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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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dr. M.S. (Matthijs) Berends
2021-08-16 21:54:34 +02:00
parent 4e1efd902c
commit a2d249962f
248 changed files with 2377 additions and 12201 deletions
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R/data.R
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@ -25,14 +25,14 @@
#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobials
#'
#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
#' @format
#' ## For the [antibiotics] data set: a [data.frame] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables:
#' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
#' - `cid`\cr Compound ID as found in PubChem
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
#' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
#' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
#' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
#' - `abbr`\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
@ -44,7 +44,7 @@
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
#'
#' ## For the [antivirals] data set: a [data.frame] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
#' - `cid`\cr Compound ID as found in PubChem
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
#' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC