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first inclusion of ITIS data
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@@ -11,18 +11,12 @@
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\alias{mo_order}
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\alias{mo_class}
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\alias{mo_phylum}
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\alias{mo_subkingdom}
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\alias{mo_type}
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\alias{mo_TSN}
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\alias{mo_gramstain}
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\alias{mo_aerobic}
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\alias{mo_taxonomy}
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\title{Property of a microorganism}
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\source{
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[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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}
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\usage{
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mo_fullname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
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@@ -42,11 +36,13 @@ mo_class(x)
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mo_phylum(x)
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mo_subkingdom(x)
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mo_type(x, language = NULL)
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mo_gramstain(x, language = NULL)
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mo_TSN(x)
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mo_aerobic(x)
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mo_gramstain(x, language = NULL)
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mo_property(x, property = "fullname", Becker = FALSE,
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Lancefield = FALSE, language = NULL)
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@@ -60,11 +56,11 @@ mo_taxonomy(x)
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This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
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\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
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\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
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\item{language}{language of the returned text, defaults to the systems language but can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
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\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
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}
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@@ -74,8 +70,24 @@ A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy})
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\description{
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Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
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}
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\section{ITIS}{
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\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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This \code{AMR} package contains the \strong{complete microbial taxonomic data} from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa (from subkingdom to the subspecies level) are included in this package.
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}
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\section{Source}{
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[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
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}
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\examples{
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# All properties
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mo_subkingdom("E. coli") # "Negibacteria"
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mo_phylum("E. coli") # "Proteobacteria"
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mo_class("E. coli") # "Gammaproteobacteria"
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mo_order("E. coli") # "Enterobacteriales"
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@@ -85,42 +97,30 @@ mo_species("E. coli") # "coli"
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mo_subspecies("E. coli") # ""
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mo_fullname("E. coli") # "Escherichia coli"
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mo_shortname("E. coli") # "E. coli"
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mo_gramstain("E. coli") # "Gram negative"
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mo_TSN("E. coli") # 285
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mo_type("E. coli") # "Bacteria"
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mo_gramstain("E. coli") # "Negative rods"
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mo_aerobic("E. coli") # TRUE
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# Abbreviations known in the field
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mo_genus("MRSA") # "Staphylococcus"
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mo_species("MRSA") # "aureus"
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mo_shortname("MRSA") # "S. aureus"
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mo_gramstain("MRSA") # "Positive cocci"
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mo_gramstain("MRSA") # "Gram positive"
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mo_genus("VISA") # "Staphylococcus"
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mo_species("VISA") # "aureus"
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# Known subspecies
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mo_genus("EHEC") # "Escherichia"
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mo_species("EHEC") # "coli"
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mo_subspecies("EHEC") # "EHEC"
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mo_fullname("EHEC") # "Escherichia coli (EHEC)"
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mo_shortname("EHEC") # "E. coli"
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mo_genus("doylei") # "Campylobacter"
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mo_species("doylei") # "jejuni"
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mo_fullname("doylei") # "Campylobacter jejuni (doylei)"
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mo_fullname("doylei") # "Campylobacter jejuni doylei"
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mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
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mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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mo_shortname("K. pneu rh") # "K. pneumoniae"
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# Anaerobic bacteria
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mo_genus("B. fragilis") # "Bacteroides"
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mo_species("B. fragilis") # "fragilis"
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mo_aerobic("B. fragilis") # FALSE
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# Becker classification, see ?as.mo
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mo_fullname("S. epi") # "Staphylococcus epidermidis"
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mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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@@ -138,10 +138,9 @@ mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
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mo_type("E. coli", language = "de") # "Bakterium"
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mo_type("E. coli", language = "nl") # "Bacterie"
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mo_type("E. coli", language = "es") # "Bakteria"
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mo_gramstain("E. coli", language = "de") # "Negative Staebchen"
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mo_gramstain("E. coli", language = "nl") # "Negatieve staven"
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mo_gramstain("E. coli", language = "es") # "Bacilos negativos"
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mo_gramstain("Giardia", language = "pt") # "Parasitas"
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mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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mo_gramstain("E. coli", language = "es") # "Gram negativo"
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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@@ -151,7 +150,7 @@ mo_fullname("S. pyogenes",
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language = "nl") # "Streptococcus groep A"
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# Complete taxonomy up to Phylum, returns a list
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# Complete taxonomy up to Subkingdom, returns a list
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mo_taxonomy("E. coli")
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}
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\seealso{
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