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parameter combine_IR
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45
R/count.R
45
R/count.R
@ -163,7 +163,8 @@ n_rsi <- function(...) {
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#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
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#' @export
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count_df <- function(data,
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translate_ab = getOption("get_antibiotic_names", "official")) {
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translate_ab = getOption("get_antibiotic_names", "official"),
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combine_IR = FALSE) {
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if (!"data.frame" %in% class(data)) {
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stop("`count_df` must be called on a data.frame")
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@ -184,23 +185,37 @@ count_df <- function(data,
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mutate(Interpretation = "S") %>%
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select(Interpretation, everything())
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resI <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = count_I) %>%
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mutate(Interpretation = "I") %>%
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select(Interpretation, everything())
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if (combine_IR == FALSE) {
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resI <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = count_I) %>%
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mutate(Interpretation = "I") %>%
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select(Interpretation, everything())
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resR <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = count_R) %>%
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mutate(Interpretation = "R") %>%
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select(Interpretation, everything())
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resR <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = count_R) %>%
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mutate(Interpretation = "R") %>%
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select(Interpretation, everything())
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data.groups <- group_vars(data)
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data.groups <- group_vars(data)
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res <- bind_rows(resS, resI, resR) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
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tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
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res <- bind_rows(resS, resI, resR) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
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tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
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} else {
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resIR <- summarise_if(.tbl = data,
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.predicate = is.rsi,
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.funs = count_IR) %>%
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mutate(Interpretation = "IR") %>%
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select(Interpretation, everything())
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data.groups <- group_vars(data)
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res <- bind_rows(resS, resIR) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("IR", "S"), ordered = TRUE)) %>%
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tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
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}
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if (!translate_ab == FALSE) {
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if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
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