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(v0.7.1.9055) algorithm improvements

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dr. M.S. (Matthijs) Berends
2019-08-13 16:15:08 +02:00
parent 6c4822164c
commit 7108454ba5
77 changed files with 644 additions and 582 deletions
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R/data.R
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@ -55,7 +55,7 @@
#'
#' 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 catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 69,854 observations and 16 variables:
#' @format A \code{\link{data.frame}} with 69,855 observations and 16 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID}
@ -64,14 +64,14 @@
#' \item{\code{rank}}{Text of the 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}
#' \item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
#' \item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
#' \item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
#' }
#' @details Manually added were:
#' \itemize{
#' \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
#' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
#' \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
#' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
#' \item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
#' }