mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 17:42:03 +02:00
update MIC comparisons
This commit is contained in:
@ -875,7 +875,7 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
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if ("logical" %in% allow_class) {
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is_in <- is_in[!is_in %in% c("TRUE", "FALSE")]
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}
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or_values <- vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class)))
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or_values <- vector_or(is_in, quotes = !isTRUE(any(c("numeric", "integer") %in% allow_class)))
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if ("logical" %in% allow_class) {
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or_values <- paste0(or_values, ", or TRUE or FALSE")
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}
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5
R/disk.R
5
R/disk.R
@ -165,11 +165,6 @@ pillar_shaft.disk <- function(x, ...) {
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create_pillar_column(out, align = "right", width = 2)
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}
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# will be exported using s3_register() in R/zzz.R
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type_sum.disk <- function(x, ...) {
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"disk"
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}
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#' @method print disk
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#' @export
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#' @noRd
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@ -175,8 +175,8 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
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#' @param row an index, such as a row number
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#' @export
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amr_distance_from_row <- function(amr_distance, row) {
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meet_criteria(amr_distance, allow_class = c("double", "numeric"), is_finite = TRUE)
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meet_criteria(row, allow_class = c("logical", "double", "numeric"))
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meet_criteria(amr_distance, allow_class = "numeric", is_finite = TRUE)
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meet_criteria(row, allow_class = c("logical", "numeric", "integer"))
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if (is.logical(row)) {
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row <- which(row)
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}
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199
R/mic.R
199
R/mic.R
@ -154,99 +154,103 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
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}
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if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
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x
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if (!identical(levels(x), VALID_MIC_LEVELS)) {
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# from an older AMR version - just update MIC factor levels
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x <- set_clean_class(factor(as.character(x), levels = VALID_MIC_LEVELS, ordered = TRUE),
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new_class = c("mic", "ordered", "factor"))
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}
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return(x)
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}
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x.bak <- NULL
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if (is.numeric(x)) {
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x.bak <- format(x, scientific = FALSE)
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# MICs never have more than 9 decimals, so:
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x <- format(round(x, 9), scientific = FALSE)
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} else {
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x.bak <- NULL
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if (is.numeric(x)) {
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x.bak <- format(x, scientific = FALSE)
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# MICs never have more than 9 decimals, so:
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x <- format(round(x, 9), scientific = FALSE)
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} else {
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x <- as.character(unlist(x))
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}
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if (isTRUE(na.rm)) {
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x <- x[!is.na(x)]
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}
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x <- trimws2(x)
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x[x == ""] <- NA
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if (is.null(x.bak)) {
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x.bak <- x
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}
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# comma to period
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x <- gsub(",", ".", x, fixed = TRUE)
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# transform scientific notation
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x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"])
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# transform Unicode for >= and <=
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x <- gsub("\u2264", "<=", x, fixed = TRUE)
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x <- gsub("\u2265", ">=", x, fixed = TRUE)
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# remove other invalid characters
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x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE)
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# remove space between operator and number ("<= 0.002" -> "<=0.002")
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x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
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# transform => to >= and =< to <=
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x <- gsub("=<", "<=", x, fixed = TRUE)
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x <- gsub("=>", ">=", x, fixed = TRUE)
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# dots without a leading zero must start with 0
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x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
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# values like "<=0.2560.512" should be 0.512
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x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
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# remove ending .0
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x <- gsub("[.]+0$", "", x, perl = TRUE)
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# remove all after last digit
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x <- gsub("[^0-9]+$", "", x, perl = TRUE)
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# keep only one zero before dot
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x <- gsub("0+[.]", "0.", x, perl = TRUE)
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# starting 00 is probably 0.0 if there's no dot yet
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x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
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# remove last zeroes
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x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
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x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
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# remove ending .0 again
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x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
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# never end with dot
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x <- gsub("[.]$", "", x, perl = TRUE)
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# trim it
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x <- trimws2(x)
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## previously unempty values now empty - should return a warning later on
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x[x.bak != "" & x == ""] <- "invalid"
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na_before <- x[is.na(x) | x == ""] %pm>% length()
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x[!x %in% VALID_MIC_LEVELS] <- NA
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na_after <- x[is.na(x) | x == ""] %pm>% length()
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if (na_before != na_after) {
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list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
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unique() %pm>%
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sort() %pm>%
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vector_and(quotes = TRUE)
