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(v1.6.0.9009) key_antibiotics update
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Package: AMR
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Version: 1.6.0.9008
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Version: 1.6.0.9009
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Date: 2021-04-23
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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5
NEWS.md
5
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.6.0.9008
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# AMR 1.6.0.9009
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## <small>Last updated: 23 April 2021</small>
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### New
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@ -25,6 +25,9 @@
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* Fixed an installation error on R-3.0
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* Added `info` argument to `as.mo()` to turn on/off the progress bar
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* Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error
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* Using `first_isolate()` with key antibiotics:
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* Fixed a bug in the algorithm when using `type == "points"`, that now leads to inclusion of slightly more isolates
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* Big speed improvement for `key_antibiotics_equal()` when using `type == "points"`
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# AMR 1.6.0
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@ -42,7 +42,7 @@
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#' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
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#' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, see *Details*
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#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see *Details*
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#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
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#' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
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#' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
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#' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
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#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
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@ -402,7 +402,7 @@ first_isolate <- function(x = NULL,
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type = type_param,
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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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na.rm = TRUE)
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# with key antibiotics
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x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
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x$newvar_row_index_sorted <= row.end &
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@ -286,93 +286,75 @@ key_antibiotics <- function(x = NULL,
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}
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#' @rdname key_antibiotics
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#' @param info unused - previously used to indicate whether a progress bar should print
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#' @param na.rm a [logical] to indicate whether comparison with `NA` should return `FALSE` (defaults to `TRUE` for backwards compatibility)
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#' @export
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key_antibiotics_equal <- function(y,
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z,
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type = c("keyantibiotics", "points"),
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE) {
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info = FALSE,
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na.rm = TRUE,
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...) {
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meet_criteria(y, allow_class = "character")
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meet_criteria(z, allow_class = "character")
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meet_criteria(type, allow_class = "character", has_length = c(1, 2))
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if (length(type) == 2) {
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type <- type[1L]
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}
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meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("keyantibiotics", "points"))
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meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
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meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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meet_criteria(na.rm, allow_class = "logical", has_length = 1)
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stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
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# y is active row, z is lag
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x <- y
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y <- z
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key2rsi <- function(val) {
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as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
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}
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y <- lapply(y, key2rsi)
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z <- lapply(z, key2rsi)
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type <- type[1]
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# only show progress bar on points or when at least 5000 isolates
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info_needed <- info == TRUE & (type == "points" | length(x) > 5000)
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result <- logical(length(x))
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p <- progress_ticker(length(x), print = info_needed)
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on.exit(close(p))
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for (i in seq_len(length(x))) {
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if (info_needed == TRUE) {
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p$tick()
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determine_equality <- function(a, b, type, points_threshold, ignore_I) {
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if (length(a) != length(b)) {
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# incomparable, so not equal
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return(FALSE)
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}
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# ignore NAs on both sides
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NA_ind <- which(is.na(a) | is.na(b))
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a[NA_ind] <- NA_real_
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b[NA_ind] <- NA_real_
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if (is.na(x[i])) {
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x[i] <- ""
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}
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if (is.na(y[i])) {
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y[i] <- ""
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}
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if (x[i] == y[i]) {
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result[i] <- TRUE
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} else if (nchar(x[i]) != nchar(y[i])) {
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result[i] <- FALSE
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if (type == "points") {
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# count points for every single character:
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# - no change is 0 points
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# - I <-> S|R is 0.5 point
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# - S|R <-> R|S is 1 point
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# use the levels of as.rsi (S = 1, I = 2, R = 3)
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(sum(abs(a - b), na.rm = TRUE) / 2) < points_threshold
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} else {
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x_split <- strsplit(x[i], "")[[1]]
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y_split <- strsplit(y[i], "")[[1]]
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if (type == "keyantibiotics") {
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if (ignore_I == TRUE) {
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x_split[x_split == "I"] <- "."
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y_split[y_split == "I"] <- "."
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}
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y_split[x_split == "."] <- "."
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x_split[y_split == "."] <- "."
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result[i] <- all(x_split == y_split)
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} else if (type == "points") {
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# count points for every single character:
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# - no change is 0 points
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# - I <-> S|R is 0.5 point
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# - S|R <-> R|S is 1 point
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# use the levels of as.rsi (S = 1, I = 2, R = 3)
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suppressWarnings(x_split <- x_split %pm>% as.rsi() %pm>% as.double())
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suppressWarnings(y_split <- y_split %pm>% as.rsi() %pm>% as.double())
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points <- (x_split - y_split) %pm>% abs() %pm>% sum(na.rm = TRUE) / 2
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result[i] <- points >= points_threshold
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} else {
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stop("`", type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
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if (ignore_I == TRUE) {
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ind <- which(a == 2 | b == 2) # since as.double(as.rsi("I")) == 2
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a[ind] <- NA_real_
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b[ind] <- NA_real_
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}
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all(a == b, na.rm = TRUE)
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}
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}
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out <- unlist(mapply(FUN = determine_equality,
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y,
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z,
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MoreArgs = list(type = type,
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points_threshold = points_threshold,
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ignore_I = ignore_I),
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SIMPLIFY = FALSE,
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USE.NAMES = FALSE))
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if (na.rm == FALSE) {
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out[is.na(y) | is.na(z)] <- NA
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} else {
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# NA means not equal if `na.rm == TRUE`, as per the manual
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out[is.na(y) | is.na(z)] <- FALSE
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}
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close(p)
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result
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out
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}
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4
R/rsi.R
4
R/rsi.R
@ -263,8 +263,8 @@ as.rsi.default <- function(x, ...) {
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x[x == 2] <- "I"
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x[x == 3] <- "R"
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} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R"))) {
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} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {
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if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
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# check if they are actually MICs or disks
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if (all_valid_mics(x)) {
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Binary file not shown.
