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set_mo_source

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dr. M.S. (Matthijs) Berends
2019-01-21 15:53:01 +01:00
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R/data.R
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@ -148,7 +148,7 @@
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
"microorganisms"
#' Data set with old taxonomic data from ITIS
@ -167,29 +167,17 @@
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old"
#' Translation table for UMCG
#' Translation table for microorganism codes
#'
#' A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
#' @format A \code{\link{data.frame}} with 1,095 observations and 2 variables:
#' A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 3,303 observations and 2 variables:
#' \describe{
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Translation table for Certe
#'
#' A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$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{data.frame}} with 2,665 observations and 2 variables:
#' \describe{
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' \item{\code{certe}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.certe"
"microorganisms.codes"
#' Data set with 2000 blood culture isolates of septic patients
#'