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cur_col <- get_current_column()
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warning_("in `as.mic()`: ", na_after - na_before, " result",
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ifelse(na_after - na_before > 1, "s", ""),
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ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
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" truncated (",
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round(((na_after - na_before) / length(x)) * 100),
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"%) that were invalid MICs: ",
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list_missing,
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call = FALSE
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)
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}
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if (keep_operators == "none" && !all(is.na(x))) {
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x <- gsub("[>=<]", "", x)
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} else if (keep_operators == "edges" && !all(is.na(x))) {
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dbls <- as.double(gsub("[>=<]", "", x))
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x[dbls == min(dbls, na.rm = TRUE)] <- paste0("<=", min(dbls, na.rm = TRUE))
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x[dbls == max(dbls, na.rm = TRUE)] <- paste0(">=", max(dbls, na.rm = TRUE))
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keep <- x[dbls == max(dbls, na.rm = TRUE) | dbls == min(dbls, na.rm = TRUE)]
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x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
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}
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set_clean_class(factor(x, levels = VALID_MIC_LEVELS, ordered = TRUE),
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new_class = c("mic", "ordered", "factor")
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x <- as.character(unlist(x))
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}
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if (isTRUE(na.rm)) {
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x <- x[!is.na(x)]
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}
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x <- trimws2(x)
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x[x == ""] <- NA
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if (is.null(x.bak)) {
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x.bak <- x
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}
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# comma to period
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x <- gsub(",", ".", x, fixed = TRUE)
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# transform scientific notation
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x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"])
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# transform Unicode for >= and <=
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x <- gsub("\u2264", "<=", x, fixed = TRUE)
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x <- gsub("\u2265", ">=", x, fixed = TRUE)
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# remove other invalid characters
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x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE)
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# remove space between operator and number ("<= 0.002" -> "<=0.002")
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x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
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# transform => to >= and =< to <=
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x <- gsub("=<", "<=", x, fixed = TRUE)
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x <- gsub("=>", ">=", x, fixed = TRUE)
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# dots without a leading zero must start with 0
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x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
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# values like "<=0.2560.512" should be 0.512
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x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
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# remove ending .0
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x <- gsub("[.]+0$", "", x, perl = TRUE)
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# remove all after last digit
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x <- gsub("[^0-9]+$", "", x, perl = TRUE)
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# keep only one zero before dot
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x <- gsub("0+[.]", "0.", x, perl = TRUE)
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# starting 00 is probably 0.0 if there's no dot yet
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x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
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# remove last zeroes
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x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
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x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
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# remove ending .0 again
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x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
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# never end with dot
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x <- gsub("[.]$", "", x, perl = TRUE)
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# trim it
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x <- trimws2(x)
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## previously unempty values now empty - should return a warning later on
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x[x.bak != "" & x == ""] <- "invalid"
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na_before <- x[is.na(x) | x == ""] %pm>% length()
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x[!x %in% VALID_MIC_LEVELS] <- NA
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na_after <- x[is.na(x) | x == ""] %pm>% length()
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if (na_before != na_after) {
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list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
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unique() %pm>%
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sort() %pm>%
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vector_and(quotes = TRUE)
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cur_col <- get_current_column()
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warning_("in `as.mic()`: ", na_after - na_before, " result",
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ifelse(na_after - na_before > 1, "s", ""),
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ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
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" truncated (",
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round(((na_after - na_before) / length(x)) * 100),
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"%) that were invalid MICs: ",
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list_missing,
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call = FALSE
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)
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}
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if (keep_operators == "none" && !all(is.na(x))) {
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x <- gsub("[>=<]", "", x)
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} else if (keep_operators == "edges" && !all(is.na(x))) {
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dbls <- as.double(gsub("[>=<]", "", x))
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x[dbls == min(dbls, na.rm = TRUE)] <- paste0("<=", min(dbls, na.rm = TRUE))
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x[dbls == max(dbls, na.rm = TRUE)] <- paste0(">=", max(dbls, na.rm = TRUE))
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keep <- x[dbls == max(dbls, na.rm = TRUE) | dbls == min(dbls, na.rm = TRUE)]
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x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
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}
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set_clean_class(factor(x, levels = VALID_MIC_LEVELS, ordered = TRUE),
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new_class = c("mic", "ordered", "factor"))
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}
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#' @rdname as.mic
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@ -375,7 +379,7 @@ type_sum.mic <- function(x, ...) {
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#' @noRd
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print.mic <- function(x, ...) {
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cat("Class 'mic'",
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ifelse(length(levels(x)) < length(VALID_MIC_LEVELS), font_red(" with dropped levels"), ""),
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ifelse(!identical(levels(x), VALID_MIC_LEVELS), font_red(" with outdated structure - convert with `as.mic()` to update"), ""),
