From 7c82d8301d032c90205d82ca6f7e199dd93c90d5 Mon Sep 17 00:00:00 2001 From: Laurent Gatto Date: Thu, 22 Feb 2024 13:47:47 +0100 Subject: [PATCH] rebuild course --- docs/404.html | 21 +- docs/index.html | 21 +- .../crosstalk-1.2.1/css/crosstalk.min.css | 1 + docs/libs/crosstalk-1.2.1/js/crosstalk.min.js | 2 + .../datatables-binding-0.31/datatables.js | 1519 +++++++++++++++++ .../css/jquery.dataTables.extra.css | 28 + .../css/jquery.dataTables.min.css | 1 + .../js/jquery.dataTables.min.js | 4 + docs/libs/htmlwidgets-1.6.4/htmlwidgets.js | 901 ++++++++++ docs/sec-anx.html | 21 +- docs/sec-bioinfo.html | 21 +- docs/sec-ccl.html | 21 +- docs/sec-dataorg.html | 21 +- docs/sec-dplyr.html | 23 +- docs/sec-join.html | 24 +- docs/sec-prog.html | 39 +- docs/sec-rr.html | 25 +- docs/sec-rrstudio.html | 42 +- docs/sec-startdata.html | 25 +- docs/sec-startr.html | 29 +- docs/sec-vis.html | 21 +- docs/session-information.html | 80 +- packages.bib | 50 +- 23 files changed, 2711 insertions(+), 229 deletions(-) create mode 100644 docs/libs/crosstalk-1.2.1/css/crosstalk.min.css create mode 100644 docs/libs/crosstalk-1.2.1/js/crosstalk.min.js create mode 100644 docs/libs/datatables-binding-0.31/datatables.js create mode 100644 docs/libs/dt-core-1.13.6/css/jquery.dataTables.extra.css create mode 100644 docs/libs/dt-core-1.13.6/css/jquery.dataTables.min.css create mode 100644 docs/libs/dt-core-1.13.6/js/jquery.dataTables.min.js create mode 100644 docs/libs/htmlwidgets-1.6.4/htmlwidgets.js diff --git a/docs/404.html b/docs/404.html index 8cd2d47..0d1c17d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -216,9 +217,9 @@

Page not found

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/index.html b/docs/index.html index 35e302c..aec0374 100644 --- a/docs/index.html +++ b/docs/index.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -458,9 +459,9 @@

