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155 lines
3.8 KiB
Markdown
155 lines
3.8 KiB
Markdown
# Data Set with 6 036 Common Microorganism Codes
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A data set containing commonly used codes for microorganisms, from
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laboratory systems and [WHONET](https://whonet.org). Define your own
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with [`set_mo_source()`](https://amr-for-r.org/reference/mo_source.md).
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They will all be searched when using
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) and consequently
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all the [`mo_*`](https://amr-for-r.org/reference/mo_property.md)
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functions.
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## Usage
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``` r
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microorganisms.codes
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```
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## Format
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A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 6
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036 observations and 2 variables:
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- `code`
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Commonly used code of a microorganism. ***This is a unique
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identifier.***
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- `mo`
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ID of the microorganism in the
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[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
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data set
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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.codes
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#> # A tibble: 6,036 × 2
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#> code mo
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#> <chr> <mo>
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#> 1 1011 B_GRAMP
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#> 2 1012 B_GRAMP
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#> 3 1013 B_GRAMN
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#> 4 1014 B_GRAMN
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#> 5 1015 F_YEAST
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#> 6 103 B_ESCHR_COLI
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#> 7 104 B_SLMNL_ENTR_ENTR
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#> 8 1100 B_STRPT
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#> 9 1101 B_STRPT_VIRI
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#> 10 1102 B_STRPT_HAEM
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#> # ℹ 6,026 more rows
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# 'ECO' or 'eco' is the WHONET code for E. coli:
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microorganisms.codes[microorganisms.codes$code == "ECO", ]
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#> # A tibble: 1 × 2
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#> code mo
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#> <chr> <mo>
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#> 1 ECO B_ESCHR_COLI
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# and therefore, 'eco' will be understood as E. coli in this package:
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mo_info("eco")
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#> $mo
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#> [1] "B_ESCHR_COLI"
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#>
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#> $rank
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#> [1] "species"
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#>
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#> $kingdom
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#> [1] "Bacteria"
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#>
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#> $phylum
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#> [1] "Pseudomonadota"
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#>
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#> $class
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#> [1] "Gammaproteobacteria"
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#>
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#> $order
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#> [1] "Enterobacterales"
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#>
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#> $family
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#> [1] "Enterobacteriaceae"
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#>
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#> $genus
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#> [1] "Escherichia"
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#>
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#> $species
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#> [1] "coli"
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#>
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#> $subspecies
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#> [1] ""
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#>
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#> $status
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#> [1] "accepted"
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#>
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#> $synonyms
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#> NULL
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#>
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#> $gramstain
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#> [1] "Gram-negative"
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#>
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#> $oxygen_tolerance
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#> [1] "facultative anaerobe"
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#>
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#> $url
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#> [1] "https://lpsn.dsmz.de/species/escherichia-coli"
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#>
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#> $ref
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#> [1] "Castellani et al., 1919"
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#>
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#> $snomed
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#> [1] "1095001000112106" "715307006" "737528008" "416989002"
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#> [5] "116397003" "414097009" "414098004" "414099007"
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#> [9] "414100004" "116395006" "735270003" "116396007"
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#> [13] "83285000" "116394005" "112283007" "710886005"
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#> [17] "710887001" "710888006" "710889003" "414132004"
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#> [21] "721892009" "416812001" "416740004" "417216001"
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#> [25] "457541006" "710253004" "416530004" "417189006"
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#> [29] "409800005" "713925008" "444771000124108" "838549008"
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#>
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#> $lpsn
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#> [1] "776057"
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#>
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#> $mycobank
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#> [1] NA
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#>
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#> $gbif
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#> [1] "11286021"
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#>
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#> $group_members
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#> character(0)
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#>
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# works for all AMR functions:
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mo_is_intrinsic_resistant("eco", ab = "vancomycin")
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#> [1] TRUE
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```
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