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first inclusion of ITIS data

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dr. M.S. (Matthijs) Berends
2018-09-24 23:33:29 +02:00
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commit 9c566585b0
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man/as.mo.Rd
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@@ -6,17 +6,13 @@
\alias{is.mo}
\alias{guess_mo}
\title{Transform to microorganism ID}
\source{
[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}
[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}
}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE)
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE)
is.mo(x)
guess_mo(x, Becker = FALSE, Lancefield = FALSE)
guess_mo(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = FALSE)
}
\arguments{
\item{x}{a character vector or a \code{data.frame} with one or two columns}
@@ -25,31 +21,62 @@ guess_mo(x, Becker = FALSE, Lancefield = FALSE)
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
\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.
\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.
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
\item{allow_uncertain}{a logical to indicate whether empty results should be checked for only a part of the input string. When results are found, a warning will be given about the uncertainty and the result.}
}
\value{
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
}
\description{
Use this function to determine a valid ID based on a genus (and species). Determination is done using Artificial Intelligence (AI), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using Artificial Intelligence (AI) and the complete taxonomic kingdoms \emph{Bacteria}, \emph{Fungi} and \emph{Protozoa} (see Source), so the input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
}
\details{
\code{guess_mo} is an alias of \code{as.mo}.
A microbial ID (class: \code{mo}) typically looks like these examples:\cr
\preformatted{
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNE Klebsiella pneumoniae
B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ----> subspecies, a 3-4 letter acronym
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
----> taxonomic kingdom, either Bacteria (B), Fungi (F) or Protozoa (P)
}
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
Thus function uses Artificial Intelligence (AI) to help getting more logical results, based on type of input and known prevalence of human pathogens. For example:
This function uses Artificial Intelligence (AI) to help getting more logical results, based on type of input and known prevalence of human pathogens. For example:
\itemize{
\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
\item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae} for the same reason}
\item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
\item{Something like \code{"stau"} or \code{"S aur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
}
Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
This means that looking up human non-pathogenic microorganisms takes a longer time compares to human pathogenic microorganisms.
\code{guess_mo} is an alias of \code{as.mo}.
}
\section{ITIS}{
\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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.
}
\section{Source}{
[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}
[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}
[3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
}
\examples{
# These examples all return "STAAUR", the ID of S. aureus:
as.mo("stau")
@@ -61,22 +88,27 @@ as.mo("Staphylococcus aureus")
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
# for the Integrated Taxonomic Information System (ITIS)
as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
as.mo("GBS") # Group B Streptococci
# guess_mo is an alias of as.mo and works the same
guess_mo("S. epidermidis") # will remain species: STAEPI
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
guess_mo("S. pyogenes") # will remain species: STCPYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `ESCCOL`
Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
mo_genus(Ecoli) # returns "Escherichia"
mo_gramstain(Ecoli) # returns "Negative rods"
mo_gramstain(Ecoli) # returns "Gram negative"
# but it uses as.mo internally too, so you could also just use:
mo_genus("E. coli") # returns "Escherichia"
\dontrun{
df$mo <- as.mo(df$microorganism_name)
@@ -98,7 +130,8 @@ df <- df \%>\%
}
}
\seealso{
\code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
\code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
}
\keyword{Becker}
\keyword{Lancefield}