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(v3.0.0.9010) in as.sir(), add note when higher taxonomic levels are used
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13
R/sir_calc.R
13
R/sir_calc.R
@ -257,12 +257,15 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
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data <- as.data.frame(data, stringsAsFactors = FALSE)
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for (i in seq_len(ncol(data))) {
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data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
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if (isTRUE(combine_SI)) {
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if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
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message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
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# transform SIR columns
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if (is.sir(data[, i, drop = TRUE])) {
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data[, i] <- as.character(data[, i, drop = TRUE])
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if (isTRUE(combine_SI)) {
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if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
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message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
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}
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data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
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}
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data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
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}
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}
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