AMR/man/as.mo.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R
\name{as.mo}
\alias{as.mo}
\alias{mo}
\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)

is.mo(x)

guess_mo(x, Becker = FALSE, Lancefield = FALSE)
}
\arguments{
\item{x}{a character vector or a \code{data.frame} with one or two columns}

\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].

  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.

  This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
}
\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.
}
\details{
\code{guess_mo} is an alias of \code{as.mo}.

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:
\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}.
}
\examples{
# These examples all return "STAAUR", the ID of S. aureus:
as.mo("stau")
as.mo("STAU")
as.mo("staaur")
as.mo("S. aureus")
as.mo("S aureus")
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("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. pyogenes")                    # will remain species: STCPYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA

# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `ESCCOL`
mo_genus(Ecoli)               # returns "Escherichia"
mo_gramstain(Ecoli)           # returns "Negative rods"

\dontrun{
df$mo <- as.mo(df$microorganism_name)

# the select function of tidyverse is also supported:
library(dplyr)
df$mo <- df \%>\%
  select(microorganism_name) \%>\%
  guess_mo()

# and can even contain 2 columns, which is convenient for genus/species combinations:
df$mo <- df \%>\%
  select(genus, species) \%>\%
  guess_mo()

# same result:
df <- df \%>\%
  mutate(mo = guess_mo(paste(genus, species)))
}
}
\seealso{
\code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
}
\keyword{Becker}
\keyword{Lancefield}
\keyword{becker}
\keyword{guess}
\keyword{lancefield}
\keyword{mo}