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added taxonomic data from ITIS

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dr. M.S. (Matthijs) Berends
2018-09-17 20:53:32 +02:00
parent 7680e4edd8
commit 5d80cef338
13 changed files with 150 additions and 80 deletions
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R/data.R
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@ -123,34 +123,28 @@
#' Data set with human pathogenic microorganisms
#'
#' A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
#' @format A \code{\link{tibble}} with 2,642 observations and 11 variables:
#' @format A \code{\link{tibble}} with 2,642 observations and 14 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode of microorganism}
#' \item{\code{family}}{Family name of microorganism}
#' \item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
#' \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{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
#' \item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
#' \item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
#' \item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
#' \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
# new <- microorganisms %>% filter(genus == "Bacteroides") %>% .[1,]
# new[1, 'mo'] <- "DIAPNU"
# new[1, 'bactsys'] <- "DIAPNU"
# new[1, 'family'] <- "Veillonellaceae"
# new[1, 'genus'] <- "Dialister"
# new[1, 'species'] <- "pneumosintes"
# new[1, 'subspecies'] <- NA
# new[1, 'fullname'] <- paste(new[1, 'genus'], new[1, 'species'])
# microorganisms <- microorganisms %>% bind_rows(new) %>% arrange(mo)
#' @source Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @seealso \code{\link{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
"microorganisms"
#' Translation table for UMCG with ~1,100 microorganisms
#' Translation table for UMCG
#'
#' A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
#' @format A \code{\link{tibble}} with 1,095 observations and 2 variables:
@ -158,7 +152,6 @@
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
# source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl}
#' @seealso \code{\link{guess_mo}} \code{\link{microorganisms}}
"microorganisms.umcg"