mirror of
https://github.com/msberends/AMR.git
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148 lines
5.3 KiB
R
Executable File
148 lines
5.3 KiB
R
Executable File
# ==================================================================== #
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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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#' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all
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rsi_calc <- function(...,
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type,
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include_I,
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minimum,
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as_percent,
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also_single_tested,
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only_count) {
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if (!is.logical(include_I)) {
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stop('`include_I` must be logical', call. = FALSE)
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}
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if (!is.numeric(minimum)) {
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stop('`minimum` must be numeric', call. = FALSE)
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}
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if (!is.logical(as_percent)) {
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stop('`as_percent` must be logical', call. = FALSE)
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}
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if (!is.logical(also_single_tested)) {
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stop('`also_single_tested` must be logical', call. = FALSE)
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}
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dots_df <- ...elt(1) # it needs this evaluation
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dots <- base::eval(base::substitute(base::alist(...)))
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ndots <- length(dots)
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if ("data.frame" %in% class(dots_df)) {
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# data.frame passed with other columns, like:
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# septic_patients %>% portion_S(amcl, gent)
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dots <- as.character(dots)
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dots <- dots[dots != "."]
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if (length(dots) == 0 | all(dots == "df")) {
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# for complete data.frames, like septic_patients %>% select(amcl, gent) %>% portion_S()
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# and the old rsi function, that has "df" as name of the first parameter
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x <- dots_df
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} else {
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x <- dots_df[, dots]
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}
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} else if (ndots == 1) {
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# only 1 variable passed (can also be data.frame), like:
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# portion_S(septic_patients$amcl)
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# septic_patients$amcl %>% portion_S()
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x <- dots_df
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} else {
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# multiple variables passed without pipe, like:
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# portion_S(septic_patients$amcl, septic_patients$gent)
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x <- NULL
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try(x <- as.data.frame(dots), silent = TRUE)
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if (is.null(x)) {
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# support for: with(septic_patients, portion_S(amcl, gent))
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x <- as.data.frame(rlang::list2(...))
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}
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}
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print_warning <- FALSE
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type_trans <- as.integer(as.rsi(type))
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type_others <- base::setdiff(1:3, type_trans)
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if (is.data.frame(x)) {
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rsi_integrity_check <- character(0)
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for (i in 1:ncol(x)) {
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# check integrity of columns: force rsi class
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if (!is.rsi(x %>% pull(i))) {
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rsi_integrity_check <- c(rsi_integrity_check, x %>% pull(i) %>% as.character())
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x[, i] <- suppressWarnings(as.rsi(x[, i])) # warning will be given later
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print_warning <- TRUE
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}
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x[, i] <- x %>% pull(i) %>% as.integer()
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}
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if (length(rsi_integrity_check) > 0) {
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# this will give a warning for invalid results, of all input columns (so only 1 warning)
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rsi_integrity_check <- as.rsi(rsi_integrity_check)
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}
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if (include_I == TRUE) {
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x <- x %>% mutate_all(funs(ifelse(. == 2, type_trans, .)))
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}
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if (also_single_tested == TRUE) {
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# THE CHANCE THAT AT LEAST ONE RESULT IS type
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found <- x %>% filter_all(any_vars(. == type_trans)) %>% nrow()
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# THE CHANCE THAT AT LEAST ONE RESULT IS type OR ALL ARE TESTED
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total <- found + x %>% filter_all(all_vars(. %in% type_others)) %>% nrow()
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} else {
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x <- apply(X = x,
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MARGIN = 1,
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FUN = min)
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found <- sum(as.integer(x) == type_trans, na.rm = TRUE)
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total <- length(x) - sum(is.na(x))
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}
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} else {
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if (!is.rsi(x)) {
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x <- as.rsi(x)
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print_warning <- TRUE
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}
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x <- as.integer(x)
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if (include_I == TRUE) {
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x[x == 2] <- type_trans
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}
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found <- sum(x == type_trans, na.rm = TRUE)
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total <- length(x) - sum(is.na(x))
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}
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if (print_warning == TRUE) {
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warning("Increase speed by transforming to class `rsi` on beforehand: df %>% mutate_if(is.rsi.eligible, as.rsi)",
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call. = FALSE)
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}
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if (only_count == TRUE) {
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return(found)
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}
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if (total < minimum) {
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warning("Introducing NA: only ", total, " results available (minimum set to ", minimum, ").", call. = FALSE)
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result <- NA
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} else {
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result <- found / total
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}
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if (as_percent == TRUE) {
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percent(result, force_zero = TRUE)
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} else {
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result
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}
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}
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