@ -81,7 +81,7 @@
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</button>
|
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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</span>
|
||||
</div>
|
||||
|
||||
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@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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||||
</span>
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||||
</div>
|
||||
|
||||
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@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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||||
</span>
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||||
</div>
|
||||
|
||||
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@ -81,7 +81,7 @@
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||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
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@ -42,7 +42,7 @@
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</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
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@ -81,7 +81,7 @@
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</button>
|
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<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1609008" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9008">
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<a href="#amr-1609008" class="anchor"></a>AMR 1.6.0.9008<small> Unreleased </small>
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<div id="amr-1609009" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9009">
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<a href="#amr-1609009" class="anchor"></a>AMR 1.6.0.9009<small> Unreleased </small>
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</h1>
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<div id="last-updated-23-april-2021" class="section level2">
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<h2 class="hasAnchor">
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@ -287,6 +287,13 @@
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<li>Fixed an installation error on R-3.0</li>
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<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
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<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
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<li>Using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> with key antibiotics:
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<ul>
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<li>Fixed a bug in the algorithm when using <code>type == "points"</code>, that now leads to inclusion of slightly more isolates</li>
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<li>Big speed improvement for <code><a href="../reference/key_antibiotics.html">key_antibiotics_equal()</a></code> when using <code>type == "points"</code>
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</li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-04-23T07:52Z
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last_built: 2021-04-23T14:13Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -82,7 +82,7 @@
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||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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</span>
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||||
</div>
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@ -346,7 +346,7 @@
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</tr>
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<tr>
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<th>info</th>
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<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
|
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<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
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</tr>
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<tr>
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<th>include_unknown</th>
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@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9007</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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||||
</span>
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||||
</div>
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@ -273,7 +273,9 @@
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type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
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ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
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points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
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info <span class='op'>=</span> <span class='cn'>FALSE</span>
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info <span class='op'>=</span> <span class='cn'>FALSE</span>,
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na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
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<span class='va'>...</span>
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<span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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@ -325,7 +327,11 @@
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</tr>
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<tr>
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<th>info</th>
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<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
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<td><p>unused - previously used to indicate whether a progress bar should print</p></td>
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</tr>
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<tr>
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<th>na.rm</th>
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||||
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether comparison with <code>NA</code> should return <code>FALSE</code> (defaults to <code>TRUE</code> for backwards compatibility)</p></td>
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</tr>
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</table>
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||||
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9008</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
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||||
</span>
|
||||
</div>
|
||||
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|
||||
@ -81,7 +81,7 @@ filter_first_weighted_isolate(
|
||||
|
||||
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
|
||||
|
||||
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
|
||||
\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}
|
||||
|
||||
\item{include_unknown}{logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}
|
||||
|
||||
|
||||
@ -36,7 +36,9 @@ key_antibiotics_equal(
|
||||
type = c("keyantibiotics", "points"),
|
||||
ignore_I = TRUE,
|
||||
points_threshold = 2,
|
||||
info = FALSE
|
||||
info = FALSE,
|
||||
na.rm = TRUE,
|
||||
...
|
||||
)
|
||||
}
|
||||
\arguments{
|
||||
@ -62,7 +64,9 @@ key_antibiotics_equal(
|
||||
|
||||
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
|
||||
|
||||
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
|
||||
\item{info}{unused - previously used to indicate whether a progress bar should print}
|
||||
|
||||
\item{na.rm}{a \link{logical} to indicate whether comparison with \code{NA} should return \code{FALSE} (defaults to \code{TRUE} for backwards compatibility)}
|
||||
}
|
||||
\description{
|
||||
These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.
|
||||
|
||||
@ -50,7 +50,7 @@ test_that("first isolates work", {
|
||||
type = "keyantibiotics",
|
||||
info = TRUE),
|
||||
na.rm = TRUE)),
|
||||
1395)
|
||||
1398)
|
||||
|
||||
# when not ignoring I
|
||||
expect_equal(
|
||||
@ -65,7 +65,7 @@ test_that("first isolates work", {
|
||||
type = "keyantibiotics",
|
||||
info = TRUE),
|
||||
na.rm = TRUE)),
|
||||
1418)
|
||||
1421)
|
||||
# when using points
|
||||
expect_equal(
|
||||
suppressWarnings(
|
||||
@ -78,7 +78,7 @@ test_that("first isolates work", {
|
||||
type = "points",
|
||||
info = TRUE),
|
||||
na.rm = TRUE)),
|
||||
1398)
|
||||
1348)
|
||||
|
||||
# first non-ICU isolates
|
||||
expect_equal(
|
||||
|
||||
Loading…
Reference in New Issue
Block a user