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feat: introduction of validation alerts
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390
R/validation.R
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390
R/validation.R
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# Description of warning with text description incl metric
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# Color coded (green (OK) or yellow (WARNING))
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# option to ignore/accept warnings ### to simplify things, this is gone for now ###
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# Only show warnings based on performed analyses
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## 250825
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## Works in demo
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## Not alert is printed in app interface
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## I believe it comes down to the reactivity
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########################################################################
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############# Server and UI
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########################################################################
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#' @title Validation module
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#'
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#' @description Check that a dataset respect some validation expectations.
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#'
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#' @param id Module's ID.
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#' @param max_height Maximum height for validation results element, useful if you have many rules.
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#' @param ... Arguments passed to \code{actionButton} or \code{uiOutput} depending on display mode,
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#' you cannot use \code{inputId}/\code{outputId}, \code{label} or \code{icon} (button only).
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#'
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#' @return
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#' * UI: HTML tags that can be included in shiny's UI
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#' * Server: a \code{list} with two slots:
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#' + **status**: a \code{reactive} function returning the best status available between \code{"OK"}, \code{"Failed"} or \code{"Error"}.
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#' + **details**: a \code{reactive} function returning a \code{list} with validation details.
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#' @export
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#'
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#' @rdname validation
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#'
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#' @example examples/validation_module_demo.R
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validation_ui <- function(id, max_height = NULL, ...) {
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ns <- shiny::NS(id)
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max_height <- if (!is.null(max_height)) {
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paste0("overflow-y: auto; max-height:", htmltools::validateCssUnit(max_height), ";")
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}
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ui <- shiny::uiOutput(
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outputId = ns("results"),
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...,
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style = max_height
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)
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htmltools::tagList(
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ui, datamods:::html_dependency_datamods()
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)
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}
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#' @export
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#'
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#' @param data a \code{reactive} function returning a \code{data.frame}.
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#'
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#' @rdname validation
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#'
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validation_server <- function(id,
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data) {
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moduleServer(
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id = id,
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module = function(input, output, session) {
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valid_ui <- reactiveValues(x = NULL)
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data_r <- if (shiny::is.reactive(data)) data else shiny::reactive(data)
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# observeEvent(data_r(), {
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# to_validate <- data()
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# valid_dims <- check_data(to_validate, n_row = n_row, n_col = n_col)
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#
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# if (all(c(valid_dims$nrows, valid_dims$ncols))) {
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# valid_status <- "OK"
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# } else {
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# valid_status <- "Failed"
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# }
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#
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# valid_results <- lapply(
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# X = c("nrows", "ncols"),
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# FUN = function(x) {
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# if (is.null(valid_dims[[x]]))
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# return(NULL)
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# label <- switch(
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# x,
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# "nrows" = n_row_label,
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# "ncols" = n_col_label
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# )
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# list(
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# status = ifelse(valid_dims[[x]], "OK", "Failed"),
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# label = paste0("<b>", label, "</b>")
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# )
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# }
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# )
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shiny::observeEvent(
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data_r(),
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{
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# browser()
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to_validate <- data_r()
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if (is.reactivevalues(to_validate))
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out <- lapply(
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reactiveValuesToList(to_validate),
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make_validation_alerts) |>
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purrr::list_flatten()
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if (length(to_validate) > 0) {
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out <- make_validation_alerts(to_validate)
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}
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valid_ui$x <- tagList(out)
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}
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)
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output$results <- renderUI({
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valid_ui$x
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})
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}
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)
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}
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########################################################################
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############# Validation functions
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########################################################################
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#' Dimensions validation
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#'
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#' @param before data before
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#' @param after data after
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#' @param fun dimension function. ncol or nrow
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#'
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#' @returns data.frame
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#'
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dim_change_call <- function(before, after, fun) {
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# browser()
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if (!0 %in% c(dim(before), dim(after))) {
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n_before <- fun(before)
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n_after <- fun(after)
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n_out <- n_before - n_after
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p_after <- n_after / fun(before) * 100
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p_out <- 100 - p_after
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data.frame(
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n_before = n_before,
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n_after = n_after,
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n_out = n_out,
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p_after = p_after,
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p_out = p_out
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) |>
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dplyr::mutate(
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dplyr::across(
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dplyr::where(
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is.numeric
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),
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\(.y) round(.y, 0)
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)
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)
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} else {
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data.frame(NULL)
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}
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}
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#' Variable filter test wrapper
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#'
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#' @param before data before
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#' @param after data after
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#'
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#' @returns vector
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#'
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#' @examples
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#' vars_filter_validate(mtcars, mtcars[1:6])
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#' vars_filter_validate(mtcars, mtcars[0])
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vars_filter_validate <- function(before, after) {
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dim_change_call(before, after, ncol)
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}
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#' Observations filter test wrapper
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#'
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#' @param before data before
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#' @param after data after
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#'
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#' @returns vector
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#'
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obs_filter_validate <- function(before, after) {
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dim_change_call(before, after, nrow)
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}
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#' Validate function of missingness in data
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#'
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#' @param data data set
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#'
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#' @returns data.frame
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#' @export
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#'
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#' @examples
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#' df <- mtcars
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#' df[1,2:4] <- NA
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#' missings_validate(df)
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missings_validate <- function(data){
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if (!0 %in% dim(data)) {
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# browser()
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p_miss <- sum(is.na(data))/prod(dim(data))*100
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data.frame(
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p_miss = p_miss
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) |>
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dplyr::mutate(
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dplyr::across(
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dplyr::where(
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is.numeric
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),
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\(.y) signif(.y, 2)
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)
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)
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} else {
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data.frame(NULL)
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}
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}
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########################################################################
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############# Collected validation functions in a library-like function
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########################################################################
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#' Validation library
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#'
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#' @param name Index name
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#'
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#' @returns list
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#'
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#' @examples
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#' validation_lib()
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#' validation_lib("missings")
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validation_lib <- function(name=NULL) {
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ls <- list(
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"obs_filter" = function(x, y) {
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## Validation function for observations filter
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list(
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string = i18n$t("You removed {p_out} % of observations."),
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summary.fun = obs_filter_validate,
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summary.fun.args = list(
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before = x,
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after = y
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),
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test.fun = function(x, var, cut) {
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test.var <- x[var]
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ifelse(test.var > cut, "warning", "succes")
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},
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test.fun.args = list(var = "p_out", cut = 50)
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)
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},
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"var_filter" = function(x, y) {
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## Validation function for variables filter
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list(
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string = i18n$t("You removed {p_out} % of variables."),
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summary.fun = vars_filter_validate,
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summary.fun.args = list(
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before = x,
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after = y
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),
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test.fun = function(x, var, cut) {
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test.var <- x[var]
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ifelse(test.var > cut, "warning", "succes")
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},
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test.fun.args = list(var = "p_out", cut = 50)
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)
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},
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"missings" = function(x, y) {
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### Placeholder for missingness validation
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list(
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string = "There are {p_miss} % missing observations.",
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summary.fun = missings_validate,
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summary.fun.args = list(
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data = x
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),
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test.fun = function(x, var, cut) {
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test.var <- x[var]
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ifelse(test.var > cut, "warning", "succes")
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},
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test.fun.args = list(var = "p_miss", cut = 30)
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)
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}
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)
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if (!is.null(name)){
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name <- match.arg(name,choices = names(ls))
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ls[[name]]
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} else {
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ls
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}
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}
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########################################################################
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############# Validation creation
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########################################################################
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#' Create validation data.frame
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#'
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#' @param ls validation list
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#' @param ... magic dots
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#'
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#' @returns data.frame
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#' @export
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#'
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#' @examples
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#' i18n <- shiny.i18n::Translator$new(translation_csvs_path = here::here("inst/translations"))
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#' i18n$set_translation_language("en")
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#' df_original <- mtcars
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#' df_original[1,2:4] <- NA
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#' df_obs <- df_original |> dplyr::filter(carb==4)
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#' df_vars <- df_original[1:7]
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#' val <- purrr::map2(
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#' .x = validation_lib(),
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#' .y = list(
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#' list(x = df_original, y = df_obs),
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#' list(x = df_original, y = df_vars),
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#' list(x=df_original)),
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#' make_validation
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#' )
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#' val |> make_validation_alerts()
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#'
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#' val2 <- purrr::map2(
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#' .x = validation_lib()[2],
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#' .y = list(list(x = mtcars, y = mtcars[0])),
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#' make_validation
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#' )
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#' val2 |> make_validation_alerts()
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#'
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#' val3 <- make_validation(
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#' ls = validation_lib()[[2]],
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#' list(x = mtcars, y = mtcars[0])
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#' )
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make_validation <- function(ls, ...) {
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ls <- do.call(ls, ...)
