mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
119 lines
3.9 KiB
R
119 lines
3.9 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This program is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This program is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License for more details. #
|
|
# ==================================================================== #
|
|
|
|
#' @importFrom dplyr %>% pull
|
|
rsi_calc <- function(...,
|
|
type,
|
|
include_I,
|
|
minimum,
|
|
as_percent,
|
|
only_count) {
|
|
|
|
if (!is.logical(include_I)) {
|
|
stop('`include_I` must be logical', call. = FALSE)
|
|
}
|
|
if (!is.numeric(minimum)) {
|
|
stop('`minimum` must be numeric', call. = FALSE)
|
|
}
|
|
if (!is.logical(as_percent)) {
|
|
stop('`as_percent` must be logical', call. = FALSE)
|
|
}
|
|
|
|
dots_df <- ...elt(1) # it needs this evaluation
|
|
dots <- base::eval(base::substitute(base::alist(...)))
|
|
ndots <- length(dots)
|
|
|
|
if ("data.frame" %in% class(dots_df)) {
|
|
# data.frame passed with other columns, like:
|
|
# septic_patients %>% portion_S(amcl, gent)
|
|
dots <- as.character(dots)
|
|
dots <- dots[dots != "."]
|
|
if (length(dots) == 0 | all(dots == "df")) {
|
|
# for complete data.frames, like septic_patients %>% select(amcl, gent) %>% portion_S()
|
|
# and the old rsi function, that has "df" as name of the first parameter
|
|
x <- dots_df
|
|
} else {
|
|
x <- dots_df[, dots]
|
|
}
|
|
} else if (ndots == 1) {
|
|
# only 1 variable passed (can also be data.frame), like:
|
|
# portion_S(septic_patients$amcl)
|
|
# septic_patients$amcl %>% portion_S()
|
|
x <- dots_df
|
|
} else {
|
|
# multiple variables passed without pipe, like:
|
|
# portion_S(septic_patients$amcl, septic_patients$gent)
|
|
x <- NULL
|
|
try(x <- as.data.frame(dots), silent = TRUE)
|
|
if (is.null(x)) {
|
|
# support for: with(septic_patients, portion_S(amcl, gent))
|
|
x <- as.data.frame(rlang::list2(...))
|
|
}
|
|
}
|
|
|
|
print_warning <- FALSE
|
|
# check integrity of columns: force rsi class
|
|
if (is.data.frame(x)) {
|
|
for (i in 1:ncol(x)) {
|
|
if (!is.rsi(x %>% pull(i))) {
|
|
x[, i] <- as.rsi(x[, i])
|
|
print_warning <- TRUE
|
|
}
|
|
x[, i] <- x %>% pull(i) %>% as.integer()
|
|
}
|
|
x <- apply(X = x,
|
|
MARGIN = 1,
|
|
FUN = min)
|
|
} else {
|
|
if (!is.rsi(x)) {
|
|
x <- as.rsi(x)
|
|
print_warning <- TRUE
|
|
}
|
|
}
|
|
|
|
if (print_warning == TRUE) {
|
|
warning("Increase speed by transforming to class `rsi` on beforehand: df %>% mutate_if(is.rsi.eligible, as.rsi)",
|
|
call. = FALSE)
|
|
}
|
|
|
|
if (type == "S") {
|
|
found <- sum(as.integer(x) <= 1 + include_I, na.rm = TRUE)
|
|
} else if (type == "I") {
|
|
found <- sum(as.integer(x) == 2, na.rm = TRUE)
|
|
} else if (type == "R") {
|
|
found <- sum(as.integer(x) >= 3 - include_I, na.rm = TRUE)
|
|
} else {
|
|
stop("invalid type")
|
|
}
|
|
|
|
if (only_count == TRUE) {
|
|
return(found)
|
|
}
|
|
|
|
total <- length(x) - sum(is.na(x))
|
|
if (total < minimum) {
|
|
return(NA)
|
|
}
|
|
|
|
if (as_percent == TRUE) {
|
|
percent(found / total, force_zero = TRUE)
|
|
} else {
|
|
found / total
|
|
}
|
|
}
|