mirror of
https://github.com/agdamsbo/FreesearchR.git
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feat: new cut option to simplify factors to only the top N levels
This commit is contained in:
parent
a06177481b
commit
0c2b061708
12 changed files with 337 additions and 236 deletions
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#' Extended cutting function with fall-back to the native base::cut
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#'
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#' @param x an object inheriting from class "hms"
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#' @param ... passed on
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#'
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#' @export
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#' @name cut_var
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cut_var <- function(x, ...) {
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UseMethod("cut_var")
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}
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#' @export
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#' @name cut_var
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cut_var.default <- function(x, ...) {
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base::cut(x, ...)
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}
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#' @name cut_var
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#'
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#' @return factor
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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_var(2)
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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_var("min")
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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_var(breaks = "hour")
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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_var(breaks = hms::as_hms(c("01:00:00", "03:01:20", "9:20:20")))
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#' d_t <- readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA))
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#' f <- d_t |> cut_var(2)
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#' readr::parse_time(c("01:00:20", "03:00:20", "01:20:20", "03:02:20", NA)) |> cut_var(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE)
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cut_var.hms <- function(x, breaks, ...) {
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## as_hms keeps returning warnings on tz(); ignored
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suppressWarnings({
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if (hms::is_hms(breaks)) {
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breaks <- lubridate::as_datetime(breaks)
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}
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x <- lubridate::as_datetime(x)
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out <- cut_var.POSIXt(x, breaks = breaks, ...)
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attr(out, which = "brks") <- hms::as_hms(lubridate::as_datetime(attr(out, which = "brks")))
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attr(out, which = "levels") <- as.character(hms::as_hms(lubridate::as_datetime(attr(out, which = "levels"))))
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})
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out
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}
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#' @name cut_var
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#' @param x an object inheriting from class "POSIXt" or "Date"
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#'
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#' @examples
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#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2)
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#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
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#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "month_only")
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#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%A-%H")
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#' readr::parse_datetime(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks=NULL,format = "%W")
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cut_var.POSIXt <- function(x, breaks, right = FALSE, include.lowest = TRUE, start.on.monday = TRUE, ...) {
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breaks_o <- breaks
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args <- list(...)
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# browser()
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if (is.numeric(breaks)) {
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breaks <- quantile(
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x,
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probs = seq(0, 1, 1 / breaks),
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right = right,
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include.lowest = include.lowest,
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na.rm = TRUE
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)
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}
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if ("format" %in% names(args)){
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assertthat::assert_that(is.character(args$format))
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out <- forcats::as_factor(format(x,format=args$format))
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} else if (identical(breaks, "weekday")) {
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## This is
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ds <- as.Date(1:7) |>
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(\(.x){
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sort_by(format(.x,"%A"),as.numeric(format(.x,"%w")))
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})()
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if (start.on.monday) {
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ds <- ds[c(7, 1:6)]
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}
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out <- factor(weekdays(x), levels = ds) |> forcats::fct_drop()
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} else if (identical(breaks, "month_only")) {
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## Simplest way to create a vector of all months in order
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## which will also follow the locale of the machine
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ms <- paste0("1970-", 1:12, "-01") |>
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as.Date() |>
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months()
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out <- factor(months(x), levels = ms) |> forcats::fct_drop()
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} else {
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## Doesn't really work very well for breaks other than the special character cases as right border is excluded
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out <- base::cut.POSIXt(x, breaks = breaks, right = right, ...) |> forcats::fct_drop()
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# browser()
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}
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l <- levels(out)
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if (is.numeric(breaks_o)) {
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l <- breaks
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} else if (is.character(breaks) && length(breaks) == 1 && !(identical(breaks, "weekday") | identical(breaks, "month_only"))) {
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if (include.lowest) {
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if (right) {
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l <- c(l, min(as.character(x)))
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} else {
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l <- c(l, max(as.character(x)))
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}
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}
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} else if (length(l) < length(breaks_o)) {
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l <- breaks_o
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}
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attr(out, which = "brks") <- l
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out
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}
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#' @name cut_var
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#' @param x an object inheriting from class "POSIXct"
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cut_var.POSIXct <- cut_var.POSIXt
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#' @name cut_var
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#' @param x an object inheriting from class "POSIXct"
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#'
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#' @examples
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#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(2)
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#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(breaks = "weekday")
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#' as.Date(c("1992-02-01 01:00:20", "1992-02-06 03:00:20", "1992-05-01 01:20:20", "1992-09-01 08:20:20", "1999-02-01 21:20:20", "1992-12-01 03:02:20")) |> cut_var(format = "%W")
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cut_var.Date <- function(x, breaks=NULL, start.on.monday = TRUE, ...) {
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args <- list(...)