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"\n",
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sep = ""
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)
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@ -533,12 +537,23 @@ Math.mic <- function(x, ...) {
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#' @export
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Ops.mic <- function(e1, e2) {
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e1_chr <- as.character(e1)
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e2_chr <- character(0)
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e1 <- as.double(e1)
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if (!missing(e2)) {
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# when e1 is `!`, e2 is missing
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e2_chr <- as.character(e2)
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e2 <- as.double(e2)
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}
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# set class to numeric, because otherwise NextMethod will be factor (since mic is a factor)
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if (as.character(.Generic) %in% c("<", "<=", "==", "!=", ">", ">=")) {
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# make sure that <0.002 is lower than 0.002
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# and that >32 is higher than 32, but equal to >=32
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e1[e1_chr %like% "<" & e1_chr %unlike% "="] <- e1[e1_chr %like% "<" & e1_chr %unlike% "="] - 0.000001
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e1[e1_chr %like% ">" & e1_chr %unlike% "="] <- e1[e1_chr %like% ">" & e1_chr %unlike% "="] + 0.000001
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e2[e2_chr %like% "<" & e2_chr %unlike% "="] <- e2[e2_chr %like% "<" & e2_chr %unlike% "="] - 0.000001
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e2[e2_chr %like% ">" & e2_chr %unlike% "="] <- e2[e2_chr %like% ">" & e2_chr %unlike% "="] + 0.000001
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}
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# set .Class to numeric, because otherwise NextMethod will be factor (since mic is a factor)
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.Class <- class(e1)
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NextMethod(.Generic)
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}
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@ -294,7 +294,7 @@ sir_confidence_interval <- function(...,
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# this applies the Clopper-Pearson method
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out <- stats::binom.test(x = x, n = n, conf.level = confidence_level)$conf.int
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out <- set_clean_class(out, "double")
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out <- set_clean_class(out, "numeric")
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if (side %in% c("left", "l", "lower", "lowest", "less", "min")) {
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out <- out[1]
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4
R/sir.R
4
R/sir.R
@ -29,7 +29,7 @@
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#' Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data
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#'
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#' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] with levels `S < I < R`.
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#' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor].
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#'
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#' Currently breakpoints are available:
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#' - For **clinical microbiology** from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
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@ -326,7 +326,7 @@ as.sir.default <- function(x, ...) {
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x.bak <- x
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x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
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if (inherits(x.bak, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
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if (inherits(x.bak, c("numeric", "integer")) && all(x %in% c(1:3, NA))) {
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# support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
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lbls <- attributes(x.bak)$labels
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if (!is.null(lbls) && all(c("S", "I", "R") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
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16
R/vctrs.R
16
R/vctrs.R
@ -102,6 +102,12 @@ vec_cast.mo.character <- function(x, to, ...) {
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}
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# S3: disk ----
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vec_ptype_full.disk <- function(x, ...) {
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"disk"
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}
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vec_ptype_abbr.disk <- function(x, ...) {
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"dsk"
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}
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vec_ptype2.disk.default <- function (x, y, ..., x_arg = "", y_arg = "") {
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x
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}
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@ -129,10 +135,16 @@ vec_cast.disk.character <- function(x, to, ...) {
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# S3: mic ----
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vec_ptype2.mic.default <- function (x, y, ..., x_arg = "", y_arg = "") {
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x
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# this will make sure that currently implemented MIC levels are returned
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as.mic(x)
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}
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vec_ptype2.mic.mic <- function(x, y, ...) {
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x
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# this will make sure that currently implemented MIC levels are returned
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as.mic(x)
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}
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vec_cast.mic.mic <- function(x, to, ...) {
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# this will make sure that currently implemented MIC levels are returned
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as.mic(x)
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}
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vec_cast.character.mic <- function(x, to, ...) {
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as.character(x)
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4
R/zzz.R
4
R/zzz.R
@ -106,7 +106,6 @@ if (pkg_is_available("cli")) {
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s3_register("pillar::type_sum", "mo")
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s3_register("pillar::type_sum", "sir")
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s3_register("pillar::type_sum", "mic")
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s3_register("pillar::type_sum", "disk")
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# Support for frequency tables from the cleaner package
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s3_register("cleaner::freq", "mo")
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s3_register("cleaner::freq", "sir")
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@ -156,6 +155,8 @@ if (pkg_is_available("cli")) {
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s3_register("vctrs::vec_cast", "character.mo")
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s3_register("vctrs::vec_cast", "mo.character")
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# S3: disk
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s3_register("vctrs::vec_ptype_full", "disk") # returns "disk"
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s3_register("vctrs::vec_ptype_abbr", "disk") # returns "dsk"
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s3_register("vctrs::vec_ptype2", "disk.default")
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s3_register("vctrs::vec_ptype2", "disk.disk")
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s3_register("vctrs::vec_cast", "integer.disk")
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@ -173,6 +174,7 @@ if (pkg_is_available("cli")) {
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s3_register("vctrs::vec_cast", "mic.character")
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s3_register("vctrs::vec_cast", "mic.double")
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s3_register("vctrs::vec_cast", "mic.integer")
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s3_register("vctrs::vec_cast", "mic.mic")
|
||||
s3_register("vctrs::vec_math", "mic")
|
||||
s3_register("vctrs::vec_arith", "mic")
|
||||
# S3: sir
|
||||
|
||||
Reference in New Issue
Block a user