AMR/R/rsi_df.R

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2019-06-13 14:28:46 +02:00
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' @rdname portion
#' @rdname count
#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
#' @export
rsi_df <- function(data,
translate_ab = "name",
language = get_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
combine_IR = FALSE) {
portions <- rsi_calc_df(type = "portion",
data = data,
translate_ab = translate_ab,
language = language,
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
counts <- rsi_calc_df(type = "count",
data = data,
translate_ab = FALSE,
language = "en",
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
data.frame(portions,
isolates = counts$value,
stringsAsFactors = FALSE)
}