Setup

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/libs/crosstalk-1.2.1/css/crosstalk.min.css b/docs/libs/crosstalk-1.2.1/css/crosstalk.min.css new file mode 100644 index 0000000..6b45382 --- /dev/null +++ b/docs/libs/crosstalk-1.2.1/css/crosstalk.min.css @@ -0,0 +1 @@ +.container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px} diff --git a/docs/libs/crosstalk-1.2.1/js/crosstalk.min.js b/docs/libs/crosstalk-1.2.1/js/crosstalk.min.js new file mode 100644 index 0000000..b7ec0ac --- /dev/null +++ b/docs/libs/crosstalk-1.2.1/js/crosstalk.min.js @@ -0,0 +1,2 @@ +!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e?@[\\\]^`{|}~])/g,"\\$1")+"']"),r=JSON.parse(n[0].innerText),i=e.factory(t,r);o(t).data("crosstalk-instance",i),o(t).addClass("crosstalk-input-bound")}if(t.Shiny){var e=new t.Shiny.InputBinding,u=t.jQuery;u.extend(e,{find:function(e){return u(e).find(".crosstalk-input")},initialize:function(e){var t,n;u(e).hasClass("crosstalk-input-bound")||(n=o(t=e),Object.keys(r).forEach(function(e){n.hasClass(e)&&!n.hasClass("crosstalk-input-bound")&&i(r[e],t)}))},getId:function(e){return e.id},getValue:function(e){},setValue:function(e,t){},receiveMessage:function(e,t){},subscribe:function(e,t){u(e).data("crosstalk-instance").resume()},unsubscribe:function(e){u(e).data("crosstalk-instance").suspend()}}),t.Shiny.inputBindings.register(e,"crosstalk.inputBinding")}}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(r,e,t){(function(e){"use strict";var t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(r("./input")),n=r("./filter");var a=e.jQuery;t.register({className:"crosstalk-input-checkboxgroup",factory:function(e,r){var i=new n.FilterHandle(r.group),o=void 0,u=a(e);return u.on("change","input[type='checkbox']",function(){var e=u.find("input[type='checkbox']:checked");if(0===e.length)o=null,i.clear();else{var t={};e.each(function(){r.map[this.value].forEach(function(e){t[e]=!0})});var n=Object.keys(t);n.sort(),o=n,i.set(n)}}),{suspend:function(){i.clear()},resume:function(){o&&i.set(o)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(r,e,t){(function(e){"use strict";var t=n(r("./input")),l=n(r("./util")),s=r("./filter");function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}var f=e.jQuery;t.register({className:"crosstalk-input-select",factory:function(e,n){var t=l.dataframeToD3(n.items),r={options:[{value:"",label:"(All)"}].concat(t),valueField:"value",labelField:"label",searchField:"label"},i=f(e).find("select")[0],o=f(i).selectize(r)[0].selectize,u=new s.FilterHandle(n.group),a=void 0;return o.on("change",function(){if(0===o.items.length)a=null,u.clear();else{var t={};o.items.forEach(function(e){n.map[e].forEach(function(e){t[e]=!0})});var e=Object.keys(t);e.sort(),a=e,u.set(e)}}),{suspend:function(){u.clear()},resume:function(){a&&u.set(a)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6,"./util":11}],9:[function(n,e,t){(function(e){"use strict";var d=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var n=[],r=!0,i=!1,o=void 0;try{for(var u,a=e[Symbol.iterator]();!(r=(u=a.next()).done)&&(n.push(u.value),!t||n.length!==t);r=!0);}catch(e){i=!0,o=e}finally{try{!r&&a.return&&a.return()}finally{if(i)throw o}}return n}(e,t);throw new TypeError("Invalid attempt to destructure non-iterable instance")},t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(n("./input")),a=n("./filter");var v=e.jQuery,p=e.strftime;function y(e,t){for(var n=e.toString();n.length 123,456,666.7890 +var markInterval = function(d, digits, interval, mark, decMark, precision) { + x = precision ? d.toPrecision(digits) : d.toFixed(digits); + if (!/^-?[\d.]+$/.test(x)) return x; + var xv = x.split('.'); + if (xv.length > 2) return x; // should have at most one decimal point + xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark); + return xv.join(decMark); +}; + +DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + var res = markInterval(d, digits, interval, mark, decMark); + res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) : + res + currency; + return res; +}; + +DTWidget.formatString = function(data, prefix, suffix) { + var d = data; + if (d === null) return ''; + return prefix + d + suffix; +}; + +DTWidget.formatPercentage = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d * 100, digits, interval, mark, decMark) + '%'; +}; + +DTWidget.formatRound = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark); +}; + +DTWidget.formatSignif = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark, true); +}; + +DTWidget.formatDate = function(data, method, params) { + var d = data; + if (d === null) return ''; + // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the + // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)', + // i.e. the date-only string is treated as UTC time instead of local time + if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) { + d = d.split(/\D/); + d = new Date(d[0], d[1] - 1, d[2]); + } else { + d = new Date(d); + } + return d[method].apply(d, params); +}; + +window.DTWidget = DTWidget; + +// A helper function to update the properties of existing filters +var setFilterProps = function(td, props) { + // Update enabled/disabled state + var $input = $(td).find('input').first(); + var searchable = $input.data('searchable'); + $input.prop('disabled', !searchable || props.disabled); + + // Based on the filter type, set its new values + var type = td.getAttribute('data-type'); + if (['factor', 'logical'].includes(type)) { + // Reformat the new dropdown options for use with selectize + var new_vals = props.params.options.map(function(item) { + return { text: item, value: item }; + }); + + // Find the selectize object + var dropdown = $(td).find('.selectized').eq(0)[0].selectize; + + // Note the current values + var old_vals = dropdown.getValue(); + + // Remove the existing values + dropdown.clearOptions(); + + // Add the new options + dropdown.addOption(new_vals); + + // Preserve the existing values + dropdown.setValue(old_vals); + + } else if (['number', 'integer', 'date', 'time'].includes(type)) { + // Apply internal scaling to new limits. Updating scale not yet implemented. + var slider = $(td).find('.noUi-target').eq(0); + var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0)); + var new_vals = [props.params.min * scale, props.params.max * scale]; + + // Note what the new limits will be just for this filter + var new_lims = new_vals.slice(); + + // Determine the current values and limits + var old_vals = slider.val().map(Number); + var old_lims = slider.noUiSlider('options').range; + old_lims = [old_lims.min, old_lims.max]; + + // Preserve the current values if filters have been applied; otherwise, apply no filtering + if (old_vals[0] != old_lims[0]) { + new_vals[0] = Math.max(old_vals[0], new_vals[0]); + } + + if (old_vals[1] != old_lims[1]) { + new_vals[1] = Math.min(old_vals[1], new_vals[1]); + } + + // Update the endpoints of the slider + slider.noUiSlider({ + start: new_vals, + range: {'min': new_lims[0], 'max': new_lims[1]} + }, true); + } +}; + +var transposeArray2D = function(a) { + return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a); +}; + +var crosstalkPluginsInstalled = false; + +function maybeInstallCrosstalkPlugins() { + if (crosstalkPluginsInstalled) + return; + crosstalkPluginsInstalled = true; + + $.fn.dataTable.ext.afnFiltering.push( + function(oSettings, aData, iDataIndex) { + var ctfilter = oSettings.nTable.ctfilter; + if (ctfilter && !ctfilter[iDataIndex]) + return false; + + var ctselect = oSettings.nTable.ctselect; + if (ctselect && !ctselect[iDataIndex]) + return false; + + return true; + } + ); +} + +HTMLWidgets.widget({ + name: "datatables", + type: "output", + renderOnNullValue: true, + initialize: function(el, width, height) { + // in order that the type=number inputs return a number + $.valHooks.number = { + get: function(el) { + var value = parseFloat(el.value); + return isNaN(value) ? "" : value; + } + }; + $(el).html(' '); + return { + data: null, + ctfilterHandle: new crosstalk.FilterHandle(), + ctfilterSubscription: null, + ctselectHandle: new crosstalk.SelectionHandle(), + ctselectSubscription: null + }; + }, + renderValue: function(el, data, instance) { + if (el.offsetWidth === 0 || el.offsetHeight === 0) { + instance.data = data; + return; + } + instance.data = null; + var $el = $(el); + $el.empty(); + + if (data === null) { + $el.append(' '); + // clear previous Shiny inputs (if any) + for (var i in instance.clearInputs) instance.clearInputs[i](); + instance.clearInputs = {}; + return; + } + + var crosstalkOptions = data.crosstalkOptions; + if (!crosstalkOptions) crosstalkOptions = { + 'key': null, 'group': null + }; + if (crosstalkOptions.group) { + maybeInstallCrosstalkPlugins(); + instance.ctfilterHandle.setGroup(crosstalkOptions.group); + instance.ctselectHandle.setGroup(crosstalkOptions.group); + } + + // if we are in the viewer then we always want to fillContainer and + // and autoHideNavigation (unless the user has explicitly set these) + if (window.HTMLWidgets.viewerMode) { + if (!data.hasOwnProperty("fillContainer")) + data.fillContainer = true; + if (!data.hasOwnProperty("autoHideNavigation")) + data.autoHideNavigation = true; + } + + // propagate fillContainer to instance (so we have it in resize) + instance.fillContainer = data.fillContainer; + + var cells = data.data; + + if (cells instanceof Array) cells = transposeArray2D(cells); + + $el.append(data.container); + var $table = $el.find('table'); + if (data.class) $table.addClass(data.class); + if (data.caption) $table.prepend(data.caption); + + if (!data.selection) data.selection = { + mode: 'none', selected: null, target: 'row', selectable: null + }; + if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' && + data.selection.target === 'row+column') { + if ($table.children('tfoot').length === 0) { + $table.append($('')); + $table.find('thead tr').clone().appendTo($table.find('tfoot')); + } + } + + // column filters + var filterRow; + switch (data.filter) { + case 'top': + $table.children('thead').append(data.filterHTML); + filterRow = $table.find('thead tr:last td'); + break; + case 'bottom': + if ($table.children('tfoot').length === 0) { + $table.append($('')); + } + $table.children('tfoot').prepend(data.filterHTML); + filterRow = $table.find('tfoot tr:first td'); + break; + } + + var options = { searchDelay: 1000 }; + if (cells !== null) $.extend(options, { + data: cells + }); + + // options for fillContainer + var bootstrapActive = typeof($.fn.popover) != 'undefined'; + if (instance.fillContainer) { + + // force scrollX/scrollY and turn off autoWidth + options.scrollX = true; + options.scrollY = "100px"; // can be any value, we'll adjust below + + // if we aren't paginating then move around the info/filter controls + // to save space at the bottom and rephrase the info callback + if (data.options.paging === false) { + + // we know how to do this cleanly for bootstrap, not so much + // for other themes/layouts + if (bootstrapActive) { + options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" + + "<'row'<'col-sm-12'tr>>"; + } + + options.fnInfoCallback = function(oSettings, iStart, iEnd, + iMax, iTotal, sPre) { + return Number(iTotal).toLocaleString() + " records"; + }; + } + } + + // auto hide navigation if requested + // Note, this only works on client-side processing mode as on server-side, + // cells (data.data) is null; In addition, we require the pageLength option + // being provided explicitly to enable this. Despite we may be able to deduce + // the default value of pageLength, it may complicate things so we'd rather + // put this responsiblity to users and warn them on the R side. + if (data.autoHideNavigation === true && data.options.paging !== false) { + // strip all nav if length >= cells + if ((cells instanceof Array) && data.options.pageLength >= cells.length) + options.dom = bootstrapActive ? "<'row'<'col-sm-12'tr>>" : "t"; + // alternatively lean things out for flexdashboard mobile portrait + else if (bootstrapActive && window.FlexDashboard && window.FlexDashboard.isMobilePhone()) + options.dom = "<'row'<'col-sm-12'f>>" + + "<'row'<'col-sm-12'tr>>" + + "<'row'<'col-sm-12'p>>"; + } + + $.extend(true, options, data.options || {}); + + var searchCols = options.searchCols; + if (searchCols) { + searchCols = searchCols.map(function(x) { + return x === null ? '' : x.search; + }); + // FIXME: this means I don't respect the escapeRegex setting + delete options.searchCols; + } + + // server-side processing? + var server = options.serverSide === true; + + // use the dataSrc function to pre-process JSON data returned from R + var DT_rows_all = [], DT_rows_current = []; + if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' && + /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) { + options.ajax.dataSrc = function(json) { + DT_rows_all = $.makeArray(json.DT_rows_all); + DT_rows_current = $.makeArray(json.DT_rows_current); + var data = json.data; + if (!colReorderEnabled()) return data; + var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row; + for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false; + if (flag) return data; + for (i = 0; i < data.length; ++i) { + row = data[i].slice(); + for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]]; + } + return data; + }; + } + + var thiz = this; + if (instance.fillContainer) $table.on('init.dt', function(e) { + thiz.fillAvailableHeight(el, $(el).innerHeight()); + }); + // If the page contains serveral datatables and one of which enables colReorder, + // the table.colReorder.order() function will exist but throws error when called. + // So it seems like the only way to know if colReorder is enabled or not is to + // check the options. + var colReorderEnabled = function() { return "colReorder" in options; }; + var table = $table.DataTable(options); + $el.data('datatable', table); + + // Unregister previous Crosstalk event subscriptions, if they exist + if (instance.ctfilterSubscription) { + instance.ctfilterHandle.off("change", instance.ctfilterSubscription); + instance.ctfilterSubscription = null; + } + if (instance.ctselectSubscription) { + instance.ctselectHandle.off("change", instance.ctselectSubscription); + instance.ctselectSubscription = null; + } + + if (!crosstalkOptions.group) { + $table[0].ctfilter = null; + $table[0].ctselect = null; + } else { + var key = crosstalkOptions.key; + function keysToMatches(keys) { + if (!keys) { + return null; + } else { + var selectedKeys = {}; + for (var i = 0; i < keys.length; i++) { + selectedKeys[keys[i]] = true; + } + var matches = {}; + for (var j = 0; j < key.length; j++) { + if (selectedKeys[key[j]]) + matches[j] = true; + } + return matches; + } + } + + function applyCrosstalkFilter(e) { + $table[0].ctfilter = keysToMatches(e.value); + table.draw(); + } + instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter); + applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys}); + + function applyCrosstalkSelection(e) { + if (e.sender !