57 UI updates (#72)

* Add missing function for has_value. Closes #71 * Change save and close buttons in file upload * Set max height to input and output options * Update bootstrap table with CI range * Updates to summary tab * Add ability to export bootstrap table * Add ui for export * Bump version and add news * Update names for exported files
Riksrevisjonen · Dec 20, 2023 · 2ec54fb · 2ec54fb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,13 @@
 Package: pioneeR
 Title: Perform productivity analyses in a web browser
-Version: 0.2.0.9000
+Version: 0.3.0
 Authors@R: c(
     person("Ove Haugland", "Jakobsen", role = c("aut", "cre"), email = "[email protected]"),
     person("Jan Roar", "Beckstrøm", role = "ctb", email = "[email protected]"),
     person("Lars Skaage", "Engebretsen", role = "ctb", email = "[email protected]"),
     person("Jonas", "Månsson", role = "ctb", email = "[email protected]"),
     person("Aleksander", "Eilertsen", role = "ctb", email = "[email protected]"),
+    person("Joachim", "Sandnes", role = "ctb", email = "[email protected]"),
     person(family = "Riksrevisjonen", role = "cph"))
 Description: What the package does (one paragraph).
 License: GPL-3 | file LICENSE

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# pioneeR 0.2.0.9000
+# pioneeR 0.3.0
 
 ## Breaking changes:
 
@@ -17,13 +17,15 @@
 - Layout changed to `layout_sidebar()` from the bslib package to improve UI and fix compatability with bslib >= 0.6.0 and Boostrap 5.3 (#44)
 - Analysis report has been updated and simplified to make the results from the app easier to reproduce (#35)
 - `runPioneeR()` has been renamed `run_pioneer()`. `runPioneeR()` will still work, but will be deprecated in a later version
-- Simplified logic in PDF report generated from the analysis tab
+- Improvements to the user interface and user experience (#57)
+- For time series data, all columns are now available to select as year/time variable. If a column with values within the range \[1900, 2100\] exists, this column will automatically be selected (#41)
 
 ## Bug fixes
 
 - If the user selects a port number that is considered unsafe, a random port number is selected instead (#40)
 - Fixed a bug where an error occurred if any of the model parameters were not found in the column names (#39)
 - Fixed a bug in the scale efficiency tab where numbers where rounded twice (#47)
+- Fixed a bug that would block Excel-files from properly uploading (#71)
 
 # pioneeR 0.2.0
 

diff --git a/inst/app/R/fct_dea-boostrap.R b/inst/app/R/fct_dea-boostrap.R
@@ -67,7 +67,8 @@ process_boot <- function(rts, orientation, h, alpha, theta, boot) {
       bias = bias,
       eff_bc = theta_tilde,
       lower = as.vector(theta_ci[, 1]),
-      upper = as.vector(theta_ci[, 2])
+      upper = as.vector(theta_ci[, 2]),
+      range = apply(theta_ci, 1, diff)
     )
   )
   invisible(out)

diff --git a/inst/app/R/fct_file-functions.R b/inst/app/R/fct_file-functions.R
@@ -27,3 +27,10 @@ check_file <- function(file) {
   file
 
 }
+
+has_value <- function(x) {
+  if (length(x) > 1L) return(sapply(x, has_value, USE.NAMES = FALSE))
+  if (is.null(x) || is.na(x)) return(FALSE)
+  if (!is.character(x)) x <- as.character(x)
+  nzchar(x)
+}
diff --git a/inst/app/R/mod_file-upload.R b/inst/app/R/mod_file-upload.R
@@ -31,8 +31,8 @@ file_upload_srv <- function(id) {
             easyClose = TRUE, size = 'xl',
             title = 'Upload file',
             footer = tagList(
-              actionButton(ns('file_save'), 'Save'),
-              bs_modal_button('Close')
+              actionButton(ns('file_save'), 'Save and close', class = 'btn-sm btn-primary', `data-bs-dismiss` = 'modal'),
+              bs_modal_button('Cancel', size = 'sm', color = 'secondary')
             ),
             div(
               class = 'input-group mb-3',

diff --git a/inst/app/server.R b/inst/app/server.R
@@ -212,10 +212,11 @@ shinyServer(function(input, output, session) {
         card_header('Select data'),
         card_body(
           'Upload a file to get started by pressing the Upload file button in the vertical
-          menu to the left. Accepted file types are Excel, Stata, R data.frames stored as
-          RDS-files, comma-, semicolon- og tabseparated files (.tsv, .csv or .txt). When you
-          upload a file, you get a preview of the contents. You can adjust the file import
-          settings if needed. Remember to save the file to the current session.'
+          menu to the left. Accepted file types are Excel, Stata (version 14 or newer), R
+          data.frames stored as DS-files, comma-, semicolon- og tabseparated files (.tsv,
+          .csv or .txt). When you upload a file, you get a preview of the contents. You can
+          adjust the file import settings if needed. Remember to save the file to the current
+          session.'
         ))
     } else {
       # Check for list wise deletion and inform the user if observations have been removed
@@ -364,7 +365,9 @@ shinyServer(function(input, output, session) {
 
