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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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R/first_isolate.R
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@@ -246,7 +246,7 @@ first_isolate <- function(x = NULL,
FUN.VALUE = logical(1),
X = x,
# check only first 10,000 rows
FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "SDD", "I", "R", "NI"), na.rm = TRUE),
FUN = function(x) any(as.character(x[1:10000]) %in% VALID_SIR_LEVELS, na.rm = TRUE),
USE.NAMES = FALSE
))
if (method == "phenotype-based" && !any_col_contains_sir) {