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remove warnings from unit tests

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dr. M.S. (Matthijs) Berends
2022-10-19 11:47:57 +02:00
parent fed3b6440f
commit 85e2fbe4a3
35 changed files with 115 additions and 110 deletions
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4
R/guess_ab_col.R
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@ -33,7 +33,7 @@
#' @param x a [data.frame]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a [logical] to indicate whether additional info should be printed
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic.
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
@ -171,7 +171,7 @@ get_column_abx <- function(x,
}
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the <rsi> class (as.rsi)
# or already have the 'rsi' class (as.rsi)
# and that they have no more than 50% invalid values
vectr_antibiotics <- unlist(AMR_env$AB_lookup$generalised_all)
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]