== instance.ctselectHandle) { + table + .rows('.' + selClass, {search: 'applied'}) + .nodes() + .to$() + .removeClass(selClass); + if (selectedRows) + changeInput('rows_selected', selectedRows(), void 0, true); + } + + if (e.sender !== instance.ctselectHandle && e.value && e.value.length) { + var matches = keysToMatches(e.value); + + // persistent selection with plotly (& leaflet) + var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {}; + if (ctOpts.persistent === true) { + var matches = $.extend(matches, $table[0].ctselect); + } + + $table[0].ctselect = matches; + table.draw(); + } else { + if ($table[0].ctselect) { + $table[0].ctselect = null; + table.draw(); + } + } + } + instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection); + // TODO: This next line doesn't seem to work when renderDataTable is used + applyCrosstalkSelection({value: instance.ctselectHandle.value}); + } + + var inArray = function(val, array) { + return $.inArray(val, $.makeArray(array)) > -1; + }; + + // search the i-th column + var searchColumn = function(i, value) { + var regex = false, ci = true; + if (options.search) { + 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') { + + filterRow.each(function(i, td) { + + var $td = $(td), type = $td.data('type'), filter; + var $input = $td.children('div').first().children('input'); + var disabled = $input.prop('disabled'); + var searchable = table.settings()[0].aoColumns[i].bSearchable; + $input.prop('disabled', !searchable || disabled); + $input.data('searchable', searchable); // for updating later + $input.on('input blur', function() { + $input.next('span').toggle(Boolean($input.val())); + }); + // Bootstrap sets pointer-events to none and we won't be able to click + // the clear button + $input.next('span').css('pointer-events', 'auto').hide().click(function() { + $(this).hide().prev('input').val('').trigger('input').focus(); + }); + var searchCol; // search string for this column + if (searchCols && searchCols[i]) { + searchCol = searchCols[i]; + $input.val(searchCol).trigger('input'); + } + var $x = $td.children('div').last(); + + // remove the overflow: hidden attribute of the scrollHead + // (otherwise the scrolling table body obscures the filters) + // The workaround and the discussion from + // https://github.com/rstudio/DT/issues/554#issuecomment-518007347 + // Otherwise the filter selection will not be anchored to the values + // when the columns number is many and scrollX is enabled. + var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot'); + var cssOverflowHead = scrollHead.css('overflow'); + var scrollBody = $(el).find('.dataTables_scrollBody'); + var cssOverflowBody = scrollBody.css('overflow'); + var scrollTable = $(el).find('.dataTables_scroll'); + var cssOverflowTable = scrollTable.css('overflow'); + if (cssOverflowHead === 'hidden') { + $x.on('show hide', function(e) { + if (e.type === 'show') { + scrollHead.css('overflow', 'visible'); + scrollBody.css('overflow', 'visible'); + scrollTable.css('overflow-x', 'scroll'); + } else { + scrollHead.css('overflow', cssOverflowHead); + scrollBody.css('overflow', cssOverflowBody); + scrollTable.css('overflow-x', cssOverflowTable); + } + }); + $x.css('z-index', 25); + } + + if (inArray(type, ['factor', 'logical'])) { + $input.on({ + click: function() { + $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus(); + }, + input: function() { + 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({ + options: $input2.data('options').map(function(v, i) { + return ({text: v, value: v}); + }), + plugins: ['remove_button'], + hideSelected: true, + onChange: function(value) { + if (value === null) value = []; // compatibility with jQuery 3.0 + $input.val(value.length ? JSON.stringify(value) : ''); + if (value.length) $input.trigger('input'); + $input.attr('title', $input.val()); + if (server) { + 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)); + filter[0].selectize.on('blur', function() { + $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur'); + }); + filter.next('div').css('margin-bottom', 'auto'); + } else if (type === 'character') { + var fun = function() { + searchColumn(i, $input.val()).draw(); + }; + if (server) { + fun = $.fn.dataTable.util.throttle(fun, options.searchDelay); + } + $input.on('input', fun); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + var $x0 = $x; + $x = $x0.children('div').first(); + $x0.css({ + 'background-color': '#fff', + 'border': '1px #ddd solid', + 'border-radius': '4px', + 'padding': data.vertical ? '35px 20px': '20px 20px 10px 20px' + }); + var $spans = $x0.children('span').css({ + 'margin-top': data.vertical ? '0' : '10px', + 'white-space': 'nowrap' + }); + var $span1 = $spans.first(), $span2 = $spans.last(); + var r1 = +$x.data('min'), r2 = +$x.data('max'); + // when the numbers are too small or have many decimal places, the + // slider may have numeric precision problems (#150) + var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0)); + r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale); + var scaleBack = function(x, scale) { + if (scale === 1) return x; + var d = Math.round(Math.log(scale) / Math.log(10)); + // to avoid problems like 3.423/100 -> 0.034230000000000003 + return (x / scale).toFixed(d); + }; + var slider_min = function() { + return filter.noUiSlider('options').range.min; + }; + var slider_max = function() { + return filter.noUiSlider('options').range.max; + }; + $input.on({ + focus: function() { + $x0.show().trigger('show'); + // first, make sure the slider div leaves at least 20px between + // the two (slider value) span's + $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20)); + // then, if the input is really wide or slider is vertical, + // make the slider the same width as the input + if ($x0.outerWidth() < $input.outerWidth() || data.vertical) { + $x0.outerWidth($input.outerWidth()); + } + // make sure the slider div does not reach beyond the right margin + if ($(window).width() < $x0.offset().left + $x0.width()) { + $x0.offset({ + 'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth() + }); + } + }, + blur: function() { + $x0.hide().trigger('hide'); + }, + input: function() { + if ($input.val() === '') filter.val([slider_min(), slider_max()]); + }, + change: function() { + var v = $input.val().replace(/\s/g, ''); + if (v === '') return; + v = v.split('...'); + if (v.length !== 2) { + $input.parent().addClass('has-error'); + return; + } + if (v[0] === '') v[0] = slider_min(); + if (v[1] === '') v[1] = slider_max(); + $input.parent().removeClass('has-error'); + // treat date as UTC time at midnight + var strTime = function(x) { + var s = type === 'date' ? 'T00:00:00Z' : ''; + var t = new Date(x + s).getTime(); + // add 10 minutes to date since it does not hurt the date, and + // it helps avoid the tricky floating point arithmetic problems, + // e.g. sometimes the date may be a few milliseconds earlier + // than the midnight due to precision problems in noUiSlider + return type === 'date' ? t + 3600000 : t; + }; + if (inArray(type, ['date', 'time'])) { + v[0] = strTime(v[0]); + v[1] = strTime(v[1]); + } + if (v[0] != slider_min()) v[0] *= scale; + if (v[1] != slider_max()) v[1] *= scale; + filter.val(v); + } + }); + var formatDate = function(d, isoFmt) { + 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); + }; + return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth()) + + '-' + pad0(x.getUTCDate()); + } else { + return x.toISOString(); + } + }; + var opts = type === 'date' ? { step: 60 * 60 * 1000 } : + type === 'integer' ? { step: 1 } : {}; + + opts.orientation = data.vertical ? 'vertical': 'horizontal'; + opts.direction = data.vertical ? 'rtl': 'ltr'; + + filter = $x.noUiSlider($.extend({ + start: [r1, r2], + range: {min: r1, max: r2}, + connect: true + }, opts)); + if (scale > 1) (function() { + var t1 = r1, t2 = r2; + var val = filter.val(); + while (val[0] > r1 || val[1] < r2) { + if (val[0] > r1) { + t1 -= val[0] - r1; + } + if (val[1] < r2) { + t2 += r2 - val[1]; + } + filter = $x.noUiSlider($.extend({ + start: [t1, t2], + range: {min: t1, max: t2}, + connect: true + }, opts), true); + val = filter.val(); + } + r1 = t1; r2 = t2; + })(); + var updateSliderText = function(v1, v2) { + $span1.text(formatDate(v1, false)); $span2.text(formatDate(v2, false)); + }; + updateSliderText(r1, r2); + var updateSlider = function(e) { + var val = filter.val(); + // turn off filter if in full range + $td.data('filter', val[0] > slider_min() || val[1] < slider_max()); + var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival; + if ($td.data('filter')) { + ival = v1 + ' ... ' + v2; + $input.attr('title', ival).val(ival).trigger('input'); + } else { + $input.attr('title', '').val(''); + } + updateSliderText(val[0], val[1]); + if (e.type === 'slide') return; // no searching when sliding only + if (server) { + searchColumn(i, $td.data('filter') ? ival : '').draw(); + return; + } + table.draw(); + }; + filter.on({ + set: updateSlider, + slide: updateSlider + }); + } + + // server-side processing will be handled by R (or whatever server + // language you use); the following code is only needed for client-side + // processing + if (server) { + // if a search string has been pre-set, search now + if (searchCol) searchColumn(i, searchCol).draw(); + return; + } + + var customFilter = function(settings, data, dataIndex) { + // there is no way to attach a search function to a specific table, + // and we need to make sure a global search function is not applied to + // all tables (i.e. a range filter in a previous table should not be + // applied to the current table); we use the settings object to + // determine if we want to perform searching on the current table, + // since settings.sTableId will be different to different tables + if (table.settings()[0] !== settings) return true; + // no filter on this column or no need to filter this column + if (typeof filter === 'undefined' || !$td.data('filter')) return true; + + var r = filter.val(), v, r0, r1; + var i_data = function(i) { + if (!colReorderEnabled()) return i; + var order = table.colReorder.order(), k; + for (k = 0; k < order.length; ++k) if (order[k] === i) return k; + return i; // in theory it will never be here... + } + v = data[i_data(i)]; + if (type === 'number' || type === 'integer') { + v = parseFloat(v); + // how to handle NaN? currently exclude these rows + if (isNaN(v)) return(false); + r0 = parseFloat(scaleBack(r[0], scale)) + r1 = parseFloat(scaleBack(r[1], scale)); + if (v >= r0 && v <= r1) return true; + } else if (type === 'date' || type === 'time') { + v = new Date(v); + r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale); + if (v >= r0 && v <= r1) return true; + } else if (type === 'factor') { + if (r.length === 0 || inArray(v, r)) return true; + } else if (type === 'logical') { + if (r.length === 0) return true; + if (inArray(v === '' ? 'na' : v, r)) return true; + } + return false; + }; + + $.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'); + } + } + + }); + + } + + // highlight search keywords + var highlight = function() { + var body = $(table.table().body()); + // removing the old highlighting first + body.unhighlight(); + + // don't highlight the "not found" row, so we get the rows using the api + if (table.rows({ filter: 'applied' }).data().length === 0) return; + // highlight global search keywords + body.highlight($.trim(table.search()).split(/\s+/)); + // then highlight keywords from individual column filters + if (filterRow) filterRow.each(function(i, td) { + var $td = $(td), type = $td.data('type'); + if (type !== 'character') return; + var $input = $td.children('div').first().children('input'); + var column = table.column(i).nodes().to$(), + val = $.trim($input.val()); + if (type !== 'character' || val === '') return; + column.highlight(val.split(/\s+/)); + }); + }; + + if (options.searchHighlight) { + table + .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight) + .on('destroy', function() { + // remove event handler + table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth'); + }); + + // Set the option for escaping regex characters in our search string. This will be used + // for all future matching. + jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex); + + // initial highlight for state saved conditions and initial states + highlight(); + } + + // run the callback function on the table instance + if (typeof data.callback === 'function') data.callback(table); + + // double click to edit the cell, row, column, or all cells + if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) { + // only bring up the editor when the cell itself is dbclicked, and ignore + // other dbclick events bubbled up (e.g. from the ) + if (e.target !