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< img src = "../logo.svg" class = "logo" alt = "" > < h1 > Data Set with 4 971 Common Microorganism Codes< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/main/R/data.R" class = "external-link" > < code > R/data.R< / code > < / a > < / small >
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< div class = "d-none name" > < code > microorganisms.codes.Rd< / code > < / div >
< / div >
< div class = "ref-description section level2" >
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< p > A data set containing commonly used codes for microorganisms, from laboratory systems and < a href = "https://whonet.org" class = "external-link" > WHONET< / a > . Define your own with < code > < a href = "mo_source.html" > set_mo_source()< / a > < / code > . They will all be searched when using < code > < a href = "as.mo.html" > as.mo()< / a > < / code > and consequently all the < code > < a href = "mo_property.html" > mo_*< / a > < / code > functions.< / p >
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< / div >
< div class = "section level2" >
< h2 id = "ref-usage" > Usage< a class = "anchor" aria-label = "anchor" href = "#ref-usage" > < / a > < / h2 >
< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span > < span class = "va" > microorganisms.codes< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level2" >
< h2 id = "format" > Format< a class = "anchor" aria-label = "anchor" href = "#format" > < / a > < / h2 >
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< p > A < a href = "https://tibble.tidyverse.org/reference/tibble.html" class = "external-link" > tibble< / a > with 4 971 observations and 2 variables:< / p > < ul > < li > < p > < code > code< / code > < br > Commonly used code of a microorganism. < em > < strong > This is a unique identifier.< / strong > < / em > < / p > < / li >
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< li > < p > < code > mo< / code > < br > ID of the microorganism in the < a href = "microorganisms.html" > microorganisms< / a > data set< / p > < / li >
< / ul > < / div >
< div class = "section level2" >
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< h2 id = "details" > Details< a class = "anchor" aria-label = "anchor" href = "#details" > < / a > < / h2 >
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< p > Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit < a href = "https://msberends.github.io/AMR/articles/datasets.html" > our website for the download links< / a > . The actual files are of course available on < a href = "https://github.com/msberends/AMR/tree/main/data-raw" class = "external-link" > our GitHub repository< / a > .< / p >
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< / div >
< div class = "section level2" >
< h2 id = "see-also" > See also< a class = "anchor" aria-label = "anchor" href = "#see-also" > < / a > < / h2 >
< div class = "dont-index" > < p > < code > < a href = "as.mo.html" > as.mo()< / a > < / code > < a href = "microorganisms.html" > microorganisms< / a > < / p > < / div >
< / div >
< div class = "section level2" >
< h2 id = "ref-examples" > Examples< a class = "anchor" aria-label = "anchor" href = "#ref-examples" > < / a > < / h2 >
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< div class = "sourceCode" > < pre class = "sourceCode r" > < code > < span class = "r-in" > < span > < span class = "va" > microorganisms.codes< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 4,971 × < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > code mo < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 1011 B_GRAMP < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 1012 B_GRAMP < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 1013 B_GRAMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 1014 B_GRAMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 1015 F_YEAST < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 103 B_ESCHR_COLI < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 104 B_SLMNL_ENTR_ENTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 1100 B_STRPT < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 1101 B_STRPT_VIRI < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 1102 B_STRPT_HAEM < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # 'ECO' or 'eco' is the WHONET code for E. coli:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > microorganisms.codes< / span > < span class = "op" > [< / span > < span class = "va" > microorganisms.codes< / span > < span class = "op" > $< / span > < span class = "va" > code< / span > < span class = "op" > ==< / span > < span class = "st" > "ECO"< / span > , < span class = "op" > ]< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 1 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > code mo < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > ECO B_ESCHR_COLI< / span >
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< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # and therefore, 'eco' will be understood as E. coli in this package:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_info< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "eco"< / span > < span class = "op" > )< / span > < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > $mo< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "B_ESCHR_COLI"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > $rank< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "species"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > $kingdom< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Bacteria"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $phylum< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Pseudomonadota"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $class< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gammaproteobacteria"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $order< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacterales"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $family< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Enterobacteriaceae"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $genus< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Escherichia"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $species< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "coli"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $subspecies< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] ""< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $status< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "accepted"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $synonyms< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > NULL< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $gramstain< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Gram-negative"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $oxygen_tolerance< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "facultative anaerobe"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $url< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "https://lpsn.dsmz.de/species/escherichia-coli"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $ref< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "Castellani et al., 1919"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $snomed< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "1095001000112106" "715307006" "737528008" "416989002" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [5] "116397003" "414097009" "414098004" "414099007" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [9] "414100004" "116395006" "735270003" "116396007" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [13] "83285000" "116394005" "112283007" "710886005" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [17] "710887001" "710888006" "710889003" "414132004" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [21] "721892009" "416812001" "416740004" "417216001" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [25] "457541006" "710253004" "416530004" "417189006" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [29] "409800005" "713925008" "444771000124108" "838549008" < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $lpsn< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "776057"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
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< span class = "r-out co" > < span class = "r-pr" > #> < / span > $mycobank< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] NA< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2023-12-03 01:14:24 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $gbif< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] "11286021"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2024-04-19 10:24:46 +02:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > $group_members< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > character(0)< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < / span >
2023-05-27 10:53:23 +02:00
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # works for all AMR functions:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "mo_property.html" > mo_is_intrinsic_resistant< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "eco"< / span > , ab < span class = "op" > =< / span > < span class = "st" > "vancomycin"< / span > < span class = "op" > )< / span > < / span > < / span >
2023-12-03 01:14:24 +01:00
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] TRUE< / span >
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< / code > < / pre > < / div >
< / div >
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< / main > < aside class = "col-md-3" > < nav id = "toc" aria-label = "Table of contents" > < h2 > On this page< / h2 >
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< / nav > < / aside > < / div >
< footer > < div class = "pkgdown-footer-left" >
2024-04-23 10:39:01 +02:00
< p > < code > AMR< / code > (for R). Free and open-source, licenced under the < a target = "_blank" href = "https://github.com/msberends/AMR/blob/main/LICENSE" class = "external-link" > GNU General Public License version 2.0 (GPL-2)< / a > .< br > Developed at the < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > University of Groningen< / a > and < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > University Medical Center Groningen< / a > in The Netherlands.< / p >
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< div class = "pkgdown-footer-right" >
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< p > < a target = "_blank" href = "https://www.rug.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_rug.svg" style = "max-width: 150px;" > < / a > < a target = "_blank" href = "https://www.umcg.nl" class = "external-link" > < img src = "https://github.com/msberends/AMR/raw/main/pkgdown/assets/logo_umcg.svg" style = "max-width: 150px;" > < / a > < / p >
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< / div >
< / footer > < / div >
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< / body > < / html >
