- hide code chunks by default

- update the README
- don't cache quarto docs for now

README.md

@@ -1,22 +1,21 @@
 # unjournaldata
-Unjournal evaluations, meta-analysis, and meta-science: data analysis and presentation
 
+This is the repository for 
+[Unjournal](https://www.unjournal.org) evaluations, meta-analysis, and meta-science. 
 
-Some goals below 
+Our current reports are available at <https://unjournal.github.io>.
 
-## Todo: Evaluation and prediction metrics
+# How it works
 
-Some things to do:
+Data is currently imported manually from airtable. We hope to automate this soon.
 
-- DONE: Import evaluation rating/predictions data
+The github site is created as a [Quarto](https://quarto.org) book. There is also
+a [Shiny](https://shiny.posit.co) app at
+<https://unjournal.shinyapps.io/DataExplorer/>. 
 
-- DONE for now: Clean and reconcile missing data, different metrics
-- [ ] Aggregations of ratings under stated uncertainty
-- [ ] Assess inter-rater reliability, etc.
-
-## Later: Track and benchmark against later outcomes
-
-## Possible: 'Claim extraction', link with predictions and replication work
-
-## House, support, link: Data and code from papers, evaluators calculations and investigations
+The site can be re-rendered by running `quarto render` from the command line,
+or `quarto::quarto_render()` from within R, and pushing changes to the `main` branch.
 
+The shiny app can be deployed by running 
+`rsconnect::deployApp("shinyapp/DataExplorer")`, or from within RStudio by
+opening `shinyapp/DataExplorer/app.R` and clicking the 'publish' button.

docs/site_libs/datatables-binding-0.28/datatables.js → _freeze/site_libs/datatables-binding-0.32/datatables.js

@@ -2,7 +2,7 @@
 
 // some helper functions: using a global object DTWidget so that it can be used
 // in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's
-// dynamic scoping, when 'code' is eval()'ed, JavaScript does not know objects
+// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects
 // from the "parent frame", e.g. JS('DTWidget') will not work unless it was made
 // a global object
 var DTWidget = {};
@@ -348,6 +348,15 @@ HTMLWidgets.widget({
     var table = $table.DataTable(options);
     $el.data('datatable', table);
 
+    if ('rowGroup' in options) {
+      // Maintain RowGroup dataSrc when columns are reordered (#1109)
+      table.on('column-reorder', function(e, settings, details) {
+        var oldDataSrc = table.rowGroup().dataSrc();
+        var newDataSrc = details.mapping[oldDataSrc];
+        table.rowGroup().dataSrc(newDataSrc);
+      });
+    }
+
     // Unregister previous Crosstalk event subscriptions, if they exist
     if (instance.ctfilterSubscription) {
       instance.ctfilterHandle.off("change", instance.ctfilterSubscription);
@@ -432,10 +441,13 @@ HTMLWidgets.widget({
         regex = options.search.regex,
         ci = options.search.caseInsensitive !== false;
       }
+      // need to transpose the column index when colReorder is enabled
+      if (table.colReorder) i = table.colReorder.transpose(i);
       return table.column(i).search(value, regex, !regex, ci);
     };
 
     if (data.filter !== 'none') {
+      if (!data.hasOwnProperty('filterSettings')) data.filterSettings = {};
 
