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first inclusion of ITIS data

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dr. M.S. (Matthijs) Berends
2018-09-24 23:33:29 +02:00
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R/data.R
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@ -120,30 +120,48 @@
#
"antibiotics"
#' Data set with human pathogenic microorganisms
#' Data set with taxonomic data from ITIS
#'
#' 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 14 variables:
#' A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' @format A \code{\link{data.frame}} with 18,831 observations and 15 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{bactsys}}{Bactsyscode 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{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
#' \item{\code{aerobic}}{Logical whether bacteria is aerobic}
#' \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
#' \item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
#' \item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
#' \item{\code{fullname}}{Full name, like \code{"Echerichia coli"}}
#' \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{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
#' \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
#' \item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
#' \item{\code{mo.old}}{The old ID for package versions 0.3.0 and lower.}
#' }
#' @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}}
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
"microorganisms"
#' Data set with old taxonomic data from ITIS
#'
#' A data set containing old, previously valid, taxonomic names. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' @format A \code{\link{data.frame}} with 58 observations and 5 variables:
#' \describe{
#' \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
#' \item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{authors}}{Authors responsible for renaming as found in ITIS, see Source}
#' \item{\code{year}}{Year in which the literature was published about the renaming as found in ITIS, see Source}
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old"
#' 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}}.
@ -152,7 +170,7 @@
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
#' @seealso \code{\link{guess_mo}} \code{\link{microorganisms}}
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Data set with 2000 blood culture isolates of septic patients