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7 changed files with 1070 additions and 200 deletions
458
R/cut-variable-dates.R
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458
R/cut-variable-dates.R
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library(datamods)
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library(toastui)
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library(phosphoricons)
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library(rlang)
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# x <- lubridate::as_datetime(seq(1,1000000,2000), origin = "2000-12-31")
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# class(x)
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#
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# lubridate::hms(c("01:00:20"))
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#
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# int_x <- classInt::classIntervals(lubridate::as_datetime(seq(1,1000000,2000), origin = "2000-12-31"), 4, style = "quantile")
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# classInt::classIntervals(readr::parse_time(c("01:00:20","03:00:20","01:20:20","03:02:20")), 2, style = "quantile")
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# int_x|> dput()
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#
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# library(hms)
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#
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# ?cut.POSIXt
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#
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# x <- readr::parse_time(c("01:00:20","03:00:20","01:20:20","03:02:20"))
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# cut(x)
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#' Title
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#'
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#' @param x an object inheriting from class "hms"
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#' @param breaks Can be "hour" or "dn"
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#' @param ... passed on
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#'
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#' @return
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#' @export
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#'
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#' @examples
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#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "08:20:20", "21:20:20", "03:02:20")) |> cut(2)
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#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) |>
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#' cut() |>
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#' dput()
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cut.hms <- function(x, breaks = "hour", ...) {
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browser()
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# For now, this function will allways try to cut to hours
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# This limits time cutting to only do hour-binning, no matter the
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if (length(breaks) != 1) {
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if ("hms" %in% class(breaks)) {
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} else {
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breaks <- "hour"
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}
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}
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if (!breaks %in% c("hour", "dn")) {
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if (is.numeric(breaks)) {
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breaks_n <- quantile(x, probs = seq(0, 1, 1 / breaks))
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## Use lapply or similar to go through levels two at a time
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} else {
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breaks <- "hour"
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}
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}
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ch <- strsplit(as.character(x), ":") |>
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lapply(\(.x).x[[1]]) |>
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unlist()
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num <- as.numeric(ch)
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if (breaks == "hour") {
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splitter <- match(
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num,
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levels(factor(num))
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)
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} else if (breaks == "dn") {
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splitter <- num %in% 8:20 + 1
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} else {
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stop("No other methods than hour cut is implemented.")
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}
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labs <- split(x, splitter) |>
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purrr::imap(\(.x, .i){
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if (breaks == "dn" && .i == 1) {
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h <- hms::as_hms(hms::hms(hours = 24) - abs(.x - hms::hms(hours = 8)))
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paste0("[", .x[match(sort(h)[1], h)], ",", .x[match(sort(h)[length(h)], h)], "]")
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} else {
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.x <- sort(.x)
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paste0("[", .x[1], ",", .x[length(.x)], "]")
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}
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}) |>
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unlist()
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structure(match(num, l), levels = labs, class = "factor")
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}
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#' Title
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#'
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#' @param data data
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#' @param class.vec vector of class names to test
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#'
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#' @return
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#' @export
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#'
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#' @examples
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#' vapply(REDCapCAST::redcapcast_data, \(.x){
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#' is_any_class(.x, c("hms", "Date", "POSIXct", "POSIXt"))
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#' }, logical(1))
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is_any_class <- function(data, class.vec) {
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any(class(data) %in% class.vec)
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}
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#' Title
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#'
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#' @param data data
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#'
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#' @return
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#' @export
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#'
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#' @examples
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#' vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1))
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is_datetime <- function(data) {
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is_any_class(data, class.vec = c("hms", "Date", "POSIXct", "POSIXt"))
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}
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#' @title Module to Convert Numeric to Factor
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#'
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#' @description
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#' This module contain an interface to cut a numeric into several intervals.
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#'
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#'
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#' @param id Module ID.
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#'
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#' @return A [shiny::reactive()] function returning the data.
