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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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4
R/ab_property.R
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@ -33,7 +33,7 @@
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
#' @param administration way of administration, either `"oral"` or `"iv"`
#' @param open browse the URL using [utils::browseURL()]
#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection like `AMX:VAN`), otherwise other arguments passed on to [as.ab()]
#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection such as `column1:column4`), otherwise other arguments passed on to [as.ab()]
#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
@ -359,7 +359,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_locale(),
} else {
df <- data
}
vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE, fn = "set_ab_names")
if (length(vars) == 0) {
message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
return(data)