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new SDD and N for as.sir()
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@ -236,7 +236,7 @@ first_isolate <- function(x = NULL,
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FUN.VALUE = logical(1),
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X = x,
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# check only first 10,000 rows
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FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "I", "R"), na.rm = TRUE),
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FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "SDD", "I", "R", "N"), na.rm = TRUE),
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USE.NAMES = FALSE
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))
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if (method == "phenotype-based" && !any_col_contains_sir) {
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