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dr. M.S. (Matthijs) Berends 2024-03-03 23:24:57 +01:00
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.1.1.9013 Version: 2.1.1.9014
Date: 2024-03-03 Date: 2024-03-03
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9013 # AMR 2.1.1.9014
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)* *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
@ -9,14 +9,14 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago * Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
## New ## New
* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* Function `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
* One Health implementation * One Health implementation
* Function `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names. * Function `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html). * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q") * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages * `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* Function `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
## Changed ## Changed
* For MICs: * For MICs:

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()]. #' 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: #' @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} #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases ab #' @aliases ab

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

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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`.** #' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
#' @export #' @export
#' @rdname atc_online #' @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 #' @examples
#' \donttest{ #' \donttest{
#' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) { #' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
@ -81,8 +81,8 @@
atc_online_property <- function(atc_code, atc_online_property <- function(atc_code,
property, property,
administration = "O", administration = "O",
url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no", url = "https://atcddd.fhi.no/atc_ddd_index/?code=%s&showdescription=no",
url_vet = "https://www.whocc.no/atcvet/atcvet_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(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(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) meet_criteria(administration, allow_class = "character", has_length = 1)

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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. #' 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: #' @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} #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases av #' @aliases av

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R/av_property.R
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@ -164,7 +164,7 @@ av_ddd <- function(x, administration = "oral", ...) {
warning_( warning_(
"in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.", "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", "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 out
@ -184,7 +184,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
warning_( warning_(
"in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.", "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", "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 out
@ -227,7 +227,7 @@ av_url <- function(x, open = FALSE, ...) {
av <- as.av(x = x, ...) av <- as.av(x = x, ...)
atcs <- av_atc(av, only_first = TRUE) 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_ u[is.na(atcs)] <- NA_character_
names(u) <- av_name(av) 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 #' # 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( #' add_custom_antimicrobials(
#' data.frame( #' data.frame(
#' ab = "COFLU", #' 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). #' 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 #' @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)`. #' * `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: #' @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. #' 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()` #' `r create_eucast_ab_documentation()`
#' @aliases EUCAST #' @aliases EUCAST

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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. #' 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: #' @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. #' 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. #' 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 #' @name WHOCC
#' @rdname WHOCC #' @rdname WHOCC

2
data-raw/extractATCs.R
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@ -4,7 +4,7 @@ library(tidyr)
library(AMR) library(AMR)
# we need J01, J02 and J04 (J03 does not exist) # we need J01, J02 and J04 (J03 does not exist)
url <- "https://www.whocc.no/atc_ddd_index/?code={code}&showdescription=no" url <- "https://atcddd.fhi.no/atc_ddd_index/?code={code}&showdescription=no"
complete_vector <- character(0) complete_vector <- character(0)
for (Jxx in c("J01", "J02", "J04")) { for (Jxx in c("J01", "J02", "J04")) {
site <- gsub("{code}", Jxx, url, fixed = TRUE) site <- gsub("{code}", Jxx, url, fixed = TRUE)

4
data-raw/reproduction_of_antibiotics.R
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@ -761,9 +761,9 @@ updated_atc <- as.list(antibiotics$atc)
get_atcs <- function(ab_name, type = "human") { get_atcs <- function(ab_name, type = "human") {
if (type == "human") { if (type == "human") {
url <- "https://www.whocc.no/atc_ddd_index/" url <- "https://atcddd.fhi.no/atc_ddd_index/"
} else if (type == "veterinary") { } else if (type == "veterinary") {
url <- "https://www.whocc.no/atcvet/atcvet_index/" url <- "https://atcddd.fhi.no/atcvet/atcvet_index/"
} else { } else {
stop("invalid type") stop("invalid type")
} }

4
data-raw/reproduction_of_antivirals.R
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@ -34,7 +34,7 @@ library(rvest)
# get all data from the WHOCC website # get all data from the WHOCC website
get_atc_table <- function(atc_group) { get_atc_table <- function(atc_group) {
# give as input J0XXX, like atc_group = "J05AB" # give as input J0XXX, like atc_group = "J05AB"
downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no")) downloaded <- read_html(paste0("https://atcddd.fhi.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
table_title <- downloaded %>% table_title <- downloaded %>%
html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>% html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
html_text() html_text()
@ -62,7 +62,7 @@ get_atc_table <- function(atc_group) {
) )
} }
# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A) # these are the relevant groups for input: https://atcddd.fhi.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX") atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX")
# get the first # get the first

4
man/WHOCC.Rd
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@ -8,13 +8,13 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi
} }
\section{WHOCC}{ \section{WHOCC}{
This package contains \strong{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, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). This package contains \strong{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, \url{https://atcddd.fhi.no}) and the Pharmaceuticals Community Register of the European Commission (\url{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. 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. 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.
\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/.} \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
} }
\examples{ \examples{

