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< h1 > Data set with previously accepted taxonomic names< / h1 >
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< small class = "dont-index" > Source: < a href = 'https://github.com/msberends/AMR/blob/master/R/data.R' > < code > R/data.R< / code > < / a > < / small >
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< div class = "hidden name" > < code > microorganisms.old.Rd< / code > < / div >
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< div class = "ref-description" >
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< p > A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > .< / p >
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< pre class = "usage" > < span class = 'kw' > microorganisms.old< / span > < / pre >
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< h2 class = "hasAnchor" id = "format" > < a class = "anchor" href = "#format" > < / a > Format< / h2 >
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< p > A < code > < a href = 'https://rdrr.io/r/base/data.frame.html' > data.frame< / a > < / code > with 12,708 observations and 4 variables:< / p > < ul >
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< li > < p > < code > fullname< / code > < br / > Old full taxonomic name of the microorganism< / p > < / li >
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< li > < p > < code > fullname_new< / code > < br / > New full taxonomic name of the microorganism< / p > < / li >
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< li > < p > < code > ref< / code > < br / > Author(s) and year of concerning scientific publication< / p > < / li >
< li > < p > < code > prevalence< / code > < br / > Prevalence of the microorganism, see < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > < / p > < / li >
< / ul >
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< h2 class = "hasAnchor" id = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
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< p > Catalogue of Life: Annual Checklist (public online taxonomic database), < a href = 'http://www.catalogueoflife.org' > http://www.catalogueoflife.org< / a > (check included annual version with < code > < a href = 'catalogue_of_life_version.html' > catalogue_of_life_version()< / a > < / code > ).< / p >
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< p > Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786< / p >
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< h2 class = "hasAnchor" id = "catalogue-of-life" > < a class = "anchor" href = "#catalogue-of-life" > < / a > Catalogue of Life< / h2 >
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< p > < img src = 'figures/logo_col.png' height = 40px style = margin-bottom:5px / > < br / >
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This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (< a href = 'http://www.catalogueoflife.org' > http://www.catalogueoflife.org< / a > ). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.< / p >
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< p > < a href = 'catalogue_of_life.html' > Click here< / a > for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with < code > < a href = 'catalogue_of_life_version.html' > catalogue_of_life_version()< / a > < / code > .< / p >
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< h2 class = "hasAnchor" id = "read-more-on-our-website-" > < a class = "anchor" href = "#read-more-on-our-website-" > < / a > Read more on our website!< / h2 >
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< p > On our website < a href = 'https://msberends.github.io/AMR' > https://msberends.github.io/AMR< / a > you can find < a href = 'https://msberends.github.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.github.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.github.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > . As we would like to better understand the backgrounds and needs of our users, please < a href = 'https://msberends.github.io/AMR/survey.html' > participate in our survey< / a > !< / p >
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< h2 class = "hasAnchor" id = "see-also" > < a class = "anchor" href = "#see-also" > < / a > See also< / h2 >
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< div class = 'dont-index' > < p > < code > < a href = 'as.mo.html' > as.mo()< / a > < / code > < code > < a href = 'mo_property.html' > mo_property()< / a > < / code > < a href = 'microorganisms.html' > microorganisms< / a > < / p > < / div >
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< p > Developed by < a href = 'https://www.rug.nl/staff/m.s.berends/' > Matthijs S. Berends< / a > , < a href = 'https://www.rug.nl/staff/c.f.luz/' > Christian F. Luz< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alexander W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > , < a href = 'https://www.rug.nl/staff/c.j.albers/' > Casper J. Albers< / a > , < a href = 'https://www.rug.nl/staff/c.glasner/' > Corinna Glasner< / a > .< / p >
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