mirror of https://github.com/msberends/AMR.git
193 lines
8.3 KiB
R
Executable File
193 lines
8.3 KiB
R
Executable File
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Join [microorganisms] to a Data Set
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#'
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#' Join the data set [microorganisms] easily to an existing data set or to a [character] vector.
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#' @rdname join
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#' @name join
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#' @aliases join inner_join
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#' @param x existing data set to join, or [character] vector. In case of a [character] vector, the resulting [data.frame] will contain a column 'x' with these values.
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#' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (such as `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("bacteria_id" = "fullname")`)
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#' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a [character] vector of length 2.
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#' @param ... ignored, only in place to allow future extensions
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#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix.
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#'
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#' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base \R will be used.
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#' @return a [data.frame]
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#' @export
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#' @examples
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#' left_join_microorganisms(as.mo("K. pneumoniae"))
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#' left_join_microorganisms("B_KLBSL_PNMN")
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#'
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#' df <- data.frame(
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#' date = seq(
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#' from = as.Date("2018-01-01"),
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#' to = as.Date("2018-01-07"),
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#' by = 1
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#' ),
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#' bacteria = as.mo(c(
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#' "S. aureus", "MRSA", "MSSA", "STAAUR",
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#' "E. coli", "E. coli", "E. coli"
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#' )),
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#' stringsAsFactors = FALSE
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#' )
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#' colnames(df)
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#'
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#' df_joined <- left_join_microorganisms(df, "bacteria")
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#' colnames(df_joined)
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#'
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#' \donttest{
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' left_join_microorganisms() %>%
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#' colnames()
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#' }
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#' }
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inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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join_microorganisms(type = "inner_join", x = x, by = by, suffix = suffix, ...)
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}
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#' @rdname join
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#' @export
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left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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join_microorganisms(type = "left_join", x = x, by = by, suffix = suffix, ...)
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}
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#' @rdname join
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#' @export
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right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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join_microorganisms(type = "right_join", x = x, by = by, suffix = suffix, ...)
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}
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#' @rdname join
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#' @export
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full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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meet_criteria(suffix, allow_class = "character", has_length = 2)
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join_microorganisms(type = "full_join", x = x, by = by, suffix = suffix, ...)
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}
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#' @rdname join
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#' @export
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semi_join_microorganisms <- function(x, by = NULL, ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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join_microorganisms(type = "semi_join", x = x, by = by, ...)
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}
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#' @rdname join
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#' @export
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anti_join_microorganisms <- function(x, by = NULL, ...) {
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meet_criteria(x, allow_class = c("data.frame", "character"))
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meet_criteria(by, allow_class = "character", allow_NULL = TRUE)
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join_microorganisms(type = "anti_join", x = x, by = by, ...)
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}
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join_microorganisms <- function(type, x, by, suffix, ...) {
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add_MO_lookup_to_AMR_env()
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if (!is.data.frame(x)) {
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if (pkg_is_available("tibble")) {
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x <- import_fn("tibble", "tibble")(mo = x)
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} else {
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x <- data.frame(mo = x, stringsAsFactors = FALSE)
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}
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by <- "mo"
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}
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x.bak <- x
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if (is.null(by)) {
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by <- search_type_in_df(x, "mo", info = FALSE)
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if (is.null(by) && NCOL(x) == 1) {
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by <- colnames(x)[1L]
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} else {
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stop_if(is.null(by), "no column with microorganism names or codes found, set this column with `by`", call = -2)
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}
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message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
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}
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if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
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x$join.mo <- as.mo(x[, by, drop = TRUE])
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by <- c("join.mo" = "mo")
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} else {
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x[, by] <- as.mo(x[, by, drop = TRUE])
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}
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if (is.null(names(by))) {
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# will always be joined to microorganisms$mo, so add name to that
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by <- stats::setNames("mo", by)
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}
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# use dplyr if available - it's much faster than poorman alternatives
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dplyr_join <- import_fn(name = type, pkg = "dplyr", error_on_fail = FALSE)
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if (!is.null(dplyr_join)) {
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join_fn <- dplyr_join
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} else {
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# otherwise use poorman, see R/aa_helper_pm_functions.R
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join_fn <- get(paste0("pm_", type), envir = asNamespace("AMR"))
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}
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MO_df <- AMR_env$MO_lookup[, colnames(AMR::microorganisms), drop = FALSE]
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if (type %like% "full|left|right|inner") {
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joined <- join_fn(x = x, y = MO_df, by = by, suffix = suffix, ...)
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} else {
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joined <- join_fn(x = x, y = MO_df, by = by, ...)
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}
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if ("join.mo" %in% colnames(joined)) {
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if ("mo" %in% colnames(joined)) {
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ind_mo <- which(colnames(joined) %in% c("mo", "join.mo"))
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colnames(joined)[ind_mo[1L]] <- paste0("mo", suffix[1L])
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colnames(joined)[ind_mo[2L]] <- paste0("mo", suffix[2L])
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} else {
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colnames(joined)[colnames(joined) == "join.mo"] <- "mo"
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}
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}
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if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
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warning_("in `", type, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
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}
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as_original_data_class(joined, class(x.bak)) # will remove tibble groups
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}
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