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added prevalence column and alterted as.mo algorith to use it, added ab_name as alias

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dr. M.S. (Matthijs) Berends
2018-09-16 16:43:29 +02:00
parent b0ca49d68d
commit b792a2754e
16 changed files with 101 additions and 79 deletions
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man/as.mo.Rd
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@ -40,12 +40,12 @@ Use this function to determine a valid ID based on a genus (and species). Determ
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
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}}
\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{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
\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}.