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(v0.8.0.9034) add cid to antivirals
This commit is contained in:
42
R/data.R
42
R/data.R
@ -19,10 +19,11 @@
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Data set with ~450 antibiotics
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#' Data sets with ~550 antimicrobials
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#'
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#' A data set containing all antibiotics. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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#' @format A \code{\link{data.frame}} with 453 observations and 13 variables:
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#' Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from the \code{antibiotics} data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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#' @format
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#' \strong{For the \code{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 13 variables:}
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#' \describe{
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#' \item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
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#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
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@ -38,7 +39,20 @@
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#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
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#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
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#' }
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#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}
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#'
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#' \strong{For the \code{antivirals} data set: a \code{\link{data.frame}} with 102 observations and 9 variables:}
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#' \describe{
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#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
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#' \item{\code{cid}}{Compound ID as found in PubChem}
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#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
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#' \item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
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#' \item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
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#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
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#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
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#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
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#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
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#' }
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#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}.
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#'
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#' Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and consequently only available where a CID is available.
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#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
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@ -48,26 +62,10 @@
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#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
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#' @inheritSection WHOCC WHOCC
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#' @inheritSection AMR Read more on our website!
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#' @seealso \code{\link{antivirals}} \code{\link{microorganisms}}
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#' @seealso \code{\link{microorganisms}}
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"antibiotics"
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#' Data set with ~100 antivirals
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#'
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#' A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).
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#' @format A \code{\link{data.frame}} with 102 observations and 7 variables:
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#' \describe{
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#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
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#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
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#' \item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
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#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
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#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
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#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
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#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
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#' }
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#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
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#' @inheritSection WHOCC WHOCC
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#' @inheritSection AMR Read more on our website!
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#' @seealso \code{\link{antibiotics}} \code{\link{microorganisms}}
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#' @rdname antibiotics
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"antivirals"
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#' Data set with ~70,000 microorganisms
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8
R/misc.R
8
R/misc.R
@ -29,6 +29,14 @@ addin_insert_like <- function() {
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rstudioapi::insertText(" %like% ")
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}
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load_AMR_package <- function() {
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if (!"package:AMR" %in% base::search()) {
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require(AMR)
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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base::invisible()
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}
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#' @importFrom crayon blue bold red
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#' @importFrom dplyr %>% pull
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search_type_in_df <- function(x, type) {
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18
R/mo.R
18
R/mo.R
@ -183,11 +183,14 @@
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#' df <- df %>%
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#' mutate(mo = as.mo(paste(genus, species)))
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source(), ...) {
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if (!"AMR" %in% base::.packages()) {
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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as.mo <- function(x,
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Becker = FALSE,
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Lancefield = FALSE,
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allow_uncertain = TRUE,
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reference_df = get_mo_source(),
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...) {
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load_AMR_package()
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# WHONET: xxx = no growth
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x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
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@ -293,10 +296,7 @@ exec_as.mo <- function(x,
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debug = FALSE,
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reference_data_to_use = microorganismsDT) {
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if (!"AMR" %in% base::.packages()) {
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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load_AMR_package()
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# WHONET: xxx = no growth
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x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
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@ -396,6 +396,8 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
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}
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mo_validate <- function(x, property, ...) {
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load_AMR_package()
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dots <- list(...)
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Becker <- dots$Becker
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@ -407,11 +409,6 @@ mo_validate <- function(x, property, ...) {
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Lancefield <- FALSE
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}
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if (!"AMR" %in% base::.packages()) {
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require("AMR")
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# check .onLoad() in R/zzz.R: data tables are created there.
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}
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# try to catch an error when inputting an invalid parameter
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% AMR::microorganisms[1, property],
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