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if ("format" %in% names(args)){
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assertthat::assert_that(is.character(args$format))
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out <- forcats::as_factor(format(x,format=args$format))
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} else if (identical(breaks, "weekday")) {
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ds <- as.Date(1:7) |>
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(\(.x){
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sort_by(format(.x,"%A"),as.numeric(format(.x,"%w")))
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})()
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if (start.on.monday) {
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ds <- ds[c(7, 1:6)]
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}
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out <- factor(weekdays(x), levels = ds) |> forcats::fct_drop()
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} else if (identical(breaks, "month_only")) {
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ms <- paste0("1970-", 1:12, "-01") |>
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as.Date() |>
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months()
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out <- factor(months(x), levels = ms) |> forcats::fct_drop()
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} else {
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## Doesn't really work very well for breaks other than the special character cases as right border is excluded
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out <- base::cut.Date(x, breaks = breaks, ...) |> forcats::fct_drop()
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# browser()
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}
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out
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}
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#' Test class
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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 factor
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#' @export
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#'
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#' @examples
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#' \dontrun{
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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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#' }
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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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#' Test is date/datetime/time
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#'
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#' @param data data
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#'
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#' @return factor
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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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cut_variable_ui <- function(id) {
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ns <- NS(id)
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tagList(
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shiny::fluidRow(
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column(
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width = 3,
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shinyWidgets::virtualSelectInput(
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inputId = ns("variable"),
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label = i18n$t("Variable to cut:"),
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choices = NULL,
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width = "100%"
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)
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),
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column(
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width = 3,
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shiny::uiOutput(ns("cut_method"))
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),
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column(
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width = 3,
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numericInput(
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inputId = ns("n_breaks"),
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label = i18n$t("Number of breaks:"),
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value = 3,
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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$t("Close intervals on the right"),
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value = TRUE
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),
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checkboxInput(
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inputId = ns("include_lowest"),
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label = i18n$t("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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toastui::datagridOutput2(outputId = ns("count")),
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actionButton(
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inputId = ns("create"),
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label = tagList(phosphoricons::ph("scissors"), i18n$t("Create factor variable")),
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class = "btn-outline-primary float-end"
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),
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tags$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, new_var_name = 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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shinyWidgets::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$variable)
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req(hasName(data, variable))
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if (is_datetime(data[[variable]])) {
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brks <- cut_var(data[[variable]],
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breaks = input$n_breaks
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)$brks
