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141 lines
6.8 KiB
R
Executable File
141 lines
6.8 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Deprecated Functions
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#'
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#' These functions are so-called '[Deprecated]'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
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#' @inheritSection lifecycle Retired Lifecycle
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#' @inheritSection AMR Read more on Our Website!
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#' @keywords internal
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#' @name AMR-deprecated
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#' @export
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p_symbol <- function(p, emptychar = " ") {
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.Deprecated(package = "AMR", new = "cleaner::p_symbol")
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p <- as.double(p)
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s <- rep(NA_character_, length(p))
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s[p <= 1] <- emptychar
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s[p <= 0.100] <- "."
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s[p <= 0.050] <- "*"
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s[p <= 0.010] <- "**"
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s[p <= 0.001] <- "***"
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s
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}
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#' @name AMR-deprecated
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#' @export
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filter_first_weighted_isolate <- function(x = NULL,
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col_date = NULL,
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col_patient_id = NULL,
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col_mo = NULL,
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...) {
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.Deprecated(old = "filter_first_weighted_isolate()",
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new = "filter_first_isolate()",
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package = "AMR")
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
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# is also fix for using a grouped df as input (a dot as first argument)
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x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
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}
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meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
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meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
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filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...)
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}
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#' @name AMR-deprecated
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#' @export
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key_antibiotics <- function(x = NULL,
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col_mo = NULL,
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universal_1 = guess_ab_col(x, "amoxicillin"),
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universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
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universal_3 = guess_ab_col(x, "cefuroxime"),
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universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
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universal_5 = guess_ab_col(x, "ciprofloxacin"),
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universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
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GramPos_1 = guess_ab_col(x, "vancomycin"),
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GramPos_2 = guess_ab_col(x, "teicoplanin"),
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GramPos_3 = guess_ab_col(x, "tetracycline"),
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GramPos_4 = guess_ab_col(x, "erythromycin"),
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GramPos_5 = guess_ab_col(x, "oxacillin"),
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GramPos_6 = guess_ab_col(x, "rifampin"),
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GramNeg_1 = guess_ab_col(x, "gentamicin"),
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GramNeg_2 = guess_ab_col(x, "tobramycin"),
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GramNeg_3 = guess_ab_col(x, "colistin"),
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GramNeg_4 = guess_ab_col(x, "cefotaxime"),
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GramNeg_5 = guess_ab_col(x, "ceftazidime"),
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GramNeg_6 = guess_ab_col(x, "meropenem"),
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warnings = TRUE,
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...) {
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.Deprecated(old = "key_antibiotics()",
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new = "key_antimicrobials()",
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package = "AMR")
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if (is_null_or_grouped_tbl(x)) {
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# when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
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# is also fix for using a grouped df as input (a dot as first argument)
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x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
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}
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key_antimicrobials(x = x,
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col_mo = col_mo,
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universal = c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6),
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gram_negative = c(GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6),
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gram_positive = c(GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6),
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antifungal = NULL,
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only_rsi_columns = FALSE,
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...)
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}
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#' @name AMR-deprecated
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#' @export
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key_antibiotics_equal <- function(y,
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z,
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type = "keyantimicrobials",
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE,
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na.rm = TRUE,
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...) {
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.Deprecated(old = "key_antibiotics_equal()",
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new = "antimicrobials_equal()",
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package = "AMR")
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antimicrobials_equal(y = y,
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z = z,
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type = type,
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ignore_I = ignore_I,
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points_threshold = points_threshold,
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info = info)
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}
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