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(v0.8.0.9036) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
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R/ab.R
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@ -21,25 +21,26 @@
#' Transform to antibiotic ID
#'
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set \code{\link{antibiotics}} will be searched for abbreviations, official names and synonyms (brand names).
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @param x character vector to determine to antibiotic ID
#' @param ... arguments passed on to internal functions
#' @rdname as.ab
#' @inheritSection WHOCC WHOCC
#' @export
#' @importFrom dplyr %>% filter slice pull
#' @details All entries in the \code{\link{antibiotics}} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
#'
#' Use the \code{\link{ab_property}} functions to get properties based on the returned antibiotic ID, see Examples.
#' Use the [ab_property()] functions to get properties based on the returned antibiotic ID, see Examples.
#' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#'
#' WHONET 2019 software: \url{http://www.whonet.org/software.html}
#'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
#' @return Character (vector) with class \code{"ab"}. Unknown values will return \code{NA}.
#' @seealso \code{\link{antibiotics}} for the dataframe that is being used to determine ATCs.
#' @aliases ab
#' @return Character (vector) with class [`ab`]. Unknown values will return `NA`.
#' @seealso [antibiotics] for the dataframe that is being used to determine ATCs.
#' @inheritSection AMR Read more on our website!
#' @export
#' @examples
#' # These examples all return "ERY", the ID of Erythromycin:
#' as.ab("J01FA01")