== this) return; + var target = [], immediate = false; + switch (data.editable.target) { + case 'cell': + target = [this]; + immediate = true; // edit will take effect immediately + break; + case 'row': + target = table.cells(table.cell(this).index().row, '*').nodes(); + break; + case 'column': + target = table.cells('*', table.cell(this).index().column).nodes(); + break; + case 'all': + target = table.cells().nodes(); + break; + default: + throw 'The editable parameter must be "cell", "row", "column", or "all"'; + } + var disableCols = data.editable.disable ? data.editable.disable.columns : null; + var numericCols = data.editable.numeric; + var areaCols = data.editable.area; + var dateCols = data.editable.date; + for (var i = 0; i < target.length; i++) { + (function(cell, current) { + var $cell = $(cell), html = $cell.html(); + var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column; + var $input; + if (inArray(index, numericCols)) { + $input = $(''); + } else if (inArray(index, areaCols)) { + $input = $(''); + } else if (inArray(index, dateCols)) { + $input = $(''); + } else { + $input = $(''); + } + if (!immediate) { + $cell.data('input', $input).data('html', html); + $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel'); + } + $input.val(value); + if (inArray(index, disableCols)) { + $input.attr('readonly', '').css('filter', 'invert(25%)'); + } + $cell.empty().append($input); + if (cell === current) $input.focus(); + $input.css('width', '100%'); + + if (immediate) $input.on('blur', function(e) { + var valueNew = $input.val(); + if (valueNew !== value) { + _cell.data(valueNew); + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'}); + } + // for server-side processing, users have to call replaceData() to update the table + if (!server) table.draw(false); + } else { + $cell.html(html); + } + }).on('keyup', function(e) { + // hit Escape to cancel editing + if (e.keyCode === 27) $input.trigger('blur'); + }); + + // bulk edit (row, column, or all) + if (!immediate) $input.on('keyup', function(e) { + var removeInput = function($cell, restore) { + $cell.data('input').remove(); + if (restore) $cell.html($cell.data('html')); + } + if (e.keyCode === 27) { + for (var i = 0; i < target.length; i++) { + removeInput($(target[i]), true); + } + } else if (e.keyCode === 13 && e.ctrlKey) { + // Ctrl + Enter + var cell, $cell, _cell, cellData = []; + for (var i = 0; i < target.length; i++) { + cell = target[i]; $cell = $(cell); _cell = table.cell(cell); + _cell.data($cell.data('input').val()); + HTMLWidgets.shinyMode && cellData.push(cellInfo(cell)); + removeInput($cell, false); + } + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"}); + } + if (!server) table.draw(false); + } + }); + })(target[i], this); + } + }); + + // interaction with shiny + if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return; + + var methods = {}; + var shinyData = {}; + + methods.updateCaption = function(caption) { + if (!caption) return; + $table.children('caption').replaceWith(caption); + } + + // register clear functions to remove input values when the table is removed + instance.clearInputs = {}; + + var changeInput = function(id, value, type, noCrosstalk, opts) { + var event = id; + id = el.id + '_' + id; + if (type) id = id + ':' + type; + // do not update if the new value is the same as old value + if (event !== 'cell_edit' && !/_clicked$/.test(event) && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value)) + return; + shinyData[id] = JSON.stringify(value); + if (HTMLWidgets.shinyMode && Shiny.setInputValue) { + Shiny.setInputValue(id, value, opts); + if (!instance.clearInputs[id]) instance.clearInputs[id] = function() { + Shiny.setInputValue(id, null); + } + } + + // HACK + if (event === "rows_selected" && !noCrosstalk) { + if (crosstalkOptions.group) { + var keys = crosstalkOptions.key; + var selectedKeys = null; + if (value) { + selectedKeys = []; + for (var i = 0; i < value.length; i++) { + // The value array's contents use 1-based row numbers, so we must + // convert to 0-based before indexing into the keys array. + selectedKeys.push(keys[value[i] - 1]); + } + } + instance.ctselectHandle.set(selectedKeys); + } + } + }; + + var addOne = function(x) { + return x.map(function(i) { return 1 + i; }); + }; + + var unique = function(x) { + var ux = []; + $.each(x, function(i, el){ + if ($.inArray(el, ux) === -1) ux.push(el); + }); + return ux; + } + + // change the row index of a cell + var tweakCellIndex = function(cell) { + var info = cell.index(); + // some cell may not be valid. e.g, #759 + // when using the RowGroup extension, datatables will + // generate the row label and the cells are not part of + // the data thus contain no row/col info + if (info === undefined) + return {row: null, col: null}; + if (server) { + info.row = DT_rows_current[info.row]; + } else { + info.row += 1; + } + return {row: info.row, col: info.column}; + } + + var cleanSelectedValues = function() { + changeInput('rows_selected', []); + changeInput('columns_selected', []); + changeInput('cells_selected', transposeArray2D([]), 'shiny.matrix'); + } + // #828 we should clean the selection on the server-side when the table reloads + cleanSelectedValues(); + + // a flag to indicates if select extension is initialized or not + var flagSelectExt = table.settings()[0]._select !== undefined; + // the Select extension should only be used in the client mode and + // when the selection.mode is set to none + if (data.selection.mode === 'none' && !server && flagSelectExt) { + var updateRowsSelected = function() { + var rows = table.rows({selected: true}); + var selected = []; + $.each(rows.indexes().toArray(), function(i, v) { + selected.push(v + 1); + }); + changeInput('rows_selected', selected); + } + var updateColsSelected = function() { + var columns = table.columns({selected: true}); + changeInput('columns_selected', columns.indexes().toArray()); + } + var updateCellsSelected = function() { + var cells = table.cells({selected: true}); + var selected = []; + cells.every(function() { + var row = this.index().row; + var col = this.index().column; + selected = selected.concat([[row + 1, col]]); + }); + changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix'); + } + table.on('select deselect', function(e, dt, type, indexes) { + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + }) + } + + var selMode = data.selection.mode, selTarget = data.selection.target; + var selDisable = data.selection.selectable === false; + if (inArray(selMode, ['single', 'multiple'])) { + var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected'; + // selected1: row indices; selected2: column indices + var initSel = function(x) { + if (x === null || typeof x === 'boolean' || selTarget === 'cell') { + return {rows: [], cols: []}; + } else if (selTarget === 'row') { + return {rows: $.makeArray(x), cols: []}; + } else if (selTarget === 'column') { + return {rows: [], cols: $.makeArray(x)}; + } else if (selTarget === 'row+column') { + return {rows: $.makeArray(x.rows), cols: $.makeArray(x.cols)}; + } + } + var selected = data.selection.selected; + var selected1 = initSel(selected).rows, selected2 = initSel(selected).cols; + // selectable should contain either all positive or all non-positive values, not both + // positive values indicate "selectable" while non-positive values means "nonselectable" + // the assertion is performed on R side. (only column indicides could be zero which indicates + // the row name) + var selectable = data.selection.selectable; + var selectable1 = initSel(selectable).rows, selectable2 = initSel(selectable).cols; + + // After users reorder the rows or filter the table, we cannot use the table index + // directly. Instead, we need this function to find out the rows between the two clicks. + // If user filter the table again between the start click and the end click, the behavior + // would be undefined, but it should not be a problem. + var shiftSelRowsIndex = function(start, end) { + var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray(); + start = indexes.indexOf(start); end = indexes.indexOf(end); + // if start is larger than end, we need to swap + if (start > end) { + var tmp = end; end = start; start = tmp; + } + return indexes.slice(start, end + 1); + } + + var serverRowIndex = function(clientRowIndex) { + return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1; + } + + // row, column, or cell selection + var lastClickedRow; + if (inArray(selTarget, ['row', 'row+column'])) { + // Get the current selected rows. It will also + // update the selected1's value based on the current row selection state + // Note we can't put this function inside selectRows() directly, + // the reason is method.selectRows() will override selected1's value but this + // function will add rows to selected1 (keep the existing selection), which is + // inconsistent with column and cell selection. + var selectedRows = function() { + var rows = table.rows('.' + selClass); + var idx = rows.indexes().toArray(); + if (!server) { + selected1 = addOne(idx); + return selected1; + } + idx = idx.map(function(i) { + return DT_rows_current[i]; + }); + selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx; + return selected1; + } + // Change selected1's value based on selectable1, then refresh the row state + var onlyKeepSelectableRows = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected1 = []; + return; + } + if (selectable1.length === 0) return; + var nonselectable = selectable1[0] <= 0; + if (nonselectable) { + // should make selectable1 positive + selected1 = $(selected1).not(selectable1.map(function(i) { return -i; })).get(); + } else { + selected1 = $(selected1).filter(selectable1).get(); + } + } + // Change selected1's value based on selectable1, then + // refresh the row selection state according to values in selected1 + var selectRows = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableRows(); + table.$('tr.' + selClass).removeClass(selClass); + if (selected1.length === 0) return; + if (server) { + table.rows({page: 'current'}).every(function() { + if (inArray(DT_rows_current[this.index()], selected1)) { + $(this.node()).addClass(selClass); + } + }); + } else { + var selected0 = selected1.map(function(i) { return i - 1; }); + $(table.rows(selected0).nodes()).addClass(selClass); + } + } + table.on('mousedown.dt', 'tbody tr', function(e) { + var $this = $(this), thisRow = table.row(this); + if (selMode === 'multiple') { + if (e.shiftKey && lastClickedRow !== undefined) { + // select or de-select depends on the last clicked row's status + var flagSel = !$this.hasClass(selClass); + var crtClickedRow = serverRowIndex(thisRow.index()); + if (server) { + var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow); + // update current page's selClass + rowsIndex.map(function(i) { + var rowIndex = DT_rows_current.indexOf(i); + if (rowIndex >= 0) { + var row = table.row(rowIndex).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + } + }); + // update selected1 + if (flagSel) { + selected1 = unique(selected1.concat(rowsIndex)); + } else { + selected1 = selected1.filter(function(index) { + return !inArray(index, rowsIndex); + }); + } + } else { + // js starts from 0 + shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) { + var row = table.row(value).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + }); + } + e.preventDefault(); + } else { + $this.toggleClass(selClass); + } + } else { + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + } else { + table.$('tr.' + selClass).removeClass(selClass); + $this.addClass(selClass); + } + } + if (server && !$this.hasClass(selClass)) { + var id = DT_rows_current[thisRow.index()]; + // remove id from selected1 since its class .selected has been removed + if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1); + } + selectedRows(); // update selected1's value based on selClass + selectRows(false); // only keep the selectable rows + changeInput('rows_selected', selected1); + changeInput('row_last_clicked', serverRowIndex(thisRow.index()), null, null, {priority: 'event'}); + lastClickedRow = serverRowIndex(thisRow.index()); + }); + selectRows(false); // in case users have specified pre-selected rows + // restore selected rows after the table is redrawn (e.g. sort/search/page); + // client-side tables will preserve the selections automatically; for + // server-side tables, we have to *real* row indices are in `selected1` + changeInput('rows_selected', selected1); + if (server) table.on('draw.dt', function(e) { selectRows(false); }); + methods.selectRows = function(selected, ignoreSelectable) { + selected1 = $.makeArray(selected); + selectRows(ignoreSelectable); + changeInput('rows_selected', selected1); + } + } + + if (inArray(selTarget, ['column', 'row+column'])) { + if (selTarget === 'row+column') { + $(table.columns().footer()).css('cursor', 'pointer'); + } + // update selected2's value based on selectable2 + var onlyKeepSelectableCols = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected2 = []; + return; + } + if (selectable2.length === 0) return; + var nonselectable = selectable2[0] <= 0; + if (nonselectable) { + // need to make selectable2 positive + selected2 = $(selected2).not(selectable2.map(function(i) { return -i; })).get(); + } else { + selected2 = $(selected2).filter(selectable2).get(); + } + } + // update selected2 and then + // refresh the col selection state according to values in selected2 + var selectCols = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCols(); + // if selected2 is not a valide index (e.g., larger than the column number) + // table.columns(selected2) will fail and result in a blank table + // this is different from the table.rows(), where the out-of-range indexes + // doesn't affect at all + selected2 = $(selected2).filter(table.columns().indexes()).get(); + table.columns().nodes().flatten().to$().removeClass(selClass); + if (selected2.length > 0) + table.columns(selected2).nodes().flatten().to$().addClass(selClass); + } + var callback = function() { + var colIdx = selTarget === 'column' ? table.cell(this).index().column : + $.inArray(this, table.columns().footer()), + thisCol = $(table.column(colIdx).nodes()); + if (colIdx === -1) return; + if (thisCol.hasClass(selClass)) { + thisCol.removeClass(selClass); + selected2.splice($.inArray(colIdx, selected2), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + thisCol.addClass(selClass); + selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx])); + } + selectCols(false); // update selected2 based on selectable + changeInput('columns_selected', selected2); + } + if (selTarget === 'column') { + $(table.table().body()).on('click.dt', 'td', callback); + } else { + $(table.table().footer()).on('click.dt', 'tr th', callback); + } + selectCols(false); // in case users have specified pre-selected columns + changeInput('columns_selected', selected2); + if (server) table.on('draw.dt', function(e) { selectCols(false); }); + methods.selectColumns = function(selected, ignoreSelectable) { + selected2 = $.makeArray(selected); + selectCols(ignoreSelectable); + changeInput('columns_selected', selected2); + } + } + + if (selTarget === 'cell') { + var selected3 = [], selectable3 = []; + if (selected !