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} else {
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brks <- classInt::classIntervals(
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var = data[[variable]],
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n = input$n_breaks,
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style = "quantile"
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)$brks
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}
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if (is_datetime(data[[variable]])) {
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lower <- min(data[[variable]], na.rm = TRUE)
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} else {
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lower <- floor(min(data[[variable]], na.rm = TRUE))
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}
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if (is_datetime(data[[variable]])) {
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upper <- max(data[[variable]], na.rm = TRUE)
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} else {
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upper <- ceiling(max(data[[variable]], na.rm = TRUE))
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}
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shinyWidgets::noUiSliderInput(
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inputId = session$ns("fixed_brks"),
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label = i18n$t("Fixed breaks:"),
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min = lower,
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max = upper,
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value = brks,
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color = datamods:::get_primary_color(),
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width = "100%"
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)
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})
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output$cut_method <- renderUI({
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data <- req(data_r())
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variable <- req(input$variable)
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choices <- c(
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# "fixed",
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# "quantile"
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)
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if (any(c("hms","POSIXct") %in% class(data[[variable]]))) {
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choices <- c(choices, "hour")
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} else if (any(c("POSIXt", "Date") %in% class(data[[variable]]))) {
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choices <- c(
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choices,
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"day",
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"weekday",
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"week",
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# "week_only",
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"month",
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"month_only",
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"quarter",
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"year"
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)
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} else {
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choices <- c(
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choices,
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"fixed",
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"quantile",
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# "sd",
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# "equal",
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# "pretty",
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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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)
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}
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choices <- unique(choices)
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shinyWidgets::virtualSelectInput(
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inputId = session$ns("method"),
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label = i18n$t("Method:"),
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choices = choices,
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selected = NULL,
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width = "100%"
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)
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})
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breaks_r <- reactive({
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data <- req(data_r())
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variable <- req(input$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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if (any(c("hms", "POSIXct") %in% class(data[[variable]]))) {
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# cut.POSIXct <- cut.POSIXt
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f <- cut_var(data[[variable]], breaks = input$fixed_brks)
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list(var = f, brks = levels(f))
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} else {
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classInt::classIntervals(
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var = as.numeric(data[[variable]]),
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n = input$n_breaks,
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style = "fixed",
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fixedBreaks = input$fixed_brks
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)
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}
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} else if (input$method == "quantile") {
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req(input$fixed_brks)
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if (any(c("hms", "POSIXt") %in% class(data[[variable]]))) {
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# cut.POSIXct <- cut.POSIXt
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f <- cut_var(data[[variable]], breaks = input$n_breaks)