       filterRow.each(function(i, td) {
 
@@ -493,11 +505,13 @@ HTMLWidgets.widget({
               $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus();
             },
             input: function() {
-              if ($input.val() === '') filter[0].selectize.setValue([]);
+              var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val();
+              if (v1 === '[]') v1 = '';
+              if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2));
             }
           });
           var $input2 = $x.children('select');
-          filter = $input2.selectize({
+          filter = $input2.selectize($.extend({
             options: $input2.data('options').map(function(v, i) {
               return ({text: v, value: v});
             }),
@@ -509,15 +523,14 @@ HTMLWidgets.widget({
               if (value.length) $input.trigger('input');
               $input.attr('title', $input.val());
               if (server) {
-                table.column(i).search(value.length ? JSON.stringify(value) : '').draw();
+                searchColumn(i, value.length ? JSON.stringify(value) : '').draw();
                 return;
               }
               // turn off filter if nothing selected
               $td.data('filter', value.length > 0);
               table.draw();  // redraw table, and filters will be applied
             }
-          });
-          if (searchCol) filter[0].selectize.setValue(JSON.parse(searchCol));
+          }, data.filterSettings.select));
           filter[0].selectize.on('blur', function() {
             $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur');
           });
@@ -526,10 +539,12 @@ HTMLWidgets.widget({
           var fun = function() {
             searchColumn(i, $input.val()).draw();
           };
-          if (server) {
-            fun = $.fn.dataTable.util.throttle(fun, options.searchDelay);
-          }
-          $input.on('input', fun);
+          // throttle searching for server-side processing
+          var throttledFun = $.fn.dataTable.util.throttle(fun, options.searchDelay);
+          $input.on('input', function(e, immediate) {
+            // always bypass throttling when immediate = true (via the updateSearch method)
+            (immediate || !server) ? fun() : throttledFun();
+          });
         } else if (inArray(type, ['number', 'integer', 'date', 'time'])) {
           var $x0 = $x;
           $x = $x0.children('div').first();
@@ -615,13 +630,11 @@ HTMLWidgets.widget({
               filter.val(v);
             }
           });
-          var formatDate = function(d, isoFmt) {
+          var formatDate = function(d) {
             d = scaleBack(d, scale);
             if (type === 'number') return d;
             if (type === 'integer') return parseInt(d);
             var x = new Date(+d);
-            var fmt = ('filterDateFmt' in data) ? data.filterDateFmt[i] : undefined;
-            if (fmt !== undefined && isoFmt === false) return x[fmt.method].apply(x, fmt.params);
             if (type === 'date') {
               var pad0 = function(x) {
                 return ('0' + x).substr(-2, 2);
@@ -642,7 +655,7 @@ HTMLWidgets.widget({
             start: [r1, r2],
             range: {min: r1, max: r2},
             connect: true
-          }, opts));
+          }, opts, data.filterSettings.slider));
           if (scale > 1) (function() {
             var t1 = r1, t2 = r2;
             var val = filter.val();
@@ -657,13 +670,28 @@ HTMLWidgets.widget({
                 start: [t1, t2],
                 range: {min: t1, max: t2},
                 connect: true
-              }, opts), true);
+              }, opts, data.filterSettings.slider), true);
               val = filter.val();
             }
             r1  = t1; r2 = t2;
           })();
+          // format with active column renderer, if defined
+          var colDef = data.options.columnDefs.find(function(def) {
+            return (def.targets === i || inArray(i, def.targets)) && 'render' in def;
+          });
           var updateSliderText = function(v1, v2) {
-            $span1.text(formatDate(v1, false)); $span2.text(formatDate(v2, false));
+            // we only know how to use function renderers
+            if (colDef && typeof colDef.render === 'function') {
+              var restore = function(v) {
+                v = scaleBack(v, scale);
+                return inArray(type, ['date', 'time']) ? new Date(+v) : v;
+              }
+              $span1.text(colDef.render(restore(v1), 'display'));
+              $span2.text(colDef.render(restore(v2), 'display'));
+            } else {
+              $span1.text(formatDate(v1));
+              $span2.text(formatDate(v2));
+            }
           };
           updateSliderText(r1, r2);
           var updateSlider = function(e) {
@@ -680,7 +708,7 @@ HTMLWidgets.widget({
             updateSliderText(val[0], val[1]);
             if (e.type === 'slide') return;  // no searching when sliding only
             if (server) {
-              table.column(i).search($td.data('filter') ? ival : '').draw();
+              searchColumn(i, $td.data('filter') ? ival : '').draw();
               return;
             }
             table.draw();
@@ -696,7 +724,7 @@ HTMLWidgets.widget({
         // processing
         if (server) {
           // if a search string has been pre-set, search now
-          if (searchCol) searchColumn(i, searchCol).draw();
+          if (searchCol) $input.trigger('input').trigger('change');
           return;
         }
 
@@ -742,15 +770,7 @@ HTMLWidgets.widget({
         $.fn.dataTable.ext.search.push(customFilter);
 
         // search for the preset search strings if it is non-empty
-        if (searchCol) {
-          if (inArray(type, ['factor', 'logical'])) {
-            filter[0].selectize.setValue(JSON.parse(searchCol));
-          } else if (type === 'character') {
-            $input.trigger('input');
-          } else if (inArray(type, ['number', 'integer', 'date', 'time'])) {
-            $input.trigger('change');
-          }
-        }
+        if (searchCol) $input.trigger('input').trigger('change');
 
       });
 
@@ -1370,7 +1390,7 @@ HTMLWidgets.widget({
     changeInput('cell_clicked', {});
 
     // do not trigger table selection when clicking on links unless they have classes
-    table.on('click.dt', 'tbody td a', function(e) {
+    table.on('mousedown.dt', 'tbody td a', function(e) {
       if (this.className === '') e.stopPropagation();
     });
 
@@ -1398,8 +1418,9 @@ HTMLWidgets.widget({
           console.log('The search keyword for column ' + i + ' is undefined')
           return;
         }
-        $(td).find('input').first().val(v);
-        searchColumn(i, v);
+        // Update column search string and values on linked filter widgets.
+        // 'input' for factor and char filters, 'change' for numeric filters.
+        $(td).find('input').first().val(v).trigger('input', [true]).trigger('change');
       });
       table.draw();
     }

_freeze/site_libs/htmltools-fill-0.5.8/fill.css

@@ -0,0 +1,21 @@
+@layer htmltools {
+  .html-fill-container {
+    display: flex;
+    flex-direction: column;
+    /* Prevent the container from expanding vertically or horizontally beyond its
+    parent's constraints. */
+    min-height: 0;
+    min-width: 0;
+  }
+  .html-fill-container > .html-fill-item {
+    /* Fill items can grow and shrink freely within
+    available vertical space in fillable container */
+    flex: 1 1 auto;
+    min-height: 0;
+    min-width: 0;
+  }
+  .html-fill-container > :not(.html-fill-item) {
+    /* Prevent shrinking or growing of non-fill items */
+    flex: 0 0 auto;
+  }
+}

_quarto.yml

@@ -18,20 +18,21 @@ book:
   date: today
 
 execute:
-  freeze: auto # re-render only when source changes
+  freeze: false # re-render only when source changes
   warning: false
   message: false
   error: true
+  echo: false
 
 comments:
     hypothesis: true
    #bibliography: references.bib
 
 format:
   html:
-    code-fold: true
-    code-link: true #note: this isn't working for me
-    code-tools: true
+    code-fold: false
+    code-link: false #note: this isn't working for me
+    code-tools: false
     theme: cosmo
     citations-hover: true
     footnotes-hover: true