   output$dea.plot.save <- downloadHandler(
     filename = function() {
-      sprintf('dea-plot-%s.%s', Sys.Date(), input$dea_dl_format)
+      sprintf(
+        'dea-plot-%s-%s.%s', model_params$rts, model_params$orientation,
+        input$dea_dl_format)
     },
     content = function(file) {
       p <- dea_plot() +
@@ -457,7 +460,9 @@ shinyServer(function(input, output, session) {
 
   output$salter.save <- downloadHandler(
     filename = function() {
-      sprintf('salterplot-%s.%s', Sys.Date(), input$salter_dl_format)
+      sprintf(
+        'salterplot-%s-%s.%s', model_params$rts, model_params$orientation,
+        input$salter_dl_format)
     },
     content = function(file) {
       ggsave_(
@@ -474,28 +479,50 @@ shinyServer(function(input, output, session) {
     eff <- dea.prod()$eff
 
     if (model_params$orientation == 'in')
-      sum.eff <- sum(dea.in() * eff) / sum(dea.in())
+      sum_eff <- sum(dea.in() * eff) / sum(dea.in())
     else if (model_params$orientation == 'out')
-      sum.eff <- sum(dea.out() * eff) / sum(dea.out())
-
-    rts <- switch(dea.prod()$RTS,
-      crs = 'constant returns to scale',
-      vrs = 'variable returns to scale',
-      drs = 'non-increasing returns to scale',
-      irs = 'non-decreasing returns to scale',
-      'UNKNOWN'
+      sum_eff <- sum(dea.out() * eff) / sum(dea.out())
+
+    rts <- switch(
+      dea.prod()$RTS,
+      crs = 'Constant',
+      vrs = 'Variable',
+      drs = 'Non-increasing',
+      irs = 'Non-decreasing'
     )
 
-    orient <- switch(dea.prod()$ORIENTATION,
-      'in' = 'input oriented',
-      'out' = 'output oriented',
-      'UNKNOWN'
+    orient <- switch(
+      dea.prod()$ORIENTATION,
+      'in' = 'Input',
+      'out' = 'Output'
     )
 
     list(
-      p(list('Technology is ', tags$em(rts), ' and orientation is ', tags$em(orient))),
-      p(paste('Mean efficiency:', round(mean(eff), input$dea_round))),
-      p(paste('Weighted efficiency:',round(sum.eff, input$dea_round))),
+      p(class = 'lead', 'Summary'),
+      layout_column_wrap(
+        width = 1/4,
+        value_box(
+          title = 'Technology',
+          rts,
+          theme = 'secondary'
+        ),
+        value_box(
+          title = 'Orientation',
+          orient,
+          theme = 'secondary'
+        ),
+        value_box(
+          'Mean efficiency',
+          round(mean(eff), input$dea_round),
+          theme = 'primary'
+        ),
+        value_box(
+          'Weighted efficiency',
+          round(sum_eff, input$dea_round),
+          theme = 'primary'
+        )
+      ),
+      p(class = 'lead', 'Statistics on efficiency scores'),
       layout_column_wrap(
         width = 1/5,
         card(
@@ -519,12 +546,25 @@ shinyServer(function(input, output, session) {
           card_body(round(max(eff), input$dea_round))
         )
       ),
-      hr(),
-      renderTable({ eff_tbl }),
-      renderPlot({
-        hist(eff, col = 'red', xlab = 'Efficiency',
-             main = 'Distribution of efficiency scores')
-      })
+      p(class = 'lead', 'Distribution'),
+      layout_columns(
+        col_widths = c(4, 8),
+        renderTable({ eff_tbl }),
+        renderPlot({
+          # Find to optimal number of bins using Freedman-Diaconis rule if N is less
+          # than 200, and Sturge's rule if N is equal or greater than 200
+          n_bins <- if (length(eff) < 200) nclass.FD(eff) else nclass.Sturges(eff)
+          bins <- pretty(range(eff), n = n_bins, min.n = 1)
+          ggplot(data.frame(eff = eff), aes(x = eff)) +
+            stat_bin(fill = '#ee2255', color = '#eeeeee', breaks = bins) +
+            geom_rug() +
+            theme_pioneer() +
+            theme(
+              axis.title.x = element_blank(),
+              axis.title.y = element_blank()
+            )
+        })
+      )
     )
 
