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(v1.5.0.9015) unit test fix, grouped first isolates

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dr. M.S. (Matthijs) Berends
2021-02-04 16:48:16 +01:00
parent 2eca8c3f01
commit 8fda473e49
44 changed files with 239 additions and 168 deletions
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9
R/guess_ab_col.R
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@ -67,6 +67,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
if (is.null(x) & is.null(search_string)) {
return(as.name("guess_ab_col"))
@ -225,9 +226,9 @@ get_column_abx <- function(x,
if (info == TRUE & !all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing_msg <- paste(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"),
collapse = ", ")
missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL),
" (", font_bold(missing, collapse = NULL), ")"),
quotes = FALSE)
message_("Reliability would be improved if these antimicrobial results would be available too: ",
missing_msg)
}
@ -243,7 +244,7 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
any_txt <- c("", "are")
}
warning_(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
paste(missing, collapse = ", ")),
vector_and(missing, quotes = FALSE)),
immediate = TRUE,
call = FALSE)
}