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#' @export
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#'
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#' @importFrom shiny NS fluidRow column numericInput checkboxInput checkboxInput plotOutput uiOutput
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#' @importFrom shinyWidgets virtualSelectInput
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#' @importFrom toastui datagridOutput2
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#'
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#' @name cut-variable
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#'
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#' @example examples/cut_variable.R
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cut_variable_ui <- function(id) {
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ns <- NS(id)
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tagList(
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fluidRow(
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column(
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width = 3,
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virtualSelectInput(
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inputId = ns("variable"),
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label = i18n("Variable to cut:"),
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choices = NULL,
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width = "100%"
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)
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),
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column(
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width = 3,
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virtualSelectInput(
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inputId = ns("method"),
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label = i18n("Method:"),
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choices = c(
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"fixed",
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# "sd",
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# "equal",
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# "pretty",
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"quantile",
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# "kmeans",
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# "hclust",
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# "bclust",
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# "fisher",
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# "jenks",
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"headtails",
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# "maximum",
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# "box",
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"hour",
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"day",
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"week",
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"month",
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"quarter",
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"year"
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),
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selected = "quantile",
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width = "100%"
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)
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),
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column(
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width = 3,
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numericInput(
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inputId = ns("n_breaks"),
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label = i18n("Number of breaks:"),
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value = 5,
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min = 2,
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max = 12,
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width = "100%"
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)
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),
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column(
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width = 3,
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checkboxInput(
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inputId = ns("right"),
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label = i18n("Close intervals on the right"),
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value = TRUE
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),
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checkboxInput(
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inputId = ns("include_lowest"),
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label = i18n("Include lowest value"),
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value = TRUE
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)
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)
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),
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conditionalPanel(
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condition = "input.method == 'fixed'",
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ns = ns,
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uiOutput(outputId = ns("slider_fixed"))
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),
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plotOutput(outputId = ns("plot"), width = "100%", height = "270px"),
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datagridOutput2(outputId = ns("count")),
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actionButton(
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inputId = ns("create"),
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label = tagList(ph("scissors"), i18n("Create factor variable")),
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class = "btn-outline-primary float-end"
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),
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tags$div(class = "clearfix")
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)
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}
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#' @param data_r A [shiny::reactive()] function returning a `data.frame`.
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#'
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#' @export
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#'
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#' @importFrom shiny moduleServer observeEvent reactive req bindEvent renderPlot
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#' @importFrom shinyWidgets updateVirtualSelect noUiSliderInput
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#' @importFrom toastui renderDatagrid2 datagrid grid_colorbar
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#' @importFrom rlang %||% call2 set_names expr syms
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#' @importFrom classInt classIntervals
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#'
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#' @rdname cut-variable
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cut_variable_server <- function(id, data_r = reactive(NULL)) {
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moduleServer(
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id,
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function(input, output, session) {
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rv <- reactiveValues(data = NULL)
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bindEvent(observe({
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data <- data_r()
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rv$data <- data
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vars_num <- vapply(data, \(.x){
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is.numeric(.x) || is_datetime(.x)
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}, logical(1))
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vars_num <- names(vars_num)[vars_num]
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updateVirtualSelect(
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inputId = "variable",
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choices = vars_num,
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selected = if (isTruthy(input$variable)) input$variable else vars_num[1]
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)
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}), data_r(), input$hidden)
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output$slider_fixed <- renderUI({
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data <- req(data_r())
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variable <- req(input$variable)
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req(hasName(data, variable))
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noUiSliderInput(
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inputId = session$ns("fixed_brks"),
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label = i18n("Fixed breaks:"),
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min = floor(min(data[[variable]], na.rm = TRUE)),
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max = ceiling(max(data[[variable]], na.rm = TRUE)),
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value = classInt::classIntervals(
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var = as.numeric(data[[variable]]),
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n = input$n_breaks,
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style = "quantile"
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)$brks,
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color = datamods:::get_primary_color(),
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width = "100%"
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)
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})
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breaks_r <- reactive({
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data <- req(data_r())
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variable <- req(input$variable)
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req(hasName(data, variable))
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req(input$n_breaks, input$method)
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if (input$method == "fixed") {
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req(input$fixed_brks)
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classInt::classIntervals(
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var = as.numeric(data[[variable]]),
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n = input$n_breaks,
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style = "fixed",
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fixedBreaks = input$fixed_brks
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)
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} else if (input$method %in% c(
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"day",
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"week",
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"month",
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"quarter",
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"year"
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)) {
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# To enable datetime cutting
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cut.POSIXct <- cut.POSIXt
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f <- cut(data[[variable]], breaks = input$method)
