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< h1 > Property of a microorganism< / h1 >
< div class = "hidden name" > < code > mo_property.Rd< / code > < / div >
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< p > Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with < code > < a href = 'as.mo.html' > as.mo< / a > < / code > , which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.< / p >
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< pre class = "usage" > < span class = 'fu' > mo_name< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_fullname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_shortname< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_subspecies< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_species< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_genus< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_family< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_order< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_class< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_phylum< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_kingdom< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_type< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_ref< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_authors< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
< span class = 'fu' > mo_year< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_rank< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_taxonomy< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_synonyms< / span > (< span class = 'no' > x< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_info< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_url< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > open< / span > < span class = 'kw' > =< / span > < span class = 'fl' > FALSE< / span > , < span class = 'no' > ...< / span > )
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< span class = 'fu' > mo_property< / span > (< span class = 'no' > x< / span > , < span class = 'kw' > property< / span > < span class = 'kw' > =< / span > < span class = 'st' > "fullname"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'fu' > < a href = 'translate.html' > get_locale< / a > < / span > (), < span class = 'no' > ...< / span > )< / pre >
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< h2 class = "hasAnchor" id = "arguments" > < a class = "anchor" href = "#arguments" > < / a > Arguments< / h2 >
< table class = "ref-arguments" >
< colgroup > < col class = "name" / > < col class = "desc" / > < / colgroup >
< tr >
< th > x< / th >
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< td > < p > any (vector of) text that can be coerced to a valid microorganism code with < code > < a href = 'as.mo.html' > as.mo< / a > < / code > < / p > < / td >
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< / tr >
< tr >
< th > language< / th >
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< td > < p > language of the returned text, defaults to system language (see < code > < a href = 'translate.html' > get_locale< / a > < / code > ) and can also be set with < code > < a href = 'https://rdrr.io/r/base/options.html' > getOption< / a > ("AMR_locale")< / code > . Use < code > language = NULL< / code > or < code > language = ""< / code > to prevent translation.< / p > < / td >
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< / tr >
< tr >
< th > ...< / th >
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< td > < p > other parameters passed on to < code > < a href = 'as.mo.html' > as.mo< / a > < / code > < / p > < / td >
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< / tr >
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< tr >
< th > open< / th >
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< td > < p > browse the URL using < code > < a href = 'https://rdrr.io/r/utils/browseURL.html' > browseURL< / a > ()< / code > < / p > < / td >
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< / tr >
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< tr >
< th > property< / th >
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< td > < p > one of the column names of the < code > < a href = 'microorganisms.html' > microorganisms< / a > < / code > data set or < code > "shortname"< / code > < / p > < / td >
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< / tr >
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< h2 class = "hasAnchor" id = "value" > < a class = "anchor" href = "#value" > < / a > Value< / h2 >
< ul >
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< li > < p > An < code > integer< / code > in case of < code > mo_year< / code > < / p > < / li >
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< li > < p > A < code > list< / code > in case of < code > mo_taxonomy< / code > < / p > < / li >
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< li > < p > A named < code > character< / code > in case of < code > mo_url< / code > < / p > < / li >
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< li > < p > A < code > character< / code > in all other cases< / p > < / li >
< / ul >
< h2 class = "hasAnchor" id = "details" > < a class = "anchor" href = "#details" > < / a > Details< / h2 >
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< p > All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for < code > mo_ref< / code > , < code > mo_authors< / code > and < code > mo_year< / code > . This leads to the following results:< / p > < ul >
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< li > < p > < code > mo_name("Chlamydia psittaci")< / code > will return < code > "Chlamydophila psittaci"< / code > (with a warning about the renaming)< / p > < / li >
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< li > < p > < code > mo_ref("Chlamydia psittaci")< / code > will return < code > "Page, 1968"< / code > (with a warning about the renaming)< / p > < / li >
< li > < p > < code > mo_ref("Chlamydophila psittaci")< / code > will return < code > "Everett et al., 1999"< / code > (without a warning)< / p > < / li >
< / ul >
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< p > The Gram stain - < code > mo_gramstain()< / code > - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value < code > NA< / code > .< / p >
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< p > All output will be < a href = 'translate.html' > translate< / a > d where possible.< / p >
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< p > The function < code > mo_url()< / code > will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.< / 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 >
< 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 = "source" > < a class = "anchor" href = "#source" > < / a > Source< / h2 >
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< p > [1] Becker K < em > et al.< / em > < strong > Coagulase-Negative Staphylococci< / strong > . 2014. Clin Microbiol Rev. 27(4): 870– < a href = 'https://dx.doi.org/10.1128/CMR.00109-13' > https://dx.doi.org/10.1128/CMR.00109-13< / a > < / p >
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< p > [2] Becker K < em > et al.< / em > < strong > Implications of identifying the recently defined members of the < em > S. aureus< / em > complex, < em > S. argenteus< / em > and < em > S. schweitzeri< / em > : A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).< / strong > 2019. Clin Microbiol Infect. < a href = 'https://doi.org/10.1016/j.cmi.2019.02.028' > https://doi.org/10.1016/j.cmi.2019.02.028< / a > < / p >
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< p > [3] Lancefield RC < strong > A serological differentiation of human and other groups of hemolytic streptococci< / strong > . 1933. J Exp Med. 57(4): 571– < a href = 'https://dx.doi.org/10.1084/jem.57.4.571' > https://dx.doi.org/10.1084/jem.57.4.571< / a > < / p >
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< p > [4] 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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< 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 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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< 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 = 'microorganisms.html' > microorganisms< / a > < / code > < / p > < / div >
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< h2 class = "hasAnchor" id = "examples" > < a class = "anchor" href = "#examples" > < / a > Examples< / h2 >
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< pre class = "examples" > < span class = 'co' > # taxonomic tree -----------------------------------------------------------< / span >
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< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria"< / span >
< span class = 'fu' > mo_phylum< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Proteobacteria"< / span >
< span class = 'fu' > mo_class< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gammaproteobacteria"< / span >
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< span class = 'fu' > mo_order< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacterales" ()< / span >
