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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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38
R/mic.R
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@ -19,15 +19,15 @@
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
#' Transform input to minimum inhibitory concentrations
#' Transform input to minimum inhibitory concentrations (MIC)
#'
#' This transforms a vector to a new class [`mic`], which is an ordered [`factor`] with valid minimum inhibitory concentrations (MIC) as levels. Invalid MIC values will be translated as `NA` with a warning.
#' This transforms a vector to a new class [`mic`], which is an ordered [factor] with valid minimum inhibitory concentrations (MIC) as levels. Invalid MIC values will be translated as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname as.mic
#' @param x vector
#' @param na.rm a logical indicating whether missing values should be removed
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
#' @return Ordered [`factor`] with new class [`mic`]
#' @return Ordered [factor] with additional class [`mic`]
#' @aliases mic
#' @export
#' @seealso [as.rsi()]
@ -55,7 +55,7 @@ as.mic <- function(x, na.rm = FALSE) {
if (is.mic(x)) {
x
} else {
x <- x %>% unlist()
x <- x %pm>% unlist()
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}
@ -109,13 +109,13 @@ as.mic <- function(x, na.rm = FALSE) {
c(t(sapply(ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
c(t(sapply(ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
na_before <- x[is.na(x) | x == ""] %>% length()
na_before <- x[is.na(x) | x == ""] %pm>% length()
x[!x %in% lvls] <- NA
na_after <- x[is.na(x) | x == ""] %>% length()
na_after <- x[is.na(x) | x == ""] %pm>% length()
if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %>%
unique() %>%
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
unique() %pm>%
sort()
list_missing <- paste0('"', list_missing, '"', collapse = ", ")
warning(na_after - na_before, " results truncated (",
@ -196,15 +196,15 @@ print.mic <- function(x, ...) {
#' @noRd
summary.mic <- function(object, ...) {
x <- object
n_total <- x %>% length()
n_total <- length(x)
x <- x[!is.na(x)]
n <- x %>% length()
c(
"Class" = "mic",
"<NA>" = n_total - n,
"Min." = sort(x)[1] %>% as.character(),
"Max." = sort(x)[n] %>% as.character()
)
n <- length(x)
value <- c("Class" = "mic",
"<NA>" = n_total - n,
"Min." = as.character(sort(x)[1]),
"Max." = as.character(sort(x)[n]))
class(value) <- c("summaryDefault", "table")
value
}
#' @method plot mic
@ -283,7 +283,7 @@ barplot.mic <- function(height,
#' @export
#' @noRd
c.mic <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
y <- unlist(lapply(list(...), as.character))
x <- as.character(x)
as.mic(c(x, y))
}