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df <- do.call(ls$summary.fun, ls$summary.fun.args)
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if (!any(dim(df) == c(0))) {
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label <- with(df, {
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glue::glue(ls$string)
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})
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# browser()
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status <- do.call(ls$test.fun, modifyList(ls$test.fun.args, list(x = df)))
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data.frame(
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label = label,
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status = status[1]
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)
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} else {
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data.frame(NULL)
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}
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}
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#' Create alert from validation data.frame
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#'
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#' @param data
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#'
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#' @export
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make_validation_alerts <- function(data) {
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# browser()
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if (is.data.frame(data)){
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ls <- list(data)
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} else {
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ls <- data
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}
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lapply(
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X = ls,
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FUN = function(x) {
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# browser()
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if (!is.null(dim(x)) && !any(dim(x) == c(0))) {
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icon <- switch(x$status,
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"succes" = phosphoricons::ph("check", title = "OK"),
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"warning" = phosphoricons::ph("warning", title = "Warning")
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)
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shinyWidgets::alert(
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icon,
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htmltools::HTML(x$label),
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status = x$status,
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style = "margin-bottom: 10px; padding: 10px;"
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)
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} else {
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return(NULL)
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}
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}
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)
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}
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133
examples/validation_module_demo.R
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133
examples/validation_module_demo.R
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#' Data and analyses validation demo
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#'
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#' @returns
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#' @export
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#'
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#' @examples
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#' \dontrun{
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#' validation_demo_app()
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#' }
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validation_demo_app <- function() {
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ui <- shiny::fluidPage(
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shiny::tags$h2("Validation"),
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IDEAFilter::IDEAFilter_ui("data_filter"),
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shiny::br(),
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DT::DTOutput("data_final"),
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shiny::br(),
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validation_ui("validation_demo_2")
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)
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server <- function(input, output, session) {
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rv <- shiny::reactiveValues(
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data_original = shiny::reactive(mtcars),
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data_filtered = NULL
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)
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rv_validation <- shiny::reactiveValues(
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obs_filter = NULL,
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vars_filter = NULL
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)
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data_filter <- IDEAFilter::IDEAFilter(
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id = "data_filter",
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data = mtcars,
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verbose = TRUE
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)
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shiny::observeEvent(
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data_filter(),
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{
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rv$data_filtered <- data_filter()
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}
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)
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output$data_final <- DT::renderDT(
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data_filter()
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)
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shiny::observeEvent(
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list(
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data_filter()
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),
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{
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to_make_validation <- data_filter()
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## Validation
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if (!is.null(to_make_validation)) {
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validation <-
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make_validation(
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ls = validation_lib("obs_filter"),
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list(
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x = mtcars,
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y = to_make_validation
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)
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)
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rv_validation$vars_filter <- validation
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validation_server(id = "validation_demo_2", data = rv_validation$vars_filter)
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}
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}
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)
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# shiny::observeEvent(
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# list(
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# shiny::reactive(rv_validation$vars_filter)(),
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# data_filter()
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# ),
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# {
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# # browser()
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# # to_make_alert <- shiny::isolate(rv_validation$vars_filter)
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# to_make_alert <- shiny::reactive(rv_validation$vars_filter)()
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# if (!is.null(rv_validation$vars_filter)) {
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# validation_server(id = "validation_demo_2", data = to_make_alert)
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# }
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# }
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# )
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}
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shiny::shinyApp(ui, server)
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}
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#' Title
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#'
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#' @returns
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#' @export
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#'
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#' @examples
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#' validation_nr_demo_app()
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validation_nr_demo_app <- function() {
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ui <- shiny::fluidPage(
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shiny::tags$h2("Validation"),
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shiny::br(),
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validation_ui("validation_demo_1", max_height = "30px"),
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shiny::br(),
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validation_ui("validation_demo_2")
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)
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server <- function(input, output, session) {
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df_original <- mtcars
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df_obs <- mtcars |> dplyr::filter(mpg > 20)
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df_vars <- df_obs[1:6]
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val1 <- purrr::map2(
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.x = validation_lib()[1],
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.y = list(list(x = df_original, y = df_obs)),
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make_validation
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)
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val2 <- make_validation(
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ls = validation_lib()[[2]],
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list(x = df_original, y = df_vars)
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)
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validation_server(id = "validation_demo_1", data = val1)
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validation_server(id = "validation_demo_2", data = val2)
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}
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shiny::shinyApp(ui, server)
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}
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169
man/validation.Rd
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169
man/validation.Rd
Normal file
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/validation.R
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\name{validation_ui}
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\alias{validation_ui}
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\alias{validation_server}
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\title{Validation module}
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\usage{
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||||
validation_ui(id, max_height = NULL, ...)