== null) selected3 = selected; + if (selectable !== null && typeof selectable !== 'boolean') selectable3 = selectable; + var findIndex = function(ij, sel) { + for (var i = 0; i < sel.length; i++) { + if (ij[0] === sel[i][0] && ij[1] === sel[i][1]) return i; + } + return -1; + } + // Change selected3's value based on selectable3, then refresh the cell state + var onlyKeepSelectableCells = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected3 = []; + return; + } + if (selectable3.length === 0) return; + var nonselectable = selectable3[0][0] <= 0; + var out = []; + if (nonselectable) { + selected3.map(function(ij) { + // should make selectable3 positive + if (findIndex([-ij[0], -ij[1]], selectable3) === -1) { out.push(ij); } + }); + } else { + selected3.map(function(ij) { + if (findIndex(ij, selectable3) > -1) { out.push(ij); } + }); + } + selected3 = out; + } + // Change selected3's value based on selectable3, then + // refresh the cell selection state according to values in selected3 + var selectCells = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCells(); + table.$('td.' + selClass).removeClass(selClass); + if (selected3.length === 0) return; + if (server) { + table.cells({page: 'current'}).every(function() { + var info = tweakCellIndex(this); + if (findIndex([info.row, info.col], selected3) > -1) + $(this.node()).addClass(selClass); + }); + } else { + selected3.map(function(ij) { + $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass); + }); + } + }; + table.on('click.dt', 'tbody td', function() { + var $this = $(this), info = tweakCellIndex(table.cell(this)); + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + selected3.splice(findIndex([info.row, info.col], selected3), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + $this.addClass(selClass); + selected3 = selMode === 'single' ? [[info.row, info.col]] : + unique(selected3.concat([[info.row, info.col]])); + } + selectCells(false); // must call this to update selected3 based on selectable3 + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + }); + selectCells(false); // in case users have specified pre-selected columns + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + + if (server) table.on('draw.dt', function(e) { selectCells(false); }); + methods.selectCells = function(selected, ignoreSelectable) { + selected3 = selected ? selected : []; + selectCells(ignoreSelectable); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + } + } + } + + // expose some table info to Shiny + var updateTableInfo = function(e, settings) { + // TODO: is anyone interested in the page info? + // changeInput('page_info', table.page.info()); + var updateRowInfo = function(id, modifier) { + var idx; + if (server) { + idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all; + } else { + var rows = table.rows($.extend({ + search: 'applied', + page: 'all' + }, modifier)); + idx = addOne(rows.indexes().toArray()); + } + changeInput('rows' + '_' + id, idx); + }; + updateRowInfo('current', {page: 'current'}); + updateRowInfo('all', {}); + } + table.on('draw.dt', updateTableInfo); + updateTableInfo(); + + // state info + table.on('draw.dt column-visibility.dt', function() { + changeInput('state', table.state()); + }); + changeInput('state', table.state()); + + // search info + var updateSearchInfo = function() { + changeInput('search', table.search()); + if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) { + return $(td).find('input').first().val(); + })); + } + table.on('draw.dt', updateSearchInfo); + updateSearchInfo(); + + var cellInfo = function(thiz) { + var info = tweakCellIndex(table.cell(thiz)); + info.value = table.cell(thiz).data(); + return info; + } + // the current cell clicked on + table.on('click.dt', 'tbody td', function() { + changeInput('cell_clicked', cellInfo(this), null, null, {priority: 'event'}); + }) + changeInput('cell_clicked', {}); + + // do not trigger table selection when clicking on links unless they have classes + table.on('mousedown.dt', 'tbody td a', function(e) { + if (this.className === '') e.stopPropagation(); + }); + + methods.addRow = function(data, rowname, resetPaging) { + var n = table.columns().indexes().length, d = n - data.length; + if (d === 1) { + data = rowname.concat(data) + } else if (d !== 0) { + console.log(data); + console.log(table.columns().indexes()); + throw 'New data must be of the same length as current data (' + n + ')'; + }; + table.row.add(data).draw(resetPaging); + } + + methods.updateSearch = function(keywords) { + if (keywords.global !== null) + $(table.table().container()).find('input[type=search]').first() + .val(keywords.global).trigger('input'); + var columns = keywords.columns; + if (!filterRow || columns === null) return; + filterRow.toArray().map(function(td, i) { + var v = typeof columns === 'string' ? columns : columns[i]; + if (typeof v === 'undefined') { + console.log('The search keyword for column ' + i + ' is undefined') + return; + } + $(td).find('input').first().val(v).trigger('input'); + searchColumn(i, v); + }); + table.draw(); + } + + methods.hideCols = function(hide, reset) { + if (reset) table.columns().visible(true, false); + table.columns(hide).visible(false); + } + + methods.showCols = function(show, reset) { + if (reset) table.columns().visible(false, false); + table.columns(show).visible(true); + } + + methods.colReorder = function(order, origOrder) { + table.colReorder.order(order, origOrder); + } + + methods.selectPage = function(page) { + if (table.page.info().pages < page || page < 1) { + throw 'Selected page is out of range'; + }; + table.page(page - 1).draw(false); + } + + methods.reloadData = function(resetPaging, clearSelection) { + // empty selections first if necessary + if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]); + if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]); + if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]); + table.ajax.reload(null, resetPaging); + } + + // update table filters (set new limits of sliders) + methods.updateFilters = function(newProps) { + // loop through each filter in the filter row + filterRow.each(function(i, td) { + var k = i; + if (filterRow.length > newProps.length) { + if (i === 0) return; // first column is row names + k = i - 1; + } + // Update the filters to reflect the updated data. + // Allow "falsy" (e.g. NULL) to signify a no-op. + if (newProps[k]) { + setFilterProps(td, newProps[k]); + } + }); + }; + + table.shinyMethods = methods; + }, + resize: function(el, width, height, instance) { + if (instance.data) this.renderValue(el, instance.data, instance); + + // dynamically adjust height if fillContainer = TRUE + if (instance.fillContainer) + this.fillAvailableHeight(el, height); + + this.adjustWidth(el); + }, + + // dynamically set the scroll body to fill available height + // (used with fillContainer = TRUE) + fillAvailableHeight: function(el, availableHeight) { + + // see how much of the table is occupied by header/footer elements + // and use that to compute a target scroll body height + var dtWrapper = $(el).find('div.dataTables_wrapper'); + var dtScrollBody = $(el).find($('div.dataTables_scrollBody')); + var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight(); + var scrollBodyHeight = availableHeight - framingHeight; + + // we need to set `max-height` to none as datatables library now sets this + // to a fixed height, disabling the ability to resize to fill the window, + // as it will be set to a fixed 100px under such circumstances, e.g., RStudio IDE, + // or FlexDashboard + // see https://github.com/rstudio/DT/issues/951#issuecomment-1026464509 + dtScrollBody.css('max-height', 'none'); + // set the height + dtScrollBody.height(scrollBodyHeight + 'px'); + }, + + // adjust the width of columns; remove the hard-coded widths on table and the + // scroll header when scrollX/Y are enabled + adjustWidth: function(el) { + var $el = $(el), table = $el.data('datatable'); + if (table) table.columns.adjust(); + $el.find('.dataTables_scrollHeadInner').css('width', '') + .children('table').css('margin-left', ''); + } +}); + + if (!HTMLWidgets.shinyMode) return; + + Shiny.addCustomMessageHandler('datatable-calls', function(data) { + var id = data.id; + var el = document.getElementById(id); + var table = el ? $(el).data('datatable') : null; + if (!table) { + console.log("Couldn't find table with id " + id); + return; + } + + var methods = table.shinyMethods, call = data.call; + if (methods[call.method]) { + methods[call.method].apply(table, call.args); + } else { + console.log("Unknown method " + call.method); + } + }); + +})(); diff --git a/docs/libs/dt-core-1.13.6/css/jquery.dataTables.extra.css b/docs/libs/dt-core-1.13.6/css/jquery.dataTables.extra.css new file mode 100644 index 0000000..b2dd141 --- /dev/null +++ b/docs/libs/dt-core-1.13.6/css/jquery.dataTables.extra.css @@ -0,0 +1,28 @@ +/* Selected rows/cells */ +table.dataTable tr.selected td, table.dataTable td.selected { + background-color: #b0bed9 !important; +} +/* In case of scrollX/Y or FixedHeader */ +.dataTables_scrollBody .dataTables_sizing { + visibility: hidden; +} + +/* The datatables' theme CSS file doesn't define +the color but with white background. It leads to an issue that +when the HTML's body color is set to 'white', the user can't +see the text since the background is white. One case happens in the +RStudio's IDE when inline viewing the DT table inside an Rmd file, +if the IDE theme is set to "Cobalt". + +See https://github.com/rstudio/DT/issues/447 for more info + +This fixes should have little side-effects because all the other elements +of the default theme use the #333 font color. + +TODO: The upstream may use relative colors for both the table background +and the color. It means the table can display well without this patch +then. At that time, we need to remove the below CSS attributes. +*/ +div.datatables { + color: #333; +} diff --git a/docs/libs/dt-core-1.13.6/css/jquery.dataTables.min.css b/docs/libs/dt-core-1.13.6/css/jquery.dataTables.min.css new file mode 100644 index 0000000..ad59f84 --- /dev/null +++ b/docs/libs/dt-core-1.13.6/css/jquery.dataTables.min.css @@ -0,0 +1 @@ +:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11;--dt-row-stripe: 0, 0, 0;--dt-row-hover: 0, 0, 0;--dt-column-ordering: 0, 0, 0;--dt-html-background: white}:root.dark{--dt-html-background: rgb(33, 37, 41)}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{display:inline-block;color:rgba(0, 0, 0, 0.5);content:"►"}table.dataTable tr.dt-hasChild td.dt-control:before{content:"▼"}html.dark table.dataTable td.dt-control:before{color:rgba(255, 255, 255, 0.5)}html.dark table.dataTable tr.dt-hasChild td.dt-control:before{color:rgba(255, 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.dataTables_wrapper .dataTables_paginate .paginate_button.current,html.dark .dataTables_wrapper .dataTables_paginate .paginate_button.current:hover{border:1px solid rgb(89, 91, 94);background:rgba(255, 255, 255, 0.15)}html.dark .dataTables_wrapper .dataTables_paginate .paginate_button.disabled,html.dark .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:hover,html.dark .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:active{color:#666 !important}html.dark .dataTables_wrapper .dataTables_paginate .paginate_button:hover{border:1px solid rgb(53, 53, 53);background:rgb(53, 53, 53)}html.dark .dataTables_wrapper .dataTables_paginate .paginate_button:active{background:#3a3a3a} diff --git a/docs/libs/dt-core-1.13.6/js/jquery.dataTables.min.js b/docs/libs/dt-core-1.13.6/js/jquery.dataTables.min.js new file mode 100644 index 0000000..f786b0d --- /dev/null +++ b/docs/libs/dt-core-1.13.6/js/jquery.dataTables.min.js @@ -0,0 +1,4 @@ +/*! DataTables 1.13.6 + * ©2008-2023 SpryMedia Ltd - datatables.net/license + */ +!function(n){"use strict";var a;"function"==typeof define&&define.amd?define(["jquery"],function(t){return n(t,window,document)}):"object"==typeof exports?(a=require("jquery"),"undefined"==typeof window?module.exports=function(t,e){return t=t||window,e=e||a(t),n(e,t,t.document)}:n(a,window,window.document)):window.DataTable=n(jQuery,window,document)}(function(P,j,v,H){"use strict";function d(t){var e=parseInt(t,10);return!isNaN(e)&&isFinite(t)?e:null}function l(t,e,n){var a=typeof t,r="string"==a;return"number"==a||"bigint"==a||!!h(t)||(e&&r&&(t=$(t,e)),n&&r&&(t=t.replace(q,"")),!isNaN(parseFloat(t))&&isFinite(t))}function a(t,e,n){var a;return!!h(t)||(h(a=t)||"string"==typeof a)&&!!l(t.replace(V,"").replace(/ - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -490,9 +491,9 @@

