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(v1.5.0.9006) major documentation update

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dr. M.S. (Matthijs) Berends
2021-01-18 16:57:56 +01:00
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R/ab.R
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@ -23,10 +23,10 @@
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Transform input to an antibiotic ID
#' Transform Input to an Antibiotic ID
#'
#' 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).
#' @inheritSection lifecycle Stable lifecycle
#' @inheritSection lifecycle Stable Lifecycle
#' @param x character vector to determine to antibiotic ID
#' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
#' @param info logical to indicate whether a progress bar should be printed
@ -42,7 +42,7 @@
#' * Switching two characters (such as "mreopenem", often the case in clinical data, when doctors typed too fast)
#' * Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
#'
#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see Examples.
#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
#'
#' Note: the [as.ab()] and [`ab_*`][ab_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
#' @section Source:
@ -56,8 +56,8 @@
#' @seealso
#' * [antibiotics] for the [data.frame] that is being used to determine ATCs
#' * [ab_from_text()] for a function to retrieve antimicrobial drugs from clinical text (from health care records)
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @export
#' @examples
#' # these examples all return "ERY", the ID of erythromycin: