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doc f fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-11-12 23:29:02 +01:00
parent fda9c15420
commit 8f021d042b
4 changed files with 19 additions and 67 deletions
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26
R/ab_property.R
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@ -241,20 +241,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
x <- as.ab(x, ...)
ddd_prop <- administration
# old behaviour
units <- list(...)$units
if (!is.null(units) && isTRUE(units)) {
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
warning_(
"in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
"This warning will be shown once per session."
)
}
ddd_prop <- paste0(ddd_prop, "_units")
} else {
ddd_prop <- paste0(ddd_prop, "_ddd")
}
ddd_prop <- paste0(administration, "_ddd")
out <- ab_validate(x = x, property = ddd_prop)
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
@ -274,16 +261,17 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
x <- as.ab(x, ...)
if (any(ab_name(x, language = NULL) %like% "/")) {
ddd_prop <- paste0(administration, "_units")
out <- ab_validate(x = x, property = ddd_prop)
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `ab_ddd_units()`: DDDs of 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",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
)
}
ddd_prop <- paste0(administration, "_units")
ab_validate(x = x, property = ddd_prop)
out
}
#' @rdname ab_property

56
R/av_property.R
View File

@ -130,35 +130,11 @@ av_group <- function(x, language = get_AMR_locale(), ...) {
}
#' @rdname av_property
#' @aliases ATC
#' @export
av_atc <- function(x, only_first = FALSE, ...) {
av_atc <- function(x, ...) {
meet_criteria(x, allow_NA = TRUE)
meet_criteria(only_first, allow_class = "logical", has_length = 1)
atcs <- av_validate(x = x, property = "atc", ...)
if (only_first == TRUE) {
atcs <- vapply(
FUN.VALUE = character(1),
# get only the first ATC code
atcs,
function(x) {
# try to get the J-group
if (any(x %like% "^J")) {
x[x %like% "^J"][1L]
} else {
as.character(x[1L])
}
}
)
} else if (length(atcs) == 1) {
atcs <- unname(unlist(atcs))
} else {
names(atcs) <- x
}
atcs
# ATCs in the antivirals data set are not a list
av_validate(x = x, property = "atc", ...)
}
#' @rdname av_property
@ -181,20 +157,7 @@ av_ddd <- function(x, administration = "oral", ...) {
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
x <- as.av(x, ...)
ddd_prop <- administration
# old behaviour
units <- list(...)$units
if (!is.null(units) && isTRUE(units)) {
if (message_not_thrown_before("av_ddd", entire_session = TRUE)) {
warning_(
"in `av_ddd()`: using `av_ddd(..., units = TRUE)` is deprecated, use `av_ddd_units()` to retrieve units instead.",
"This warning will be shown once per session."
)
}
ddd_prop <- paste0(ddd_prop, "_units")
} else {
ddd_prop <- paste0(ddd_prop, "_ddd")
}
ddd_prop <- paste0(administration, "_ddd")
out <- av_validate(x = x, property = ddd_prop)
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
@ -214,16 +177,17 @@ av_ddd_units <- function(x, administration = "oral", ...) {
meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
x <- as.av(x, ...)
if (any(av_name(x, language = NULL) %like% "/")) {
ddd_prop <- paste0(administration, "_units")
out <- av_validate(x = x, property = ddd_prop)
if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_(
"in `av_ddd_units()`: DDDs of 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",
"www.whocc.no/ddd/list_of_ddds_combined_products/"
)
}
ddd_prop <- paste0(administration, "_units")
av_validate(x = x, property = ddd_prop)
out
}
#' @rdname av_property