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/sec-bioinfo.html b/docs/sec-bioinfo.html index ae8ba5f..e6c1173 100644 --- a/docs/sec-bioinfo.html +++ b/docs/sec-bioinfo.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -1147,9 +1148,9 @@

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/sec-ccl.html b/docs/sec-ccl.html index 180291f..0e189d4 100644 --- a/docs/sec-ccl.html +++ b/docs/sec-ccl.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -332,9 +333,9 @@

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/sec-dataorg.html b/docs/sec-dataorg.html index 4528d42..79887c4 100644 --- a/docs/sec-dataorg.html +++ b/docs/sec-dataorg.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -1132,9 +1133,9 @@

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/sec-dplyr.html b/docs/sec-dplyr.html index 52971bb..c044ae7 100644 --- a/docs/sec-dplyr.html +++ b/docs/sec-dplyr.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -317,7 +318,7 @@

tidyverse package readr, instead of read.csv().

rna <- read_csv("data/rnaseq.csv")
## Rows: 32428 Columns: 19
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (14): gene, sample, organism, sex, infection, strain, tissue, product, e...
 ## dbl  (5): expression, age, time, mouse, ENTREZID
@@ -2011,9 +2012,9 @@ 

 
 

 
Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 
 
diff --git a/docs/sec-join.html b/docs/sec-join.html
index 6656df0..e91d217 100644
--- a/docs/sec-join.html
+++ b/docs/sec-join.html
@@ -13,7 +13,7 @@
 
 
 
-
+
 
 
-
+
 
-
+
 
-
-
-
-
-
+
+
+
+
+
 
 
 
@@ -149,6 +149,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;
@@ -558,7 +559,8 @@ 

 
## Warning in inner_join(jdf6, jdf7): Detected an unexpected many-to-many relationship between `x` and `y`.
 ## ℹ Row 2 of `x` matches multiple rows in `y`.
 ## ℹ Row 1 of `y` matches multiple rows in `x`.
-## ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence this warning.

+## ℹ If a many-to-many relationship is expected, set `relationship = "many-to-many"` to silence this
+##   warning.
## # A tibble: 4 × 9
 ##   uniprot organelle     entry isoform gene_name description organism isoform_num
 ##   <chr>   <chr>         <chr>   <dbl> <chr>     <chr>       <chr>          <dbl>
@@ -834,9 +836,9 @@ 

 
 

 
Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 
 
diff --git a/docs/sec-prog.html b/docs/sec-prog.html
index 55a626e..769b27f 100644
--- a/docs/sec-prog.html
+++ b/docs/sec-prog.html
@@ -13,7 +13,7 @@
 
 
 
-
+
 
 
-
+
 
-
+
 
-
-
-
-
-
+
+
+
+
+
 
 
 
@@ -149,6 +149,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;
@@ -470,7 +471,7 @@ 
Which iteration to use?
## Rows: 570 Columns: 4
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (3): sampleID, patient, type
 ## dbl (1): A1BG
@@ -493,7 +494,7 @@ 
Which iteration to use?