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< span class = 'fu' > mo_family< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Enterobacteriaceae"< / span >
< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "coli"< / span >
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< span class = 'fu' > mo_subspecies< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # ""< / span >
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< span class = 'co' > # colloquial properties ----------------------------------------------------< / span >
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< span class = 'fu' > mo_name< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia coli"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Escherichia coli", same as mo_name()< / span >
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< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "E. coli"< / span >
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< span class = 'co' > # other properties ---------------------------------------------------------< / span >
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Gram-negative"< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" (equal to kingdom, but may be translated)< / span >
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< span class = 'fu' > mo_rank< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "species"< / span >
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< span class = 'fu' > mo_url< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # get the direct url to the online database entry< / span >
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< span class = 'fu' > mo_synonyms< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # get previously accepted taxonomic names< / span >
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< span class = 'co' > # scientific reference -----------------------------------------------------< / span >
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< span class = 'fu' > mo_ref< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani et al., 1919"< / span >
< span class = 'fu' > mo_authors< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Castellani et al."< / span >
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< span class = 'fu' > mo_year< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # 1919< / span >
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< span class = 'co' > # abbreviations known in the field -----------------------------------------< / span >
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< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "Staphylococcus"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "MRSA"< / span > ) < span class = 'co' > # "aureus"< / span >
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< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "S. aureus"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "VISA"< / span > ) < span class = 'co' > # "Gram-positive"< / span >
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< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "EHEC"< / span > ) < span class = 'co' > # "Escherichia"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "EHEC"< / span > ) < span class = 'co' > # "coli"< / span >
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< span class = 'co' > # known subspecies ---------------------------------------------------------< / span >
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< span class = 'fu' > mo_name< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter jejuni doylei"< / span >
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< span class = 'fu' > mo_genus< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "Campylobacter"< / span >
< span class = 'fu' > mo_species< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "jejuni"< / span >
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< span class = 'fu' > mo_subspecies< / span > (< span class = 'st' > "doylei"< / span > ) < span class = 'co' > # "doylei"< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "Klebsiella pneumoniae rhinoscleromatis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "K. pneu rh"< / span > ) < span class = 'co' > # "K. pneumoniae"< / span >
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< span class = 'co' > # \donttest{< / span >
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< span class = 'co' > # Becker classification, see ?as.mo ----------------------------------------< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "Staphylococcus epidermidis"< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Coagulase-negative Staphylococcus (CoNS)"< / span >
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< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > ) < span class = 'co' > # "S. epidermidis"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. epi"< / span > , < span class = 'kw' > Becker< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "CoNS"< / span >
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< span class = 'co' > # Lancefield classification, see ?as.mo ------------------------------------< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "Streptococcus pyogenes"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "Streptococcus group A"< / span >
< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > ) < span class = 'co' > # "S. pyogenes"< / span >
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< span class = 'fu' > mo_shortname< / span > (< span class = 'st' > "S. pyo"< / span > , < span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ) < span class = 'co' > # "GAS" (='Group A Streptococci')< / span >
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< span class = 'co' > # language support for German, Dutch, Spanish, Portuguese, Italian and French< / span >
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< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Gramnegativ"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Gram-negatief"< / span >
< span class = 'fu' > mo_gramstain< / span > (< span class = 'st' > "E. coli"< / span > , < span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "es"< / span > ) < span class = 'co' > # "Gram negativo"< / span >
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< span class = 'co' > # mo_type is equal to mo_kingdom, but mo_kingdom will remain official< / span >
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< span class = 'fu' > mo_kingdom< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bakterien" on a German system< / span >
< span class = 'fu' > mo_type< / span > (< span class = 'st' > "E. coli"< / span > ) < span class = 'co' > # "Bacteria" on an English system< / span >
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< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "de"< / span > ) < span class = 'co' > # "Streptococcus Gruppe A"< / span >
< span class = 'fu' > mo_fullname< / span > (< span class = 'st' > "S. pyogenes"< / span > ,
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< span class = 'kw' > Lancefield< / span > < span class = 'kw' > =< / span > < span class = 'fl' > TRUE< / span > ,
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< span class = 'kw' > language< / span > < span class = 'kw' > =< / span > < span class = 'st' > "nl"< / span > ) < span class = 'co' > # "Streptococcus groep A"< / span >
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< span class = 'co' > # get a list with the complete taxonomy (from kingdom to subspecies)< / span >
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< span class = 'fu' > mo_taxonomy< / span > (< span class = 'st' > "E. coli"< / span > )
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< span class = 'co' > # get a list with the taxonomy, the authors and the URL to the online database< / span >
< span class = 'fu' > mo_info< / span > (< span class = 'st' > "E. coli"< / span > )
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< span class = 'co' > # }< / span > < / pre >
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< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< h2 > Contents< / h2 >
< ul class = "nav nav-pills nav-stacked" >
< li > < a href = "#arguments" > Arguments< / a > < / li >
< li > < a href = "#value" > Value< / a > < / li >
< 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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< li > < a href = "#source" > Source< / a > < / li >
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< li > < a href = "#read-more-on-our-website-" > Read more on our website!< / a > < / li >
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< li > < a href = "#see-also" > See also< / a > < / li >
< li > < a href = "#examples" > Examples< / 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/a.w.friedrich/' > Alex 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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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
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