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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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6
R/amr_selectors.R
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@@ -839,10 +839,10 @@ c.amr_selector <- function(...) {
all_any_amr_selector <- function(type, ..., na.rm = TRUE) {
cols_ab <- c(...)
result <- cols_ab[toupper(cols_ab) %in% c("S", "SDD", "I", "R", "NI")]
result <- cols_ab[toupper(cols_ab) %in% VALID_SIR_LEVELS]
if (length(result) == 0) {
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
result <- c("S", "SDD", "I", "R", "NI")
result <- VALID_SIR_LEVELS
}
cols_ab <- cols_ab[!cols_ab %in% result]
df <- get_current_data(arg_name = NA, call = -3)
@@ -951,7 +951,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
}
}
# this is `!=`, so turn around the values
sir <- c("S", "SDD", "I", "R", "NI")
sir <- VALID_SIR_LEVELS
e2 <- sir[sir != e2]
structure(all_any_amr_selector(type = type, e1, e2),
class = c("amr_selector_any_all", "logical")