 
## Rows: 570 Columns: 4
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (3): sampleID, patient, type
 ## dbl (1): A1CF
@@ -690,11 +691,11 @@ 

 ##     }
 ##     return(sum(res))
 ## }
-## <bytecode: 0x5643f7f896b0>

-
set.seed(1L)
+## <bytecode: 0x55b7ec83ad60>

+
set.seed(1L)
 fun(5, 15)

 
## [1] 4825.278

-
set.seed(1L)
+
set.seed(1L)
 fun(15, 5)

 
## [1] 23

 

@@ -826,7 +827,7 @@ 

 for (i in seq_along(fls))
     l[[i]] <- read_csv(fls[i])

 
## Rows: 100 Columns: 8
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -834,7 +835,7 @@ 

 ## ℹ Use `spec()` to retrieve the full column specification for this data.
 ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 ## Rows: 105 Columns: 8
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -862,7 +863,7 @@ 

 
or

 
l <- lapply(fls, read_csv)

 
## Rows: 100 Columns: 8
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -870,7 +871,7 @@ 

 ## ℹ Use `spec()` to retrieve the full column specification for this data.
 ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
 ## Rows: 105 Columns: 8
-## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: ","
 ## chr (2): id, gender
 ## dbl (6): height, X, interro1, interro2, interro3, interro4
@@ -1107,9 +1108,9 @@ 

 
 

 
Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 

 
diff --git a/docs/sec-rr.html b/docs/sec-rr.html
index 56f2e66..a96026d 100644
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ip <- installed.packages()
 DT::datatable(ip[, c(1, 3, 5, 6, 10)], rownames = FALSE)

-

-
    
+
    
+
      
 
    • It is always useful to finish a Rmarkdown report with a section
 providing all the session information details with the
 sessionInfo() function, such at the end of this material. This
@@ -548,9 +549,9 @@ 
      
 
 
      
 
      Page built: 
-2023-11-01
+2024-02-22
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+R version 4.3.2 Patched (2023-12-27 r85757)
 
      
 
 
diff --git a/docs/sec-rrstudio.html b/docs/sec-rrstudio.html
index 6348b40..b553e09 100644
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@@ -747,13 +748,13 @@ 
      Asking for help
+## [1] cli_3.6.2 knitr_1.45 rlang_1.1.3 xfun_0.41 +## [5] stringi_1.8.3 highr_0.10 png_0.1-8 jsonlite_1.8.8 +## [9] glue_1.7.0 htmltools_0.5.7 sass_0.4.8 msmbstyle_0.0.19 +## [13] rmarkdown_2.25 evaluate_0.23 jquerylib_0.1.4 fastmap_1.1.1 +## [17] yaml_2.3.8 lifecycle_1.0.4 bookdown_0.34.2 stringr_1.5.1 +## [21] compiler_4.3.2 rstudioapi_0.15.0 digest_0.6.34 R6_2.5.1 +## [25] magrittr_2.0.3 bslib_0.6.1 tools_4.3.2 xml2_1.3.6 +## [29] cachem_1.0.8

Where to ask for help?
@@ -908,9 +910,9 @@

Page built: -2023-11-01 +2024-02-22 using -R version 4.3.1 Patched (2023-07-10 r84676) +R version 4.3.2 Patched (2023-12-27 r85757)

diff --git a/docs/sec-startdata.html b/docs/sec-startdata.html index 65c663c..3cab8bb 100644 --- a/docs/sec-startdata.html +++ b/docs/sec-startdata.html @@ -13,7 +13,7 @@ - + - + - + - - - - - + + + + + @@ -149,6 +149,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging div.csl-entry { margin-left:2em; @@ -1150,9 +1151,9 @@ 

## List of 5
 ##  $ : int [1:10] 1 2 3 4 5 6 7 8 9 10
 ##  $ : chr [1:26] "a" "b" "c" "d" ...
-##  $ : chr [1:667, 1:16] "abind" "affy" "affyio" "airway" ...
+##  $ : chr [1:734, 1:16] "abind" "affy" "affyio" "airway" ...
 ##   ..- attr(*, "dimnames")=List of 2
-##   .. ..$ : chr [1:667] "abind" "affy" "affyio" "airway" ...
+##   .. ..$ : chr [1:734] "abind" "affy" "affyio" "airway" ...
 ##   .. ..$ : chr [1:16] "Package" "LibPath" "Version" "Priority" ...
 ##  $ :'data.frame':    50 obs. of  2 variables:
 ##   ..$ speed: num [1:50] 4 4 7 7 8 9 10 10 10 11 ...
@@ -1729,9 +1730,9 @@ 

 
 

 
Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 
 
diff --git a/docs/sec-startr.html b/docs/sec-startr.html
index 5ce3284..e1ab467 100644
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+++ b/docs/sec-startr.html
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@@ -742,13 +743,13 @@ 

 use the “or” operator | to test for equality to multiple values, but
 this can quickly become tedious. The function %in% allows you to
 test if any of the elements of a search vector are found:

-
molecules <- c("dan", "rna", "protein", "peptide")
+
molecules <- c("dna", "rna", "protein", "peptide")
 molecules[molecules == "rna" | molecules == "dna"] # returns both rna and dna

-
## [1] "rna"

+
## [1] "dna" "rna"

 
molecules %in% c("rna", "dna", "metabolite", "peptide", "glycerol")

-
## [1] FALSE  TRUE FALSE  TRUE

+
## [1]  TRUE  TRUE FALSE  TRUE

 
molecules[molecules %in% c("rna", "dna", "metabolite", "peptide", "glycerol")]

-
## [1] "rna"     "peptide"

+
## [1] "dna"     "rna"     "peptide"

 

 

 ► Question
@@ -1340,9 +1341,9 @@ 

 
 

 
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+2024-02-22
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-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 

 

diff --git a/docs/sec-vis.html b/docs/sec-vis.html
index d0f4cf3..249c6d3 100644
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Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 
 
diff --git a/docs/session-information.html b/docs/session-information.html
index 5a2b3fe..bba61c5 100644
--- a/docs/session-information.html
+++ b/docs/session-information.html
@@ -13,7 +13,7 @@
 
 
 
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@@ -213,13 +214,13 @@ 

 Chapter 13 Session information

 
The following packages have been used to generate this document.

 
sessionInfo()

-
## R version 4.3.1 Patched (2023-07-10 r84676)
+
## R version 4.3.2 Patched (2023-12-27 r85757)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Manjaro Linux
 ## 
 ## Matrix products: default
-## BLAS:   /usr/lib/libblas.so.3.11.0 
-## LAPACK: /usr/lib/liblapack.so.3.11.0
+## BLAS:   /usr/lib/libblas.so.3.12.0 
+## LAPACK: /usr/lib/liblapack.so.3.12.0
 ## 
 ## locale:
 ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
@@ -239,41 +240,42 @@ 

 ## other attached packages:
 ##  [1] rWSBIM1322_0.3.2            BiocStyle_2.30.0           
 ##  [3] SummarizedExperiment_1.32.0 Biobase_2.62.0             
-##  [5] GenomicRanges_1.54.0        GenomeInfoDb_1.38.0        
-##  [7] IRanges_2.36.0              S4Vectors_0.40.0           
-##  [9] BiocGenerics_0.48.0         MatrixGenerics_1.14.0      
-## [11] matrixStats_1.0.0           gridExtra_2.3              
-## [13] patchwork_1.1.3             hexbin_1.28.3              
+##  [5] GenomicRanges_1.54.1        GenomeInfoDb_1.38.5        
+##  [7] IRanges_2.36.0              S4Vectors_0.40.2           
+##  [9] BiocGenerics_0.48.1         MatrixGenerics_1.14.0      
+## [11] matrixStats_1.2.0           gridExtra_2.3              
+## [13] patchwork_1.2.0             hexbin_1.28.3              
 ## [15] magrittr_2.0.3              rWSBIM1207_0.1.17          
-## [17] forcats_1.0.0               stringr_1.5.0              
-## [19] dplyr_1.1.3                 purrr_1.0.2                
-## [21] readr_2.1.4                 tidyr_1.3.0                
+## [17] forcats_1.0.0               stringr_1.5.1              
+## [19] dplyr_1.1.4                 purrr_1.0.2                
+## [21] readr_2.1.5                 tidyr_1.3.1                
 ## [23] tibble_3.2.1                ggplot2_3.4.4              
 ## [25] tidyverse_2.0.0             lubridate_1.9.3            
 ## 
 ## loaded via a namespace (and not attached):
 ##  [1] tidyselect_1.2.0        farver_2.1.1            bitops_1.0-7           
-##  [4] fastmap_1.1.1           RCurl_1.98-1.12         digest_0.6.33          
-##  [7] timechange_0.2.0        lifecycle_1.0.3         ellipsis_0.3.2         
-## [10] compiler_4.3.1          rlang_1.1.1             sass_0.4.7             
-## [13] tools_4.3.1             utf8_1.2.4              yaml_2.3.7             
-## [16] knitr_1.44              S4Arrays_1.2.0          labeling_0.4.3         
-## [19] htmlwidgets_1.6.2       bit_4.0.5               DelayedArray_0.28.0    
-## [22] xml2_1.3.5              RColorBrewer_1.1-3      abind_1.4-5            
-## [25] withr_2.5.1             grid_4.3.1              fansi_1.0.5            
-## [28] colorspace_2.1-0        scales_1.2.1            cli_3.6.1              
+##  [4] fastmap_1.1.1           RCurl_1.98-1.14         digest_0.6.34          
+##  [7] timechange_0.3.0        lifecycle_1.0.4         ellipsis_0.3.2         
+## [10] compiler_4.3.2          rlang_1.1.3             sass_0.4.8             
+## [13] tools_4.3.2             utf8_1.2.4              yaml_2.3.8             
+## [16] knitr_1.45              S4Arrays_1.2.0          labeling_0.4.3         
+## [19] htmlwidgets_1.6.4       bit_4.0.5               DelayedArray_0.28.0    
+## [22] xml2_1.3.6              RColorBrewer_1.1-3      abind_1.4-5            
+## [25] withr_3.0.0             grid_4.3.2              fansi_1.0.6            
+## [28] colorspace_2.1-0        scales_1.3.0            cli_3.6.2              
 ## [31] rmarkdown_2.25          crayon_1.5.2            generics_0.1.3         
 ## [34] rstudioapi_0.15.0       tzdb_0.4.0              cachem_1.0.8           
-## [37] zlibbioc_1.48.0         parallel_4.3.1          BiocManager_1.30.22    
-## [40] XVector_0.42.0          vctrs_0.6.4             Matrix_1.6-1.1         
-## [43] jsonlite_1.8.7          bookdown_0.34.2         hms_1.1.3              
-## [46] bit64_4.0.5             crosstalk_1.2.0         jquerylib_0.1.4        
-## [49] glue_1.6.2              DT_0.30                 stringi_1.7.12         
+## [37] zlibbioc_1.48.0         parallel_4.3.2          BiocManager_1.30.22    
+## [40] XVector_0.42.0          vctrs_0.6.5             Matrix_1.6-5           
+## [43] jsonlite_1.8.8          bookdown_0.34.2         hms_1.1.3              
+## [46] bit64_4.0.5             crosstalk_1.2.1         jquerylib_0.1.4        
+## [49] glue_1.7.0              DT_0.31                 stringi_1.8.3          
 ## [52] gtable_0.3.4            munsell_0.5.0           msmbstyle_0.0.19       
-## [55] pillar_1.9.0            htmltools_0.5.6.1       GenomeInfoDbData_1.2.11
-## [58] R6_2.5.1                vroom_1.6.4             evaluate_0.22          
-## [61] lattice_0.22-5          png_0.1-8               bslib_0.5.1            
-## [64] SparseArray_1.2.0       xfun_0.40               pkgconfig_2.0.3

