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Becker classification

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Lancefield classification
Added Lancefield groups to `microorganisms` data set
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dr. M.S. (Matthijs) Berends
2018-08-02 13:15:45 +02:00
parent edd2dd09dc
commit 6262315527
10 changed files with 161 additions and 26 deletions
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24
man/as.bactid.Rd
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@ -5,15 +5,25 @@
\alias{guess_bactid}
\alias{is.bactid}
\title{Transform to bacteria ID}
\source{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \cr
\url{https://dx.doi.org/10.1128/CMR.00109-13} \cr
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \cr
\url{https://dx.doi.org/10.1084/jem.57.4.571}
}
\usage{
as.bactid(x)
as.bactid(x, Becker = FALSE, Lancefield = FALSE)
guess_bactid(x)
guess_bactid(x, Becker = FALSE, Lancefield = FALSE)
is.bactid(x)
}
\arguments{
\item{x}{a character vector or a dataframe 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. Groups D and E will be ignored, since they are \emph{Enterococci}.}
}
\value{
Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
@ -22,9 +32,9 @@ Character (vector) with class \code{"bactid"}. Unknown values will return \code{
Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
}
\details{
\code{guess_bactid} does exactly the same as \code{as.bactid}.
\code{guess_bactid} is an alias of \code{as.bactid}.
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
\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}}
@ -46,6 +56,12 @@ as.bactid("MRSA") # Methicillin Resistant S. aureus
as.bactid("VISA") # Vancomycin Intermediate S. aureus
as.bactid("VRSA") # Vancomycin Resistant S. aureus
guess_bactid("S. epidermidis") # will remain species: STAEPI
guess_bactid("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
guess_bactid("S. pyogenes") # will remain species: STCAGA
guess_bactid("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
\dontrun{
df$bactid <- as.bactid(df$microorganism_name)

4
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Dataset with ~2500 microorganisms}
\format{A data.frame with 2453 observations and 12 variables:
\format{A data.frame with 2456 observations and 12 variables:
\describe{
\item{\code{bactid}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism}
@ -23,7 +23,7 @@
microorganisms
}
\description{
A dataset containing 2453 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
A dataset containing 2456 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
}
\seealso{
\code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}