|
||||
|
||||
validation_server(id, data)
|
||||
}
|
||||
\arguments{
|
||||
\item{id}{Module's ID.}
|
||||
|
||||
\item{max_height}{Maximum height for validation results element, useful if you have many rules.}
|
||||
|
||||
\item{...}{Arguments passed to \code{actionButton} or \code{uiOutput} depending on display mode,
|
||||
you cannot use \code{inputId}/\code{outputId}, \code{label} or \code{icon} (button only).}
|
||||
|
||||
\item{data}{a \code{reactive} function returning a \code{data.frame}.}
|
||||
}
|
||||
\value{
|
||||
\itemize{
|
||||
\item UI: HTML tags that can be included in shiny's UI
|
||||
\item Server: a \code{list} with two slots:
|
||||
\itemize{
|
||||
\item \strong{status}: a \code{reactive} function returning the best status available between \code{"OK"}, \code{"Failed"} or \code{"Error"}.
|
||||
\item \strong{details}: a \code{reactive} function returning a \code{list} with validation details.
|
||||
}
|
||||
}
|
||||
}
|
||||
\description{
|
||||
Check that a dataset respect some validation expectations.
|
||||
}
|
||||
\examples{
|
||||
#' Data and analyses validation demo
|
||||
#'
|
||||
#' @returns
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' \dontrun{
|
||||
#' validation_demo_app()
|
||||
#' }
|
||||
validation_demo_app <- function() {
|
||||
ui <- shiny::fluidPage(
|
||||
shiny::tags$h2("Validation"),
|
||||
IDEAFilter::IDEAFilter_ui("data_filter"),
|
||||
shiny::br(),
|
||||
DT::DTOutput("data_final"),
|
||||
shiny::br(),
|
||||
validation_ui("validation_demo_2")
|
||||
)
|
||||
|
||||
server <- function(input, output, session) {
|
||||
rv <- shiny::reactiveValues(
|
||||
data_original = shiny::reactive(mtcars),
|
||||
data_filtered = NULL
|
||||
)
|
||||
|
||||
rv_validation <- shiny::reactiveValues(
|
||||
obs_filter = NULL,
|
||||
vars_filter = NULL
|
||||
)
|
||||
|
||||
data_filter <- IDEAFilter::IDEAFilter(
|
||||
id = "data_filter",
|
||||
data = mtcars,
|
||||
verbose = TRUE
|
||||
)
|
||||
|
||||
shiny::observeEvent(
|
||||
data_filter(),
|
||||
{
|
||||
rv$data_filtered <- data_filter()
|
||||
}
|
||||
)
|
||||
|
||||
output$data_final <- DT::renderDT(
|
||||
data_filter()
|
||||
)
|
||||
|
||||
shiny::observeEvent(
|
||||
list(
|
||||
data_filter()
|
||||
),
|
||||
{
|
||||
to_make_validation <- data_filter()
|
||||
## Validation
|
||||
if (!is.null(to_make_validation)) {
|
||||
validation <-
|
||||
make_validation(
|
||||
ls = validation_lib("obs_filter"),
|
||||
list(
|
||||
x = mtcars,
|
||||
y = to_make_validation
|
||||
)
|
||||
)
|
||||
|
||||
rv_validation$vars_filter <- validation
|
||||
|
||||
validation_server(id = "validation_demo_2", data = rv_validation$vars_filter)
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
)
|
||||
|
||||
# shiny::observeEvent(
|
||||
# list(
|
||||