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list(var = f, brks = levels(f))
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} else if (input$method %in% c("hour")) {
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# To enable datetime cutting
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cut.POSIXct <- cut.POSIXt
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f <- cut(data[[variable]], breaks = "hour")
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list(var = f, brks = levels(f))
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} else {
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classInt::classIntervals(
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var = as.numeric(data[[variable]]),
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n = input$n_breaks,
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style = input$method
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)
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}
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})
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output$plot <- renderPlot({
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data <- req(data_r())
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variable <- req(input$variable)
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plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
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})
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data_cutted_r <- reactive({
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data <- req(data_r())
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variable <- req(input$variable)
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data[[paste0(variable, "_cut")]] <- cut(
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x = data[[variable]],
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breaks = if (input$method %in% c("day","week","month","quarter","year","hour")) input$method else breaks_r()$brks,
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include.lowest = input$include_lowest,
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right = input$right
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)
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code <- call2(
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"mutate",
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!!!set_names(
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list(
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expr(cut(
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!!!syms(list(x = variable)),
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!!!list(breaks = breaks_r()$brks, include.lowest = input$include_lowest, right = input$right)
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))
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),
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paste0(variable, "_cut")
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)
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)
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attr(data, "code") <- Reduce(
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f = function(x, y) expr(!!x %>% !!y),
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x = c(attr(data, "code"), code)
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)
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data
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})
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output$count <- renderDatagrid2({
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data <- req(data_cutted_r())
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variable <- req(input$variable)
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count_data <- as.data.frame(
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table(
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breaks = data[[paste0(variable, "_cut")]],
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useNA = "ifany"
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),
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responseName = "count"
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)
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gridTheme <- getOption("datagrid.theme")
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if (length(gridTheme) < 1) {
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datamods:::apply_grid_theme()
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}
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on.exit(toastui::reset_grid_theme())
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grid <- datagrid(
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data = count_data,
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colwidths = "guess",
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theme = "default",
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bodyHeight = "auto"
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)
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grid <- toastui::grid_columns(grid, className = "font-monospace")
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grid_colorbar(
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grid,
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column = "count",
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label_outside = TRUE,
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label_width = "40px",
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bar_bg = datamods:::get_primary_color(),
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from = c(0, max(count_data$count) + 1)
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)
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})
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data_returned_r <- observeEvent(input$create, {
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rv$data <- data_cutted_r()
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})
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return(reactive(rv$data))
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}
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)
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}
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#' @inheritParams shiny::modalDialog
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#' @export
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#'
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#' @importFrom shiny showModal modalDialog textInput
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#' @importFrom htmltools tagList
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#'
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#' @rdname cut-variable
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modal_cut_variable <- function(id,
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title = i18n("Convert Numeric to Factor"),
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easyClose = TRUE,
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size = "l",
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footer = NULL) {
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ns <- NS(id)
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showModal(modalDialog(
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title = tagList(title, datamods:::button_close_modal()),
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cut_variable_ui(id),
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tags$div(
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style = "display: none;",
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textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId())
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),
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easyClose = easyClose,
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size = size,
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footer = footer
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))
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}
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#' @inheritParams shinyWidgets::WinBox
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#' @export
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#'
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#' @importFrom shinyWidgets WinBox wbOptions wbControls
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#' @importFrom htmltools tagList
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#' @rdname cut-variable
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winbox_cut_variable <- function(id,
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title = i18n("Convert Numeric to Factor"),
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options = shinyWidgets::wbOptions(),
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controls = shinyWidgets::wbControls()) {
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ns <- NS(id)
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WinBox(
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title = title,
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ui = tagList(
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cut_variable_ui(id),
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tags$div(
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style = "display: none;",
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textInput(inputId = ns("hidden"), label = NULL, value = genId())
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)
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),
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options = modifyList(
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shinyWidgets::wbOptions(height = "750px", modal = TRUE),
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options
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),
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controls = controls,
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auto_height = FALSE
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)
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}
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#' @importFrom graphics abline axis hist par plot.new plot.window
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plot_histogram <- function(data, column, bins = 30, breaks = NULL, color = "#112466") {
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x <- data[[column]]
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x <- as.numeric(x)
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op <- par(mar = rep(1.5, 4))
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on.exit(par(op))
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plot.new()
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plot.window(xlim = range(pretty(x)), ylim = range(pretty(hist(x, breaks = bins, plot = FALSE)$counts)))
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abline(v = pretty(x), col = "#D8D8D8")
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abline(h = pretty(hist(x, breaks = bins, plot = FALSE)$counts), col = "#D8D8D8")
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hist(x, breaks = bins, xlim = range(pretty(x)), xaxs = "i", yaxs = "i", col = color, add = TRUE)
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axis(side = 1, at = pretty(x), pos = 0)
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axis(side = 2, at = pretty(hist(x, breaks = bins, plot = FALSE)$counts), pos = min(pretty(x)))
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abline(v = breaks, col = "#FFFFFF", lty = 1, lwd = 1.5)
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abline(v = breaks, col = "#2E2E2E", lty = 2, lwd = 1.5)
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}
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