   })
@@ -612,7 +652,9 @@ shinyServer(function(input, output, session) {
 
   output$exporttable <- downloadHandler(
     filename = function() {
-      paste0('dea-model-', Sys.Date(), '.', input$exportfileformat)
+      sprintf(
+        'dea-model-%s-%s.%s', model_params$rts, model_params$orientation,
+        input$exportfileformat)
     },
     content = function(file) {
       df <- dea.tbl()
@@ -867,20 +909,16 @@ shinyServer(function(input, output, session) {
     # Add DMU names and round inputs
     df <- cbind(data.frame(DMU = names(dea.prod()$eff)), round(res$tbl, input$boot_round))
 
-    tbl <- reactable(
-      df,
-      class = 'small',
-      striped = TRUE,
-      defaultPageSize = 30,
-      pageSizeOptions = c(10, 30, 50, 100),
-      columns = list(
+    opts <- list2(!!!reactable_opts, data = df, columns = list(
         eff = colDef(show = input$boot_show_eff, name = 'Efficiency'),
         bias = colDef(show = input$boot_show_bias, name = 'Bias'),
         eff_bc = colDef(name = 'Bias corr. score'),
         lower = colDef(name = 'Lower bound'),
-        upper = colDef(name = 'Upper bound')
+        upper = colDef(name = 'Upper bound'),
+        range = colDef(name = 'CI range')
       )
     )
+    tbl <- do.call(reactable, opts)
 
     # Add warning if there are any missing observations
     if (!is.null(res$missing)) {
@@ -900,6 +938,28 @@ shinyServer(function(input, output, session) {
     }
   })
 
+  output$boot_export <- downloadHandler(
+    filename = function() {
+      sprintf(
+        'bootstrap-%s-%s.%s', model_params$rts, model_params$orientation,
+        input$boot_fileformat)
+    },
+    content = function(file) {
+      res <- dea_boostrap()
+      df <- cbind(data.frame(DMU = names(dea.prod()$eff)), round(res$tbl, input$boot_round))
+      # Export based on chosen file format
+      if (input$boot_fileformat == 'dta') {
+        colnames(df) <- gsub('\\s', '_', colnames(df))
+        colnames(df) <- gsub('[^A-Za-z0-9_]', '', colnames(df))
+        haven::write_dta(df, file)
+      } else if (input$boot_fileformat == 'xlsx') {
+        writexl::write_xlsx(df, file)
+      } else if (input$boot_fileformat == 'csv') {
+        write.csv2(df, file, fileEncoding = 'CP1252', row.names = FALSE)
+      }
+    }
+  )
+
   # ---- Malmquist ----
 
   output$malm.dt <- renderUI({
@@ -982,7 +1042,9 @@ shinyServer(function(input, output, session) {
   )
 
   output$`export-dea-rds` <- downloadHandler(
-    filename = 'dea.rds',
+    filename = function() {
+      sprintf('dea-%s-%s.rds', model_params$rts, model_params$orientation)
+    },
     content = function(file) {
       d <- selection()
       saveRDS(d, file = file)

diff --git a/inst/app/ui.R b/inst/app/ui.R
@@ -228,6 +228,16 @@ ui <- function(request) { page_navbar(
             numericInput('boot_round', 'Number of decimals', min = 1L, max = 15L, step = 1L, value = 4L),
             checkboxInput('boot_show_eff', 'Show original efficiency score', value = TRUE),
             checkboxInput('boot_show_bias', 'Show bias', value = FALSE)
+          ),
+          accordion_panel(
+            title = 'Export',
+            downloadButton('boot_export', 'Export results', class = 'btn-dark'),
+            p(class = 'small', helpText(
+              'Download the bootstrap results as shown in the table to the right.'
+            )),
+            selectizeInput(
+              'boot_fileformat', 'Choose file format',
+              choices = c('Excel' = 'xlsx', 'Stata' = 'dta', 'Comma separated values' = 'csv'))
           )
         ),
         actionButton('run_boot', 'Run bootstrap', class = 'btn-primary btn-sm')

diff --git a/inst/app/www/style.css b/inst/app/www/style.css
@@ -12,17 +12,13 @@ h2 {
     background-color: #edf389;
 }
 
-.irs-grid-pol.small {
-    display: none;
-}
-
-.dataTables_info, .dt-buttons {
-    width: 50%;
-    text-align: left;
+#ui_inputs .selectize-input, #ui_outputs .selectize-input  {
+  max-height: 4rem;
+  overflow-y: scroll;
 }
 
-.dataTables_length, .dataTables_paginate {
-    width: 50%;
+.irs-grid-pol.small {
+    display: none;
 }
 
 .form-control {