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bring back antibiogram(), without deps

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dr. M.S. (Matthijs) Berends
2023-02-10 16:18:00 +01:00
parent 70a7ba0206
commit bc434db835
42 changed files with 11307 additions and 4734 deletions
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6
R/mo.R
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@ -158,7 +158,7 @@ as.mo <- function(x,
meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
meet_criteria(minimum_matching_score, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE)
meet_criteria(minimum_matching_score, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive_or_zero = TRUE, is_finite = TRUE)
meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
language <- validate_language(language)
@ -627,7 +627,7 @@ freq.mo <- function(x, ...) {
.add_header = list(
`Gram-negative` = paste0(
format(sum(grams == "Gram-negative", na.rm = TRUE),
big.mark = ",",
big.mark = " ",
decimal.mark = "."
),
" (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams),
@ -637,7 +637,7 @@ freq.mo <- function(x, ...) {
),
`Gram-positive` = paste0(
format(sum(grams == "Gram-positive", na.rm = TRUE),
big.mark = ",",
big.mark = " ",
decimal.mark = "."
),
" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams),