mirror of https://github.com/msberends/AMR.git
(v1.2.0.9016) fix in rsi_calc()
This commit is contained in:
parent
033ca49817
commit
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.2.0.9015
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Date: 2020-06-25
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Version: 1.2.0.9016
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Date: 2020-06-26
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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6
NEWS.md
6
NEWS.md
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@ -1,5 +1,5 @@
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# AMR 1.2.0.9015
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## <small>Last updated: 25-Jun-2020</small>
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# AMR 1.2.0.9016
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## <small>Last updated: 26-Jun-2020</small>
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### New
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* Function `ab_from_text()` to retrieve antimicrobial drugs from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally:
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@ -31,7 +31,7 @@
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* Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set
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### Changed
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* Fixed a bug for using `susceptibility` or `resistance()` outside `summarise()`
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* Using unexisting columns in all `count_*()`, `proportion_*()`, `susceptibility()` and `resistance()` functions wil now return an error instead of dropping them silently
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* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
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* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
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* Fixed a bug where `as.ab()` would return an error on invalid input values
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@ -202,33 +202,33 @@ import_fn <- function(name, pkg) {
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}
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stop_if <- function(expr, ..., call = TRUE) {
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msg <- paste0(c(...), collapse = "")
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if (!isFALSE(call)) {
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if (isTRUE(call)) {
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call <- as.character(sys.call(-1)[1])
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} else {
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# so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
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call <- as.character(sys.call(call)[1])
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}
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msg <- paste0("in ", call, "(): ", msg)
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}
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if (isTRUE(expr)) {
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msg <- paste0(c(...), collapse = "")
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if (!isFALSE(call)) {
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if (isTRUE(call)) {
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call <- as.character(sys.call(-1)[1])
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} else {
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# so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
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call <- as.character(sys.call(call)[1])
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}
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msg <- paste0("in ", call, "(): ", msg)
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}
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stop(msg, call. = FALSE)
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}
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}
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stop_ifnot <- function(expr, ..., call = TRUE) {
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msg <- paste0(c(...), collapse = "")
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if (!isFALSE(call)) {
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if (isTRUE(call)) {
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call <- as.character(sys.call(-1)[1])
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} else {
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# so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
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call <- as.character(sys.call(call)[1])
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}
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msg <- paste0("in ", call, "(): ", msg)
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}
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if (!isTRUE(expr)) {
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msg <- paste0(c(...), collapse = "")
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if (!isFALSE(call)) {
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if (isTRUE(call)) {
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call <- as.character(sys.call(-1)[1])
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} else {
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# so you can go back more than 1 call, as used in rsi_calc(), that now throws a reference to e.g. n_rsi()
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call <- as.character(sys.call(call)[1])
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}
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msg <- paste0("in ", call, "(): ", msg)
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}
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stop(msg, call. = FALSE)
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}
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}
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2
R/ab.R
2
R/ab.R
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@ -209,7 +209,7 @@ as.ab <- function(x, ...) {
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# correct for digital reading text (OCR)
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x_spelling <- gsub("[NRD]", "[NRD]", x_spelling)
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}
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# try if name starts with it
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found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
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if (length(found) > 0) {
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@ -58,12 +58,17 @@ ab_from_text <- function(text, collapse = NULL, translate_ab = "name", ...) {
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}
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text_split <- unlist(strsplit(text, "[ ;.,:/\\|-]"))
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result <- as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
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text_split[grep(to_regex(names), text_split)],
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# regular expression must not be too long, so split synonyms in two:
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text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
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text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
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...)
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result <- suppressWarnings(
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as.ab(unique(c(text_split[grep(to_regex(abbr), text_split)],
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text_split[grep(to_regex(names), text_split)],
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# regular expression must not be too long, so split synonyms in two:
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text_split[grep(to_regex(synonyms[c(1:0.5 * length(synonyms))]), text_split)],
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text_split[grep(to_regex(synonyms[c(0.5 * length(synonyms):length(synonyms))]), text_split)])),
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...))
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result <- result[!is.na(result)]
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if (length(result) == 0) {
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result <- as.ab(NA)
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}
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translate_ab <- get_translate_ab(translate_ab)
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if (!isFALSE(translate_ab)) {
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result <- ab_property(result, property = translate_ab)
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3
R/mic.R
3
R/mic.R
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@ -130,7 +130,8 @@ as.mic <- function(x, na.rm = FALSE) {
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}
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all_valid_mics <- function(x) {
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x_mic <- suppressWarnings(as.mic(x[!is.na(x)]))
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x_mic <- tryCatch(suppressWarnings(as.mic(x[!is.na(x)])),
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error = function(e) NA)
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!any(is.na(x_mic)) & !all(is.na(x))
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}
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6
R/rsi.R
6
R/rsi.R
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@ -166,10 +166,10 @@ as.rsi.default <- function(x, ...) {
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}
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}
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x <- x %>% unlist()
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x <- as.character(unlist(x))
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x.bak <- x
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na_before <- x[is.na(x) | x == ""] %>% length()
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na_before <- length(x[is.na(x) | x == ""])
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# remove all spaces
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x <- gsub(" +", "", x)
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# remove all MIC-like values: numbers, operators and periods
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@ -188,7 +188,7 @@ as.rsi.default <- function(x, ...) {
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x <- gsub("^I+$", "I", x)
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x <- gsub("^R+$", "R", x)
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x[!x %in% c("S", "I", "R")] <- NA
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na_after <- x[is.na(x) | x == ""] %>% length()
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na_after <- length(x[is.na(x) | x == ""])
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if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
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if (na_before != na_after) {
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15
R/rsi_calc.R
15
R/rsi_calc.R
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@ -48,18 +48,23 @@ rsi_calc <- function(...,
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"Please read Details in the help page (`?proportion`) as this may have a considerable impact on your analysis.", call = -2)
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ndots <- length(dots)
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if ("data.frame" %in% class(dots_df)) {
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if (is.data.frame(dots_df)) {
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# data.frame passed with other columns, like: example_isolates %>% proportion_S(AMC, GEN)
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dots <- as.character(dots)
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dots <- dots[dots != "."]
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# remove first element, it's the data.frame
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if (length(dots) == 1) {
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dots <- character(0)
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} else {
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dots <- dots[2:length(dots)]
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}
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if (length(dots) == 0 | all(dots == "df")) {
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# for complete data.frames, like example_isolates %>% select(AMC, GEN) %>% proportion_S()
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# and the old rsi function, which has "df" as name of the first parameter
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x <- dots_df
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} else if (length(dots) == 1 | all(!dots %in% colnames(dots_df))) {
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x <- dots_df
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} else {
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x <- dots_df[, dots[dots %in% colnames(dots_df)], drop = FALSE]
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dots_not_exist <- dots[!dots %in% colnames(dots_df)]
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stop_if(length(dots_not_exist) > 0, "column(s) not found: ", paste0("'", dots_not_exist, "'", collapse = ", "), call = -2)
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x <- dots_df[, dots, drop = FALSE]
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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: proportion_S(example_isolates$AMC) and example_isolates$AMC %>% proportion_S()
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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="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -229,13 +229,13 @@
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<small>Source: <a href='https://gitlab.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-1209015" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9015">
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<a href="#amr-1209015" class="anchor"></a>AMR 1.2.0.9015<small> Unreleased </small>
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<div id="amr-1209016" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9016">
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<a href="#amr-1209016" class="anchor"></a>AMR 1.2.0.9016<small> Unreleased </small>
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</h1>
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<div id="last-updated-25-jun-2020" class="section level2">
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<div id="last-updated-26-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-25-jun-2020" class="anchor"></a><small>Last updated: 25-Jun-2020</small>
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<a href="#last-updated-26-jun-2020" class="anchor"></a><small>Last updated: 26-Jun-2020</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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@ -274,8 +274,7 @@
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<h3 class="hasAnchor">
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<a href="#changed" class="anchor"></a>Changed</h3>
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<ul>
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<li>Fixed a bug for using <code>susceptibility</code> or <code><a href="../reference/proportion.html">resistance()</a></code> outside <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>
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</li>
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<li>Using unexisting columns in all <code>count_*()</code>, <code>proportion_*()</code>, <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> functions wil now return an error instead of dropping them silently</li>
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<li>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</li>
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<li>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</li>
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<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would return an error on invalid input values</li>
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-25T17:20Z
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last_built: 2020-06-26T08:20Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -82,7 +82,7 @@
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -82,7 +82,7 @@
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -82,7 +82,7 @@
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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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>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9016</span>
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</span>
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</div>
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