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(v0.8.0.9033) antivirals data set, cleanup

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dr. M.S. (Matthijs) Berends
2019-11-18 12:10:47 +01:00
parent 67f3f4387b
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R/data.R
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@ -34,7 +34,7 @@
#' \item{\code{abbr}}{List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)}
#' \item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{ddd_units}}
#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' }
@ -48,9 +48,28 @@
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{microorganisms}}
#' @seealso \code{\link{antivirals}} \code{\link{microorganisms}}
"antibiotics"
#' Data set with ~100 antivirals
#'
#' A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).
#' @format A \code{\link{data.frame}} with 102 observations and 7 variables:
#' \describe{
#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
#' \item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' }
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{antibiotics}} \code{\link{microorganisms}}
"antivirals"
#' Data set with ~70,000 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}}.
@ -126,9 +145,9 @@ catalogue_of_life <- list(
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.codes"
#' Data set with 2,000 blood culture isolates
#' Data set with 2,000 example isolates
#'
#' An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
#' A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
#' @format A \code{\link{data.frame}} with 2,000 observations and 49 variables:
#' \describe{
#' \item{\code{date}}{date of receipt at the laboratory}
@ -138,7 +157,7 @@ catalogue_of_life <- list(
#' \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
#' \item{\code{age}}{age of the patient}
#' \item{\code{gender}}{gender of the patient}
#' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
#' \item{\code{patient_id}}{ID of the patient}
#' \item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
#' \item{\code{PEN:RIF}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{ab_name}}}
#' }
@ -183,17 +202,17 @@ catalogue_of_life <- list(
#' Data set for RSI interpretation
#'
#' Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link{as.rsi}} to transform MICs or disks measurements to RSI values.
#' @format A \code{\link{data.frame}} with 11,559 observations and 9 variables:
#' @format A \code{\link{data.frame}} with 13,975 observations and 9 variables:
#' \describe{
#' \item{\code{guideline}}{Name of the guideline}
#' \item{\code{method}}{Either "MIC" or "DISK"}
#' \item{\code{site}}{Body site, e.g. "Oral" or "Respiratory"}
#' \item{\code{mo}}{Microbial ID, see \code{\link{as.mo}}}
#' \item{\code{ab}}{Antibiotic ID, see \code{\link{as.ab}}}
#' \item{\code{ref_tbl}}{Info about where the guideline rule can be found}
#' \item{\code{S_mic}}{Lowest MIC value that leads to "S"}
#' \item{\code{R_mic}}{Highest MIC value that leads to "R"}
#' \item{\code{dose_disk}}{Dose of the used disk diffusion method}
#' \item{\code{S_disk}}{Lowest number of millimeters that leads to "S"}
#' \item{\code{R_disk}}{Highest number of millimeters that leads to "R"}
#' \item{\code{disk_dose}}{Dose of the used disk diffusion method}
#' \item{\code{breakpoint_S}}{Lowest MIC value or highest number of millimeters that leads to "S"}
#' \item{\code{breakpoint_R}}{Highest MIC value or lowest number of millimeters that leads to "R"}
#' }
#' @inheritSection AMR Read more on our website!
"rsi_translation"