# shiny::reactive(rv_validation$vars_filter)(),
|
||||
# data_filter()
|
||||
# ),
|
||||
# {
|
||||
# # browser()
|
||||
# # to_make_alert <- shiny::isolate(rv_validation$vars_filter)
|
||||
# to_make_alert <- shiny::reactive(rv_validation$vars_filter)()
|
||||
# if (!is.null(rv_validation$vars_filter)) {
|
||||
# validation_server(id = "validation_demo_2", data = to_make_alert)
|
||||
# }
|
||||
# }
|
||||
# )
|
||||
}
|
||||
shiny::shinyApp(ui, server)
|
||||
}
|
||||
|
||||
|
||||
#' Title
|
||||
#'
|
||||
#' @returns
|
||||
#' @export
|
||||
#'
|
||||
#' @examples
|
||||
#' validation_nr_demo_app()
|
||||
validation_nr_demo_app <- function() {
|
||||
ui <- shiny::fluidPage(
|
||||
shiny::tags$h2("Validation"),
|
||||
shiny::br(),
|
||||
validation_ui("validation_demo_1", max_height = "30px"),
|
||||
shiny::br(),
|
||||
validation_ui("validation_demo_2")
|
||||
)
|
||||
|
||||
server <- function(input, output, session) {
|
||||
df_original <- mtcars
|
||||
|
||||
df_obs <- mtcars |> dplyr::filter(mpg > 20)
|
||||
|
||||
df_vars <- df_obs[1:6]
|
||||
|
||||
val1 <- purrr::map2(
|
||||
.x = validation_lib()[1],
|
||||
.y = list(list(x = df_original, y = df_obs)),
|
||||
make_validation
|
||||
)
|
||||
|
||||
val2 <- make_validation(
|
||||
ls = validation_lib()[[2]],
|
||||
list(x = df_original, y = df_vars)
|
||||
)
|
||||
|
||||
validation_server(id = "validation_demo_1", data = val1)
|
||||
|
||||
validation_server(id = "validation_demo_2", data = val2)
|
||||
}
|
||||
shiny::shinyApp(ui, server)
|
||||
}
|
||||
}
|
||||
21
man/validation_lib.Rd
Normal file
21
man/validation_lib.Rd
Normal file
|
|
@ -0,0 +1,21 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/validation.R
|
||||
\name{validation_lib}
|
||||
\alias{validation_lib}
|
||||
\title{Validation library}
|
||||
\usage{
|
||||
validation_lib(name = NULL)
|
||||
}
|
||||
\arguments{
|
||||
\item{name}{Index name}
|
||||
}
|
||||
\value{
|
||||
list
|
||||
}
|
||||
\description{
|
||||
Validation library
|
||||
}
|
||||
\examples{
|
||||
validation_lib()
|
||||
validation_lib("missings")
|
||||
}
|
||||
23
man/vars_filter_validate.Rd
Normal file
23
man/vars_filter_validate.Rd
Normal file
|
|
@ -0,0 +1,23 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/validation.R
|
||||
\name{vars_filter_validate}
|
||||
\alias{vars_filter_validate}
|
||||
\title{Variable filter test wrapper}
|
||||
\usage{
|
||||
vars_filter_validate(before, after)
|
||||
}
|
||||
\arguments{
|
||||
\item{before}{data before}
|
||||
|
||||
\item{after}{data after}
|
||||
}
|
||||
\value{
|
||||
vector
|
||||
}
|
||||
\description{
|
||||
Variable filter test wrapper
|
||||
}
|
||||
\examples{
|
||||
vars_filter_validate(mtcars, mtcars[1:6])
|
||||
vars_filter_validate(mtcars, mtcars[0])
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue