mirror of https://github.com/msberends/AMR.git
59 lines
2.8 KiB
R
59 lines
2.8 KiB
R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' @rdname portion
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#' @rdname count
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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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rsi_df <- function(data,
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translate_ab = "name",
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language = get_locale(),
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minimum = 30,
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as_percent = FALSE,
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combine_SI = TRUE,
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combine_IR = FALSE) {
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portions <- rsi_calc_df(type = "portion",
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data = data,
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translate_ab = translate_ab,
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language = language,
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minimum = minimum,
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as_percent = as_percent,
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combine_SI = combine_SI,
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combine_IR = combine_IR,
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combine_SI_missing = missing(combine_SI))
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counts <- rsi_calc_df(type = "count",
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data = data,
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translate_ab = FALSE,
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language = "en",
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minimum = minimum,
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as_percent = as_percent,
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combine_SI = combine_SI,
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combine_IR = combine_IR,
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combine_SI_missing = missing(combine_SI))
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data.frame(portions,
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isolates = counts$value,
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stringsAsFactors = FALSE)
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}
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