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(v0.7.1.9100) bug_drug speed, MIC levels
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@ -39,6 +39,7 @@
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#' The language of the output can be overwritten with \code{options(AMR_locale)}, please see \link{translate}.
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#' @export
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#' @rdname bug_drug_combinations
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#' @return The function \code{bug_drug_combinations} returns a \code{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
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#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
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#' @inheritSection AMR Read more on our website!
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#' @examples
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@ -58,7 +59,6 @@
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#' }
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bug_drug_combinations <- function(x,
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col_mo = NULL,
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minimum = 30,
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FUN = mo_shortname,
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...) {
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if (!is.data.frame(x)) {
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@ -77,17 +77,17 @@ bug_drug_combinations <- function(x,
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x <- x %>%
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as.data.frame(stringsAsFactors = FALSE) %>%
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mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>%
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filter(mo %in% (freq(mo) %>%
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filter(count >= minimum) %>%
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pull(item))) %>%
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group_by(mo) %>%
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AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>%
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select(-value) %>%
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spread(interpretation, isolates) %>%
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select_if(is.rsi) %>%
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gather("ab", "value", -mo) %>%
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group_by(mo, ab) %>%
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summarise(S = sum(value == "S", na.rm = TRUE),
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I = sum(value == "I", na.rm = TRUE),
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R = sum(value == "R", na.rm = TRUE)) %>%
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ungroup() %>%
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mutate(total = S + I + R) %>%
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filter(total >= minimum) %>%
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rename(ab = antibiotic)
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as.data.frame(stringsAsFactors = FALSE)
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structure(.Data = x, class = c("bug_drug_combinations", class(x)))
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}
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@ -107,6 +107,8 @@ format.bug_drug_combinations <- function(x,
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decimal.mark = getOption("OutDec"),
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big.mark = ifelse(decimal.mark == ",", ".", ","),
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...) {
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x <- x %>% filter(total >= minimum)
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if (remove_intrinsic_resistant == TRUE) {
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x <- x %>% filter(R != total)
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}
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@ -133,7 +135,6 @@ format.bug_drug_combinations <- function(x,
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}
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y <- x %>%
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filter(total >= minimum) %>%
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mutate(ab = as.ab(ab),
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ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>%
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group_by(ab, ab_txt, mo) %>%
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