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(v1.5.0.9012) ampc_cephalosporin_resistance for I

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dr. M.S. (Matthijs) Berends
2021-01-25 21:58:00 +01:00
parent 24eb4453db
commit 331c1f6508
19 changed files with 73 additions and 35 deletions
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16
R/aa_helper_functions.R
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@ -442,7 +442,7 @@ create_ab_documentation <- function(ab) {
out
}
vector_or <- function(v, quotes = TRUE, reverse = FALSE) {
vector_or <- function(v, quotes = TRUE, reverse = FALSE, last_sep = " or ") {
# makes unique and sorts, and this also removed NAs
v <- sort(unique(v))
if (length(v) == 1) {
@ -451,9 +451,18 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE) {
if (reverse == TRUE) {
v <- rev(v)
}
if (identical(v, c("I", "R", "S"))) {
# class <rsi> should be sorted like this
v <- c("R", "S", "I")
}
if (isTRUE(quotes)) {
quotes <- '"'
} else if (isFALSE(quotes)) {
quotes <- ""
}
# all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
paste0(paste0(ifelse(quotes, '"', ""), v[seq_len(length(v) - 1)], ifelse(quotes, '"', ""), collapse = ", "),
" or ", paste0(ifelse(quotes, '"', ""), v[length(v)], ifelse(quotes, '"', "")))
paste0(paste0(quotes, v[seq_len(length(v) - 1)], quotes, collapse = ", "),
last_sep, paste0(quotes, v[length(v)], quotes))
}
format_class <- function(class, plural) {
@ -562,6 +571,7 @@ meet_criteria <- function(object,
"` must be ",
ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1, "either ", ""),
vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class))),
ifelse(allow_NA == TRUE, ", or NA", ""),
call = call_depth)
}
if (!is.null(is_positive)) {