+## [55] pillar_1.9.0            htmltools_0.5.7         GenomeInfoDbData_1.2.11
+## [58] R6_2.5.1                vroom_1.6.5             evaluate_0.23          
+## [61] lattice_0.22-5          highr_0.10              png_0.1-8              
+## [64] bslib_0.6.1             SparseArray_1.2.3       xfun_0.41              
+## [67] pkgconfig_2.0.3

 

 

 13.1 R package setup

@@ -298,9 +300,9 @@ 

 
 

 
Page built: 
-2023-11-01
+2024-02-22
  using 
-R version 4.3.1 Patched (2023-07-10 r84676)
+R version 4.3.2 Patched (2023-12-27 r85757)
 

 

 
diff --git a/packages.bib b/packages.bib
index 5e4c162..8eda560 100644
--- a/packages.bib
+++ b/packages.bib
@@ -20,7 +20,7 @@ @Manual{R-BiocGenerics
   title = {BiocGenerics: S4 generic functions used in Bioconductor},
   author = {The Bioconductor Dev Team},
   year = {2023},
-  note = {R package version 0.48.0},
+  note = {R package version 0.48.1},
   url = {https://bioconductor.org/packages/BiocGenerics},
   doi = {10.18129/B9.bioc.BiocGenerics},
 }
@@ -46,7 +46,7 @@ @Manual{R-dplyr
   title = {dplyr: A Grammar of Data Manipulation},
   author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
   year = {2023},
-  note = {R package version 1.1.3},
+  note = {R package version 1.1.4},
   url = {https://dplyr.tidyverse.org},
 }
 
@@ -54,7 +54,8 @@ @Manual{R-forcats
   title = {forcats: Tools for Working with Categorical Variables (Factors)},
   author = {Hadley Wickham},
   year = {2023},
-  note = {R package version 1.0.0},
+  note = {R package version 1.0.0, 
+https://github.com/tidyverse/forcats},
   url = {https://forcats.tidyverse.org/},
 }
 
@@ -63,7 +64,7 @@ @Manual{R-GenomeInfoDb
 them to follow a particular naming style},
   author = {Sonali Arora and Martin Morgan and Marc Carlson and Hervé Pagès},
   year = {2023},
-  note = {R package version 1.38.0},
+  note = {R package version 1.38.5},
   url = {https://bioconductor.org/packages/GenomeInfoDb},
   doi = {10.18129/B9.bioc.GenomeInfoDb},
 }
@@ -72,7 +73,7 @@ @Manual{R-GenomicRanges
   title = {GenomicRanges: Representation and manipulation of genomic intervals},
   author = {Patrick Aboyoun and Hervé Pagès and Michael Lawrence},
   year = {2023},
-  note = {R package version 1.54.0},
+  note = {R package version 1.54.1},
   url = {https://bioconductor.org/packages/GenomicRanges},
   doi = {10.18129/B9.bioc.GenomicRanges},
 }
@@ -81,7 +82,8 @@ @Manual{R-ggplot2
   title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},
   author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},
   year = {2023},
-  note = {R package version 3.4.4},
+  note = {R package version 3.4.4, 
+https://github.com/tidyverse/ggplot2},
   url = {https://ggplot2.tidyverse.org},
 }
 
@@ -107,7 +109,7 @@ @Manual{R-knitr
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
   year = {2023},
-  note = {R package version 1.44},
+  note = {R package version 1.45},
   url = {https://yihui.org/knitr/},
 }
 
@@ -115,7 +117,8 @@ @Manual{R-lubridate
   title = {lubridate: Make Dealing with Dates a Little Easier},
   author = {Vitalie Spinu and Garrett Grolemund and Hadley Wickham},
   year = {2023},
-  note = {R package version 1.9.3},
+  note = {R package version 1.9.3, 
+https://github.com/tidyverse/lubridate},
   url = {https://lubridate.tidyverse.org},
 }
 
@@ -123,7 +126,8 @@ @Manual{R-magrittr
   title = {magrittr: A Forward-Pipe Operator for R},
   author = {Stefan Milton Bache and Hadley Wickham},
   year = {2022},
-  note = {R package version 2.0.3},
+  note = {R package version 2.0.3, 
+https://github.com/tidyverse/magrittr},
   url = {https://magrittr.tidyverse.org},
 }
 
@@ -142,7 +146,7 @@ @Manual{R-matrixStats
 Vectors)},
   author = {Henrik Bengtsson},
   year = {2023},
-  note = {R package version 1.0.0},
+  note = {R package version 1.2.0},
   url = {https://github.com/HenrikBengtsson/matrixStats},
 }
 
@@ -150,8 +154,9 @@ @Manual{R-matrixStats
 @Manual{R-patchwork,
   title = {patchwork: The Composer of Plots},
   author = {Thomas Lin Pedersen},
-  year = {2023},
-  note = {R package version 1.1.3},
+  year = {2024},
+  note = {R package version 1.2.0, 
+https://github.com/thomasp85/patchwork},
   url = {https://patchwork.data-imaginist.com},
 }
 
@@ -166,8 +171,8 @@ @Manual{R-purrr
 @Manual{R-readr,
   title = {readr: Read Rectangular Text Data},
   author = {Hadley Wickham and Jim Hester and Jennifer Bryan},
-  year = {2023},
-  note = {R package version 2.1.4},
+  year = {2024},
+  note = {R package version 2.1.5},
   url = {https://readr.tidyverse.org},
 }
 
@@ -175,7 +180,8 @@ @Manual{R-rmarkdown
   title = {rmarkdown: Dynamic Documents for R},
   author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
   year = {2023},
-  note = {R package version 2.25},
+  note = {R package version 2.25, 
+https://pkgs.rstudio.com/rmarkdown/},
   url = {https://github.com/rstudio/rmarkdown},
 }
 
@@ -186,7 +192,7 @@ @Manual{R-S4Vectors
 Bioconductor},
   author = {Hervé Pagès and Michael Lawrence and Patrick Aboyoun},
   year = {2023},
-  note = {R package version 0.40.0},
+  note = {R package version 0.40.2},
   url = {https://bioconductor.org/packages/S4Vectors},
   doi = {10.18129/B9.bioc.S4Vectors},
 }
@@ -194,8 +200,9 @@ @Manual{R-S4Vectors
 @Manual{R-stringr,
   title = {stringr: Simple, Consistent Wrappers for Common String Operations},
   author = {Hadley Wickham},
-  year = {2022},
-  note = {R package version 1.5.0},
+  year = {2023},
+  note = {R package version 1.5.1, 
+https://github.com/tidyverse/stringr},
   url = {https://stringr.tidyverse.org},
 }
 
@@ -219,8 +226,8 @@ @Manual{R-tibble
 @Manual{R-tidyr,
   title = {tidyr: Tidy Messy Data},
   author = {Hadley Wickham and Davis Vaughan and Maximilian Girlich},
-  year = {2023},
-  note = {R package version 1.3.0},
+  year = {2024},
+  note = {R package version 1.3.1},
   url = {https://tidyr.tidyverse.org},
 }
 
@@ -228,7 +235,8 @@ @Manual{R-tidyverse
   title = {tidyverse: Easily Install and Load the Tidyverse},
   author = {Hadley Wickham},
   year = {2023},
-  note = {R package version 2.0.0},
+  note = {R package version 2.0.0, 
+https://github.com/tidyverse/tidyverse},
   url = {https://tidyverse.tidyverse.org},
 }