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< h1 > Data set with ~60,000 microorganisms< / h1 >
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< div class = "hidden name" > < code > microorganisms.Rd< / code > < / div >
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< p > A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using < code > < a href = 'as.mo.html' > as.mo< / a > < / code > .< / p >
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< / div >
< pre class = "usage" > < span class = 'no' > microorganisms< / span > < / pre >
< h2 class = "hasAnchor" id = "format" > < a class = "anchor" href = "#format" > < / a > Format< / h2 >
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< p > A < code > < a href = 'https://www.rdocumentation.org/packages/base/topics/data.frame' > data.frame< / a > < / code > with 59,985 observations and 15 variables:< / p > < dl class = 'dl-horizontal' >
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< dt > < code > mo< / code > < / dt > < dd > < p > ID of microorganism as used by this package< / p > < / dd >
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< dt > < code > col_id< / code > < / dt > < dd > < p > Catalogue of Life ID< / p > < / dd >
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< dt > < code > fullname< / code > < / dt > < dd > < p > Full name, like < code > "Echerichia coli"< / code > < / p > < / dd >
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< dt > < code > kingdom< / code > < / dt > < dd > < p > Taxonomic kingdom of the microorganism< / p > < / dd >
< dt > < code > phylum< / code > < / dt > < dd > < p > Taxonomic phylum of the microorganism< / p > < / dd >
< dt > < code > class< / code > < / dt > < dd > < p > Taxonomic class of the microorganism< / p > < / dd >
< dt > < code > order< / code > < / dt > < dd > < p > Taxonomic order of the microorganism< / p > < / dd >
< dt > < code > family< / code > < / dt > < dd > < p > Taxonomic family of the microorganism< / p > < / dd >
< dt > < code > genus< / code > < / dt > < dd > < p > Taxonomic genus of the microorganism< / p > < / dd >
< dt > < code > species< / code > < / dt > < dd > < p > Taxonomic species of the microorganism< / p > < / dd >
< dt > < code > subspecies< / code > < / dt > < dd > < p > Taxonomic subspecies of the microorganism< / p > < / dd >
< dt > < code > rank< / code > < / dt > < dd > < p > Taxonomic rank of the microorganism, like < code > "species"< / code > or < code > "genus"< / code > < / p > < / dd >
< dt > < code > ref< / code > < / dt > < dd > < p > Author(s) and year of concerning scientific publication< / p > < / dd >
< dt > < code > species_id< / code > < / dt > < dd > < p > ID of the species as used by the Catalogue of Life< / p > < / dd >
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< dt > < code > prevalence< / code > < / dt > < dd > < p > Prevalence of the microorganism, see < code > < a href = 'as.mo.html' > ?as.mo< / a > < / code > < / p > < / dd >
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< / dl >
< 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 database), < a href = 'www.catalogueoflife.org' > www.catalogueoflife.org< / a > .< / p >
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< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
< p > Manually added were:< / p > < ul >
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< li > < p > 9 species of < em > Streptococcus< / em > (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)< / p > < / li >
< li > < p > 2 species of < em > Staphylococcus< / em > (coagulase-negative [CoNS] and coagulase-positive [CoPS])< / p > < / li >
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< li > < p > 2 other undefined (unknown Gram negatives and unknown Gram positives)< / p > < / li >
< / ul >
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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 / >
This package contains the complete taxonomic tree of almost all microorganisms (~60,000 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 >
< p > < a href = 'catalogue_of_life.html' > Click here< / a > for more information about the included taxa. The Catalogue of Life releases updates annually; check which version 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.gitlab.io/AMR' > https://msberends.gitlab.io/AMR< / a > you can find < a href = 'https://msberends.gitlab.io/AMR/articles/AMR.html' > a comprehensive tutorial< / a > about how to conduct AMR analysis, the < a href = 'https://msberends.gitlab.io/AMR/reference' > complete documentation of all functions< / a > (which reads a lot easier than here in R) and < a href = 'https://msberends.gitlab.io/AMR/articles/WHONET.html' > an example analysis using WHONET data< / a > .< / p >
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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 > , < code > < a href = 'microorganisms.codes.html' > microorganisms.codes< / a > < / code > < / p > < / div >
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< h2 > Contents< / h2 >
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< li > < a href = "#details" > Details< / a > < / li >
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< li > < a href = "#catalogue-of-life" > Catalogue of Life< / a > < / li >
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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/c.glasner/' > Corinna Glasner< / a > , < a href = 'https://www.rug.nl/staff/a.w.friedrich/' > Alex W. Friedrich< / a > , < a href = 'https://www.rug.nl/staff/b.sinha/' > Bhanu N. M. Sinha< / a > .< / p >
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