_PRBCT_DSTS Bacteroides fragilis complex Parabacteroides dist…
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```
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