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new Norwegian link

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dr. M.S. (Matthijs) Berends
2024-03-03 23:24:57 +01:00
parent f2d245b0cb
commit bc4f8515e2
26 changed files with 50 additions and 50 deletions
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2
R/ab.R
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@ -51,7 +51,7 @@
#'
#' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
#' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
#'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases ab

8
R/ab_property.R
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@ -245,7 +245,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
warning_(
"in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
}
out
@ -265,7 +265,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
warning_(
"in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
}
out
@ -312,8 +312,8 @@ ab_url <- function(x, open = FALSE, ...) {
atcs <- ab_atc(ab, only_first = TRUE)
u <- character(length(atcs))
# veterinary codes
u[atcs %like% "^Q"] <- paste0("https://www.whocc.no/atcvet/atcvet_index/?code=", atcs[atcs %like% "^Q"], "&showdescription=no")
u[atcs %unlike% "^Q"] <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs[atcs %unlike% "^Q"], "&showdescription=no")
u[atcs %like% "^Q"] <- paste0("https://atcddd.fhi.no/atcvet/atcvet_index/?code=", atcs[atcs %like% "^Q"], "&showdescription=no")
u[atcs %unlike% "^Q"] <- paste0("https://atcddd.fhi.no/atc_ddd_index//?code=", atcs[atcs %unlike% "^Q"], "&showdescription=no")
u[is.na(atcs)] <- NA_character_
names(u) <- ab_name(ab)

6
R/atc_online.R
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@ -64,7 +64,7 @@
#' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
#' @export
#' @rdname atc_online
#' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
#' @source <https://atcddd.fhi.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
#' @examples
#' \donttest{
#' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
@ -81,8 +81,8 @@
atc_online_property <- function(atc_code,
property,
administration = "O",
url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
url = "https://atcddd.fhi.no/atc_ddd_index/?code=%s&showdescription=no",
url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
meet_criteria(atc_code, allow_class = "character", allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "unit", "Adm.R", "Note", "groups"), ignore.case = TRUE)
meet_criteria(administration, allow_class = "character", has_length = 1)

2
R/av.R
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@ -49,7 +49,7 @@
#'
#' Note: the [as.av()] and [`av_*`][av_property()] functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
#' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
#'
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases av

6
R/av_property.R
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@ -164,7 +164,7 @@ av_ddd <- function(x, administration = "oral", ...) {
warning_(
"in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
}
out
@ -184,7 +184,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
warning_(
"in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
"atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
)
}
out
@ -227,7 +227,7 @@ av_url <- function(x, open = FALSE, ...) {
av <- as.av(x = x, ...)
atcs <- av_atc(av, only_first = TRUE)
u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
u <- paste0("https://atcddd.fhi.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
u[is.na(atcs)] <- NA_character_
names(u) <- av_name(av)

2
R/custom_antimicrobials.R
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@ -96,7 +96,7 @@
#'
#'
#' # Add Co-fluampicil, which is one of the many J01CR50 codes, see
#' # https://www.whocc.no/ddd/list_of_ddds_combined_products/
#' # https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/
#' add_custom_antimicrobials(
#' data.frame(
#' ab = "COFLU",

2
R/data.R
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@ -67,7 +67,7 @@
#' Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
#' @source
#'
#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://atcddd.fhi.no/atc_ddd_index/>
#'
#' * `r TAXONOMY_VERSION$LOINC$citation` Accessed from <`r TAXONOMY_VERSION$LOINC$url`> on `r documentation_date(TAXONOMY_VERSION$LOINC$accessed_date)`.
#'

2
R/eucast_rules.R
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@ -103,7 +103,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @section Antibiotics:
#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
#'
#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://atcddd.fhi.no/atc/structure_and_principles/))', sorted alphabetically:
#'
#' `r create_eucast_ab_documentation()`
#' @aliases EUCAST

4
R/whocc.R
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@ -31,13 +31,13 @@
#'
#' 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:
#' This package contains **all ~550 antibiotic, antimycotic and antiviral 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, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
#' This package contains **all ~550 antibiotic, antimycotic and antiviral 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, <https://atcddd.fhi.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
#'
#' These have become the gold standard for international drug utilisation monitoring and research.
#'
#' The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
#'
#' **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.** See <https://www.whocc.no/copyright_disclaimer/.>
#' **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.** See <https://atcddd.fhi.no/copyright_disclaimer/.>
#' @name WHOCC
#' @rdname WHOCC