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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$n_breaks,
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style = "quantile"
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)
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}
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} else if (input$method %in% c(
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"day",
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"weekday",
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"week",
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"month",
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"month_only",
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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_var(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")) {
|
||||
# To enable datetime cutting
|
||||
# cut.POSIXct <- cut.POSIXt
|
||||
f <- cut_var(data[[variable]], breaks = "hour")
|
||||
list(var = f, brks = levels(f))
|
||||
# } else if (input$method %in% c("week_only")) {
|
||||
# # As a proof of concept a single option to use "format" parameter
|
||||
# # https://www.stat.berkeley.edu/~s133/dates.html
|
||||
# f <- cut_var(data[[variable]], format = "%W")
|
||||
# list(var = f, brks = levels(f))
|
||||
} else {
|
||||
classInt::classIntervals(
|
||||
var = as.numeric(data[[variable]]),
|
||||
n = input$n_breaks,
|
||||
style = input$method
|
||||
)
|
||||
}
|
||||
})
|
||||
|
||||
output$plot <- renderPlot({
|
||||
data <- req(data_r())
|
||||
variable <- req(input$variable)
|
||||
plot_histogram(data, variable, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
|
||||
# plot_histogram(data = breaks_r()$var, breaks = breaks_r()$brks, color = datamods:::get_primary_color())
|
||||
})
|
||||
|
||||
|
||||
data_cutted_r <- reactive({
|
||||
req(input$method)
|
||||
data <- req(data_r())
|
||||
variable <- req(input$variable)
|
||||
|
||||
|
||||
if (input$method %in% c("day", "weekday", "week", "month", "month_only", "quarter", "year", "hour")) {
|
||||
breaks <- input$method
|
||||
} else {
|
||||
breaks <- breaks_r()$brks
|
||||
}
|
||||
|
||||
parameters <- list(
|
||||
x = data[[variable]],
|
||||
breaks = breaks,
|
||||
include.lowest = input$include_lowest,
|
||||
right = input$right
|
||||
)
|
||||
|
||||
new_variable <- tryCatch(
|
||||
{
|
||||
rlang::exec(cut_var, !!!parameters)
|
||||
},
|
||||
error = function(err) {
|
||||
showNotification(paste0("We encountered the following error creating your report: ", err), type = "err")
|
||||
}
|
||||
)
|
||||
|
||||
# new_variable <- do.call(
|
||||
# cut,
|
||||
# parameters
|
||||
# )
|
||||
|
||||
|
||||
data <- append_column(data, column = new_variable, name = paste0(variable, "_cut"), index = "right")
|
||||
|
||||
# setNames(paste0(variable, "_cut"))
|
||||
#
|
||||
# data <- dplyr::bind_cols(data, new_variable, .name_repair = "unique_quiet")
|
||||
|
||||
# rv$new_var_name <- names(data)[length(data)]
|
||||
# browser()
|
||||
|
||||
# browser()
|
||||
code <- rlang::call2(
|
||||
"append_column",
|
||||
!!!list(
|
||||
column = rlang::call2("cut_var",
|
||||
!!!modifyList(parameters, list(x = as.symbol(paste0("data$", variable)))),
|
||||
.ns = "FreesearchR"),
|
||||
name = paste0(variable, "_cut"), index = "right"
|
||||
),
|
||||
.ns = "FreesearchR"
|
||||
)
|
||||
attr(data, "code") <- code
|
||||
|
||||
# attr(data, "code") <- Reduce(
|
||||
# f = function(x, y) expr(!!x %>% !!y),
|
||||
# x = c(attr(data, "code"), code)
|
||||
# )
|
||||
data
|
||||
})
|
||||
|
||||
output$count <- toastui::renderDatagrid2({
|
||||
# shiny::req(rv$new_var_name)
|
||||
data <- req(data_cutted_r())
|
||||
# variable <- req(input$variable)
|
||||
count_data <- as.data.frame(
|
||||
table(
|
||||
breaks = data[[length(data)]],
|
||||
useNA = "ifany"
|
||||
),
|
||||
responseName = "count"
|
||||
)
|
||||
gridTheme <- getOption("datagrid.theme")
|
||||
if (length(gridTheme) < 1) {
|
||||
datamods:::apply_grid_theme()
|
||||
}
|
||||
on.exit(toastui::reset_grid_theme())
|
||||
grid <- toastui::datagrid(
|
||||
data = count_data,
|
||||
colwidths = "guess",
|
||||
theme = "default",
|
||||
bodyHeight = "auto"
|
||||
)
|
||||
grid <- toastui::grid_columns(grid, className = "font-monospace")
|
||||
toastui::grid_colorbar(
|
||||
grid,
|
||||
column = "count",
|
||||
label_outside = TRUE,
|
||||
label_width = "40px",
|
||||
bar_bg = datamods:::get_primary_color(),
|
||||
from = c(0, max(count_data$count) + 1)
|
||||
)
|
||||
})
|
||||
|
||||
data_returned_r <- observeEvent(input$create, {
|
||||
rv$data <- data_cutted_r()
|
||||
})
|
||||
return(reactive(rv$data))
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
|
||||
#' @inheritParams shiny::modalDialog
|
||||
#' @export
|
||||
#'
|
||||
#' @importFrom shiny showModal modalDialog textInput
|
||||
#' @importFrom htmltools tagList
|
||||
#'
|
||||
#' @rdname cut-variable
|
||||
modal_cut_variable <- function(id,
|
||||
title = i18n$t("Convert Numeric to Factor"),
|
||||
easyClose = TRUE,
|
||||
size = "l",
|
||||
footer = NULL) {
|
||||
ns <- NS(id)
|
||||
showModal(modalDialog(
|
||||
title = tagList(title, datamods:::button_close_modal()),
|
||||
cut_variable_ui(id),
|
||||
tags$div(
|
||||
style = "display: none;",
|
||||
textInput(inputId = ns("hidden"), label = NULL, value = datamods:::genId())
|
||||
),
|
||||
easyClose = easyClose,
|
||||
size = size,
|
||||
footer = footer
|
||||
))
|
||||
}
|
||||
|
||||
|
||||
#' @importFrom graphics abline axis hist par plot.new plot.window
|
||||
plot_histogram <- function(data, column=NULL, bins = 30, breaks = NULL, color = "#112466") {
|
||||
if (is.vector(data)){
|
||||
x <- data
|
||||
} else {
|
||||
x <- data[[column]]
|
||||
|
||||
}
|
||||
x <- as.numeric(x)
|
||||
op <- par(mar = rep(1.5, 4))
|
||||
on.exit(par(op))
|
||||
plot.new()
|
||||
plot.window(xlim = range(pretty(x)), ylim = range(pretty(hist(x, breaks = bins, plot = FALSE)$counts)))
|
||||
abline(v = pretty(x), col = "#D8D8D8")
|
||||
abline(h = pretty(hist(x, breaks = bins, plot = FALSE)$counts), col = "#D8D8D8")
|
||||
hist(x, breaks = bins, xlim = range(pretty(x)), xaxs = "i", yaxs = "i", col = color, add = TRUE)
|
||||
axis(side = 1, at = pretty(x), pos = 0)
|
||||
axis(side = 2, at = pretty(hist(x, breaks = bins, plot = FALSE)$counts), pos = min(pretty(x)))
|
||||
abline(v = breaks, col = "#FFFFFF", lty = 1, lwd = 1.5)
|
||||
abline(v = breaks, col = "#2E2E2E", lty = 2, lwd = 1.5)
|
||||
}
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue