mirror of https://github.com/msberends/AMR.git
(v0.8.0.9012) mdro improvement
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Package: AMR
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Version: 0.8.0.9011
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Date: 2019-11-04
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Version: 0.8.0.9012
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Date: 2019-11-05
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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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@ -1,10 +1,10 @@
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# AMR 0.8.0.9011
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<small>Last updated: 04-Nov-2019</small>
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# AMR 0.8.0.9012
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<small>Last updated: 05-Nov-2019</small>
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### New
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* Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012).
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* This is now the new default guideline for the `mdro()` function
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* The new Verbose mode (`mdro(...., verbose = TRUE)`) returns an informative data set where the reason for MDRO determination is given for every isolate
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* The new Verbose mode (`mdro(...., verbose = TRUE)`) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents
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### Changes
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* When running `as.rsi()` over a data set, it will now print the guideline that will be used if it is not specified by the user
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75
R/mdro.R
75
R/mdro.R
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@ -48,7 +48,7 @@
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#' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests}
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#' }
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#' @rdname mdro
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#' @importFrom dplyr %>% filter_at vars all_vars pull
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#' @importFrom dplyr %>% filter_at vars all_vars pull mutate_at
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#' @importFrom crayon blue bold italic
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#' @importFrom cleaner percentage
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#' @export
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@ -439,6 +439,15 @@ mdro <- function(x,
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cols <- cols[!ab_missing(cols)]
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cols <- cols[!is.na(cols)]
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if (length(rows) > 0 & length(cols) > 0) {
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#print(cols)
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x <<- x %>% mutate_at(vars(cols), as.rsi)
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x[rows, "columns_nonsusceptible"] <<- sapply(rows,
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function(row, group_vct = cols) {
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cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y == "R")
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paste(sort(c(unlist(strsplit(x[row, "columns_nonsusceptible", drop = TRUE], ", ")),
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names(cols_nonsus)[cols_nonsus])),
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collapse = ", ")
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})
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if (any_all == "any") {
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row_filter <- which(x[, cols] == "R")
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} else if (any_all == "all") {
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@ -449,8 +458,7 @@ mdro <- function(x,
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}
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rows <- rows[rows %in% row_filter]
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x[rows, "MDRO"] <<- to
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x[rows, "reason"] <<- paste0(any_all, " of these ", ifelse(any_all == "any", "is", "are"), " R: ",
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paste(cols, collapse = ", "))
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x[rows, "reason"] <<- paste0(any_all, " of the required antibiotics ", ifelse(any_all == "any", "is", "are"), " R")
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}
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}
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trans_tbl2 <- function(txt, rows, lst) {
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@ -460,16 +468,20 @@ mdro <- function(x,
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if (length(rows) > 0) {
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# function specific for the CMI paper of 2012 (Magiorakos et al.)
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lst_vector <- unlist(lst)[!is.na(unlist(lst))]
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x <<- x %>% mutate_at(vars(lst_vector), as.rsi)
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x[rows, "classes_in_guideline"] <<- length(lst)
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x[rows, "classes_available"] <<- sapply(rows,
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl, function(group) !all(is.na(group))))
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})
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# now the hard part - using two sapply()s for super fast results:
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# [1] run through all `rows` with sapply()
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# [2] within each row, run through all antibiotic classes with another sapply()
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# [3] determine for each antibiotic group in that row if at least 1 drug is R of I
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# [4] sum the number of TRUEs of this determination
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl, function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))))
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})
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if (verbose == TRUE) {
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x[rows, "columns_nonsusceptible"] <<- sapply(rows,
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function(row, group_vct = lst_vector) {
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cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y %in% c("I", "R"))
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paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
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})
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}
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x[rows, "classes_affected"] <<- sapply(rows,
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function(row, group_tbl = lst) {
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sum(sapply(group_tbl,
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@ -479,7 +491,7 @@ mdro <- function(x,
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}),
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na.rm = TRUE)
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})
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x[filter_at(x[rows,],
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x[filter_at(x[rows, ],
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vars(lst_vector),
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all_vars(. %in% c("R", "I")))$row_number, "classes_affected"] <<- 999
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}
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@ -496,7 +508,8 @@ mdro <- function(x,
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# add unavailable to where genus is available
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mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
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row_number = seq_len(nrow(.)),
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reason = paste0("not covered by ", toupper(guideline$code), " guideline")) %>%
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reason = paste0("not covered by ", toupper(guideline$code), " guideline"),
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columns_nonsusceptible = "") %>%
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# transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
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as.data.frame(stringsAsFactors = FALSE)
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@ -690,29 +703,30 @@ mdro <- function(x,
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x[which(x$classes_affected >= 3), "reason"] <- paste0("at least 3 classes contain R or I: ", x$classes_affected[which(x$classes_affected >= 3)],
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" out of ", x$classes_available[which(x$classes_affected >= 3)], " available classes")
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}
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# XDR (=3): all but <=2 classes affected
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x[which((x$classes_in_guideline - x$classes_affected) <= 2), "MDRO"] <- 3
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if (verbose == TRUE) {
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x[which((x$classes_in_guideline - x$classes_affected) <= 2), "reason"] <- paste0("less than 3 classes remain susceptible (", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)] - x$classes_affected[which((x$classes_in_guideline - x$classes_affected) <= 2)],
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" out of ", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)], " classes)")
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x[which(x$MDRO == 3), "reason"] <- paste0("less than 3 classes remain susceptible (", x$classes_in_guideline[which((x$classes_in_guideline - x$classes_affected) <= 2)] - x$classes_affected[which(x$MDRO == 3)],
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" out of ", x$classes_in_guideline[which(x$MDRO == 3)], " classes)")
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}
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# PDR (=4): all agents are R
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x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4
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if (verbose == TRUE) {
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x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "reason"] <- paste("all antibiotics in all", x$classes_in_guideline[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available)], "classes were tested R or I")
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x[which(x$MDRO == 4), "reason"] <- paste("all antibiotics in all", x$classes_in_guideline[which(x$MDRO == 4)], "classes were tested R or I")
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}
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# not enough classes available
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x[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes)), "MDRO"] <- -1
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x[which(x$MDRO %in% c(1, 3) & x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes)), "MDRO"] <- -1
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if (verbose == TRUE) {
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x[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes)), "reason"] <- paste0("not enough classes available: ", x$classes_available[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))],
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" instead of ", (base::floor(x$classes_in_guideline * pct_required_classes))[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))],
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" (~", percentage(pct_required_classes), " of ", x$classes_in_guideline[which(x$classes_available < base::floor(x$classes_in_guideline * pct_required_classes))], ")")
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}
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# some more info on negative results
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if (verbose == TRUE) {
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x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
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x[which(x$MDRO == -1), "reason"] <- paste0("not enough classes available: ", x$classes_available[which(x$MDRO == -1)],
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" of required ", (base::floor(x$classes_in_guideline * pct_required_classes))[which(x$MDRO == -1)],
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" (~", percentage(pct_required_classes), " of ", x$classes_in_guideline[which(x$MDRO == -1)], ")")
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}
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# add antibiotic names of resistant ones to verbose output
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}
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if (guideline$code == "eucast") {
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@ -973,6 +987,15 @@ mdro <- function(x,
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" tested isolates (", percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO))), ")\n")))
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}
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# some more info on negative results
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if (verbose == TRUE ) {
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if (guideline$code == "cmi2012") {
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x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)")
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} else {
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x[which(x$MDRO == 1), "reason"] <- "too few antibiotics are R"
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}
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}
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# Results ----
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if (guideline$code == "cmi2012") {
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if (any(x$MDRO == -1, na.rm = TRUE)) {
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@ -1008,7 +1031,9 @@ mdro <- function(x,
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x[, c("row_number",
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col_mo,
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"MDRO",
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"reason")]
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"reason",
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"columns_nonsusceptible")]
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#x
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} else {
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x$MDRO
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}
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6
R/rsi.R
6
R/rsi.R
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@ -99,6 +99,12 @@ as.rsi.default <- function(x, ...) {
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x
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} else if (identical(levels(x), c("S", "I", "R"))) {
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structure(x, class = c("rsi", "ordered", "factor"))
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} else if (identical(class(x), "integer") & all(x %in% c(1:3, NA))) {
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x[x == 1] <- "S"
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x[x == 2] <- "I"
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x[x == 3] <- "R"
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structure(.Data = factor(x, levels = c("S", "I", "R"), ordered = TRUE),
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class = c("rsi", "ordered", "factor"))
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} else {
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x <- x %>% unlist()
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -231,11 +231,11 @@
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</div>
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<div id="amr-0-8-0-9011" class="section level1">
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<div id="amr-0-8-0-9012" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-8-0-9011" class="anchor"></a>AMR 0.8.0.9011<small> Unreleased </small>
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<a href="#amr-0-8-0-9012" class="anchor"></a>AMR 0.8.0.9012<small> Unreleased </small>
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</h1>
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<p><small>Last updated: 04-Nov-2019</small></p>
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<p><small>Last updated: 05-Nov-2019</small></p>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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<a href="#new" class="anchor"></a>New</h3>
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@ -1333,7 +1333,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-8-0-9011">0.8.0.9011</a></li>
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<li><a href="#amr-0-8-0-9012">0.8.0.9012</a></li>
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<li><a href="#amr-0-8-0">0.8.0</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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@ -84,7 +84,7 @@
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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">0.8.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9012</span>
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</span>
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</div>
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@ -32,7 +32,7 @@ test_that("mdro works", {
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expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
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expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
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outcome <- mdro(example_isolates)
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outcome <- suppressWarnings(mdro(example_isolates))
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outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
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# check class
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expect_equal(outcome %>% class(), c("ordered", "factor"))
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