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(v0.7.1.9009) note for WHOCC

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dr. M.S. (Matthijs) Berends
2019-07-09 11:22:46 +02:00
parent d9e257f8db
commit b15d59cf03
34 changed files with 711 additions and 41 deletions
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4
R/mdro.R
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@ -496,8 +496,8 @@ mdro <- function(x,
#' @rdname mdro
#' @export
brmo <- function(..., guideline = "BRMO") {
mdro(..., guideline = "BRMO")
brmo <- function(x, guideline = "BRMO", ...) {
mdro(x, guideline = "BRMO", ...)
}
#' @rdname mdro

2
R/mo.R
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@ -483,7 +483,7 @@ exec_as.mo <- function(x,
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
# remove genus as first word
x <- gsub("^Genus ", "", x)
# allow characters that resemble others
# allow characters that resemble others, but not on first try
if (initial_search == FALSE) {
x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x)

2
R/mo_property.R
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@ -157,7 +157,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
# exceptions for Staphylococci
shortnames[shortnames == "S. coagulase-negative" ] <- "CoNS"
shortnames[shortnames == "S. coagulase-positive" ] <- "CoPS"
# exceptions for Streptococci
# exceptions for Streptococci: Streptococcus Group A -> GAS
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
load_mo_failures_uncertainties_renamed(metadata)

2
R/whocc.R
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@ -24,7 +24,7 @@
#' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
#' @section WHOCC:
#' \if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
#' This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
#' This package contains \strong{all ~450 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
#'
#' These have become the gold standard for international drug utilisation monitoring and research.
#'