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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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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}}