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Support for German and Spanish microorganism properties, cleanup

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dr. M.S. (Matthijs) Berends
2018-09-04 11:33:30 +02:00
parent 5405002119
commit b388e3fee7
20 changed files with 256 additions and 157 deletions
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R/data.R
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@ -123,7 +123,7 @@
#' Data set with human pathogenic microorganisms
#'
#' A data set containing 2,664 (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
#' @format A \code{\link{tibble}} with 2,664 observations and 12 variables:
#' @format A \code{\link{tibble}} with 2,664 observations and 16 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism}
@ -132,11 +132,15 @@
#' \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
#' \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
#' \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
#' \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{aerobic}}{Logical whether bacteria is aerobic}
#' \item{\code{type_de}}{Type of microorganism in German, like \code{"Bakterien"} and \code{"Pilz/Hefe"}}
#' \item{\code{gramstain_de}}{Gram of microorganism in German, like \code{"Negative Staebchen"}}
#' \item{\code{type_nl}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
#' \item{\code{gramstain_nl}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
#' \item{\code{type_es}}{Type of microorganism in Spanish, like \code{"Bacteria"} and \code{"Hongo/levadura"}}
#' \item{\code{gramstain_es}}{Gram of microorganism in Spanish, like \code{"Bacilos negativos"}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
# new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,]