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

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This commit is contained in:
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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12
man/ab_property.Rd
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@ -4,7 +4,7 @@
\alias{ab_property}
\alias{ab_atc}
\alias{ab_official}
\alias{ab_official_nl}
\alias{ab_name}
\alias{ab_trivial_nl}
\alias{ab_certe}
\alias{ab_umcg}
@ -15,9 +15,9 @@ ab_property(x, property = "official")
ab_atc(x)
ab_official(x)
ab_official(x, language = NULL)
ab_official_nl(x)
ab_name(x, language = NULL)
ab_trivial_nl(x)
@ -31,6 +31,8 @@ ab_tradenames(x)
\item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}}
\item{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}}
\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).}
}
\value{
A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
@ -40,8 +42,8 @@ Use these functions to return a specific property of an antibiotic from the \cod
}
\examples{
ab_atc("amcl") # J01CR02
ab_official("amcl") # Amoxicillin and beta-lactamase inhibitor
ab_official_nl("amcl") # Amoxicilline met enzymremmer
ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
ab_name("amcl", "nl") # Amoxicilline met enzymremmer
ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
ab_certe("amcl") # amcl
ab_umcg("amcl") # AMCL

6
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}.

5
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,630 observations and 10 variables:
\format{A \code{\link{tibble}} with 2,642 observations and 11 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism}
@ -16,12 +16,13 @@
\item{\code{aerobic}}{Logical whether bacteria is aerobic}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
}}
\usage{
microorganisms
}
\description{
A data set containing 2,630 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
}
\seealso{
\code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}