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speed improvement for as.mo, more old taxonomic names

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dr. M.S. (Matthijs) Berends
2018-09-27 23:23:48 +02:00
parent 450992baea
commit 2b0080995e
18 changed files with 481 additions and 441 deletions
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17
R/data.R
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@ -148,9 +148,9 @@
#' 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}}.
#' 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
#' @format A \code{\link{data.frame}} with 1,682 observations and 5 variables:
#' @format A \code{\link{data.frame}} with 2,384 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}
@ -168,10 +168,21 @@
#' @format A \code{\link{tibble}} with 1,095 observations and 2 variables:
#' \describe{
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' }
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Translation table for Certe
#'
#' A data set containing all bacteria codes of Certe 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 2,664 observations and 2 variables:
#' \describe{
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.umcg"
"microorganisms.certe"
#' Data set with 2000 blood culture isolates of septic patients
#'