2
man/ab_property.Rd
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@ -97,7 +97,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
} }
\section{Source}{ \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} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }

2
man/add_custom_antimicrobials.Rd
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@ -77,7 +77,7 @@ ab_info("testab")
# Add Co-fluampicil, which is one of the many J01CR50 codes, see # 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( add_custom_antimicrobials(
data.frame( data.frame(
ab = "COFLU", ab = "COFLU",

6
man/antibiotics.Rd
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@ -45,7 +45,7 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w
} }
\source{ \source{
\itemize{ \itemize{
\item World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/} \item World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://atcddd.fhi.no/atc_ddd_index/}
\item Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from \url{https://loinc.org} on October 19th, 2023. \item Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from \url{https://loinc.org} on October 19th, 2023.
\item European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} \item European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }
@ -69,13 +69,13 @@ Like all data sets in this package, these data sets are publicly available for d
} }
\section{WHOCC}{ \section{WHOCC}{
This package contains \strong{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, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). This package contains \strong{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, \url{https://atcddd.fhi.no}) and the Pharmaceuticals Community Register of the European Commission (\url{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. 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. 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.
\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/.} \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
} }
\examples{ \examples{

6
man/as.ab.Rd
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@ -44,20 +44,20 @@ You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab(
} }
\section{Source}{ \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} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }
\section{WHOCC}{ \section{WHOCC}{
This package contains \strong{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, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). This package contains \strong{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, \url{https://atcddd.fhi.no}) and the Pharmaceuticals Community Register of the European Commission (\url{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. 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. 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.
\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/.} \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
} }
\section{Reference Data Publicly Available}{ \section{Reference Data Publicly Available}{

6
man/as.av.Rd
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@ -42,20 +42,20 @@ Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} fun
} }
\section{Source}{ \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} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }
\section{WHOCC}{ \section{WHOCC}{
This package contains \strong{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, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). This package contains \strong{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, \url{https://atcddd.fhi.no}) and the Pharmaceuticals Community Register of the European Commission (\url{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. 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. 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.
\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/.} \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
} }
\section{Reference Data Publicly Available}{ \section{Reference Data Publicly Available}{

6
man/atc_online.Rd
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@ -7,15 +7,15 @@
\alias{atc_online_ddd_units} \alias{atc_online_ddd_units}
\title{Get ATC Properties from WHOCC Website} \title{Get ATC Properties from WHOCC Website}
\source{ \source{
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/} \url{https://atcddd.fhi.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
} }
\usage{ \usage{
atc_online_property( atc_online_property(
atc_code, atc_code,
property, property,
administration = "O", administration = "O",
url = "https://www.whocc.no/atc_ddd_index/?code=\%s&showdescription=no", url = "https://atcddd.fhi.no/atc_ddd_index/?code=\%s&showdescription=no",
url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=\%s&showdescription=no" url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=\%s&showdescription=no"
) )
atc_online_groups(atc_code, ...) atc_online_groups(atc_code, ...)

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man/av_property.Rd
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@ -72,7 +72,7 @@ The function \code{\link[=av_url]{av_url()}} will return the direct URL to the o
} }
\section{Source}{ \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} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
} }

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pkgdown/extra.css
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@ -34,7 +34,7 @@
--bs-primary-color: #a7dbc3 !important; --bs-primary-color: #a7dbc3 !important;
--bs-primary-rgb: 167, 219, 195 !important; --bs-primary-rgb: 167, 219, 195 !important;
--bs-secondary: #ffffff !important; --bs-secondary: #ffffff !important;
--bs-secondary-color: #ffffff !important; --bs-secondary-color: var(--bs-success) !important;
--bs-secondary-rgb: 255, 255, 255 !important; --bs-secondary-rgb: 255, 255, 255 !important;
--bs-navbar-brand-color: var(--bs-body-color) !important; --bs-navbar-brand-color: var(--bs-body-color) !important;
--bs-navbar-brand-color-hover: var(--bs-body-color) !important; --bs-navbar-brand-color-hover: var(--bs-body-color) !important;

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vignettes/datasets.Rmd
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@ -170,7 +170,7 @@ The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stat
This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration. This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use) * [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://atcddd.fhi.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov) * [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
* [WHONET software 2019](https://whonet.org) * [WHONET software 2019](https://whonet.org)
* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org) * [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)
@ -198,7 +198,7 @@ The tab-separated text file and Microsoft Excel workbook, and SAS, SPSS and Stat
This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration. This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.
* [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://www.whocc.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use) * [ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology](https://atcddd.fhi.no/atc_ddd_index/) (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)
* [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov) * [PubChem by the US National Library of Medicine](https://pubchem.ncbi.nlm.nih.gov)
* [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org) * [LOINC (Logical Observation Identifiers Names and Codes)](https://loinc.org)