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Catalogue of life

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dr. M.S. (Matthijs) Berends
2019-02-20 00:04:48 +01:00
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@ -133,26 +133,25 @@
#' Data set with ~60,000 microorganisms
#'
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection ITIS ITIS
#' @format A \code{\link{data.frame}} with 56,659 observations and 15 variables:
#' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 56,672 observations and 14 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID}
#' \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{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
#' \item{\code{kingdom}}{Taxonomic kingdom of the microorganism as found in ITIS, see Source}
#' \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
#' \item{\code{prevalence}}{An integer based on estimated prevalence of the microorganism in humans. Used internally by \code{\link{as.mo}}, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
#' \item{\code{kingdom}}{Taxonomic kingdom of the microorganism}
#' \item{\code{phylum}}{Taxonomic phylum of the microorganism}
#' \item{\code{class}}{Taxonomic class of the microorganism}
#' \item{\code{order}}{Taxonomic order of the microorganism}
#' \item{\code{family}}{Taxonomic family of the microorganism}
#' \item{\code{genus}}{Taxonomic genus of the microorganism}
#' \item{\code{species}}{Taxonomic species of the microorganism}
#' \item{\code{subspecies}}{Taxonomic subspecies of the microorganism}
#' \item{\code{rank}}{Taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
#' \item{\code{ref}}{Author(s) and year of concerning scientific publication}
#' \item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
#' }
#' @source Integrated Taxonomic Information System (ITIS) public online database, \url{https://www.itis.gov}.
#' @source Catalogue of Life: Annual Checklist (public online database), \url{www.catalogueoflife.org}.
#' @details Manually added were:
#' \itemize{
#' \item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
@ -160,21 +159,37 @@
#' \item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
#' @seealso \code{\link{as.mo}}, \code{\link{mo_property}}, \code{\link{microorganisms.codes}}
"microorganisms"
catalogue_of_life <- list(
version = "Catalogue of Life: 2018 Annual Checklist",
url = "http://www.catalogueoflife.org/annual-checklist/2018"
)
#' Version info of included Catalogue of Life
#' @seealso \code{\link{microorganisms}}
#' @inheritSection catalogue_of_life Catalogue of Life
#' @export
catalogue_of_life_version <- function() {
list(version = catalogue_of_life$version,
url = catalogue_of_life$url,
no_of_species = nrow(AMR::microorganisms),
no_of_synonyms = nrow(AMR::microorganisms.old))
}
#' Data set with previously accepted taxonomic names
#'
#' A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 14,506 observations and 4 variables:
#' \describe{
#' \item{\code{col_id}}{Catalogue of Life ID}
#' \item{\code{tsn_new}}{New Catalogue of Life ID}
#' \item{\code{fullname}}{Old taxonomic name of the microorganism as found in the CoL, see Source}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in the CoL, see Source}
#' \item{\code{fullname}}{Old taxonomic name of the microorganism}
#' \item{\code{ref}}{Author(s) and year of concerning scientific publication}
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @source [3] Catalogue of Life: Annual Checklist (public online database), \url{www.catalogueoflife.org}.
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old"
@ -187,7 +202,7 @@
#' \item{\code{certe}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}
#' }
#' @inheritSection ITIS ITIS
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.codes"